A User-centric Framework for Accessing Biological Sources and Tools

Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists’ needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself – the strategy followed – differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies

A Variational Procedure for Time-Dependent Processes

A simple variational Lagrangian is proposed for the time development of an arbitrary density matrix, employing the "factorization" of the density. Only the "kinetic energy" appears in the Lagrangian. The formalism applies to pure and mixed state cases, the Navier-Stokes equations of hydrodynamics, transport theory, etc. It recaptures the Least Dissipation Function condition of Rayleigh-Onsager {\bf and in practical applications is flexible}. The variational proposal is tested on a two level system interacting that is subject, in one instance, to an interaction with a single oscillator and, in another, that evolves in a dissipative mode.Comment: 25 pages, 4 figure

Fear of the unknown: a pre-departure qualitative study of Turkish international students

This paper presents findings from eleven in-depth interviews with Turkish undergraduate students, who were, by the time of data collection, about to spend a semester at a European university under the Erasmus exchange scheme. The students all agreed to be interviewed about their feelings about studying in a foreign culture, and were found to be anxious prior to departure about the quality of accommodation in the new destination, their language ability and the opportunity to form friendships. Fears were expressed about possible misconceptions over Turkey as a Muslim and a developing country. Suggestions are made for HEI interventions to allay student travellers’ concerns

Pathogenesis of non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) represents a spectrum of disease ranging from hepatocellular steatosis through steatohepatitis to fibrosis and irreversible cirrhosis. The prevalence of NAFLD has risen rapidly in parallel with the dramatic rise in obesity and diabetes, and is rapidly becoming the most common cause of liver disease in Western countries. Indeed, NAFLD is now recognized to be the aetiology in many cases previously labelled as cryptogenic cirrhosis

Expansions of algebras and superalgebras and some applications

After reviewing the three well-known methods to obtain Lie algebras and superalgebras from given ones, namely, contractions, deformations and extensions, we describe a fourth method recently introduced, the expansion of Lie (super)algebras. Expanded (super)algebras have, in general, larger dimensions than the original algebra, but also include the Inonu-Wigner and generalized IW contractions as a particular case. As an example of a physical application of expansions, we discuss the relation between the possible underlying gauge symmetry of eleven-dimensional supergravity and the superalgebra osp(1|32).Comment: Invited lecture delivered at the 'Deformations and Contractions in Mathematics and Physics Workshop', 15-21 January 2006, Mathematisches Forschungsinstitut Oberwolfach, German

Rapid Rule-out of Acute Myocardial Infarction With a Single High-Sensitivity Cardiac Troponin T Measurement Below the Limit of Detection: A Collaborative Meta-analysis.

Background: High-sensitivity assays for cardiac troponin T (hs-cTnT) are sometimes used to rapidly rule out acute myocardial infarction (AMI). Purpose: To estimate the ability of a single hs-cTnT concentration below the limit of detection (<0.005 µg/L) and a nonischemic electrocardiogram (ECG) to rule out AMI in adults presenting to the emergency department (ED) with chest pain. Data Sources: EMBASE and MEDLINE without language restrictions (1 January 2008 to 14 December 2016). Study Selection: Cohort studies involving adults presenting to the ED with possible acute coronary syndrome in whom an ECG and hs-cTnT measurements were obtained and AMI outcomes adjudicated during initial hospitalization. Data Extraction: Investigators of studies provided data on the number of low-risk patients (no new ischemia on ECG and hs-cTnT measurements <0.005 µg/L) and the number who had AMI during hospitalization (primary outcome) or a major adverse cardiac event (MACE) or death within 30 days (secondary outcomes), by risk classification (low or not low risk). Two independent epidemiologists rated risk of bias of studies. Data Synthesis: Of 9241 patients in 11 cohort studies, 2825 (30.6%) were classified as low risk. Fourteen (0.5%) low-risk patients had AMI. Sensitivity of the risk classification for AMI ranged from 87.5% to 100% in individual studies. Pooled estimated sensitivity was 98.7% (95% CI, 96.6% to 99.5%). Sensitivity for 30-day MACEs ranged from 87.9% to 100%; pooled sensitivity was 98.0% (CI, 94.7% to 99.3%). No low-risk patients died. Limitation: Few studies, variation in timing and methods of reference standard troponin tests, and heterogeneity of risk and prevalence of AMI across studies. Conclusion: A single hs-cTnT concentration below the limit of detection in combination with a nonischemic ECG may successfully rule out AMI in patients presenting to EDs with possible emergency acute coronary syndrome. Primary Funding Source: Emergency Care Foundation

Observer weighting of interaural cues in positive and negative envelope slopes of amplitude-modulated waveforms

The auditory system can encode interaural delays in highpass-filtered complex sounds by phase locking to their slowly modulating envelopes. Spectrotemporal analysis of interaurally time-delayed highpass waveforms reveals the presence of a concomitant interaural level cue. The current study systematically investigated the contribution of time and concomitant level cues carried by positive and negative envelope slopes of a modified sinusoidally amplitude-modulated (SAM) high-frequency carrier. The waveforms were generated from concatenation of individual modulation cycles whose envelope peaks were extended by the desired interaural delay, allowing independent control of delays in the positive and negative modulation slopes. In experiment 1, thresholds were measured using a 2-interval forced-choice adaptive task for interaural delays in either the positive or negative modulation slopes. In a control condition, thresholds were measured for a standard SAM tone. In experiment 2, decision weights were estimated using a multiple-observation correlational method in a single-interval forced-choice task for interaural delays carried simultaneously by the positive, and independently, negative slopes of the modulation envelope. In experiment 3, decision weights were measured for groups of 3 modulation cycles at the start, middle, and end of the waveform to determine the influence of onset dominance or recency effects. Results were consistent across experiments: thresholds were equal for the positive and negative modulation slopes. Decision weights were positive and equal for the time cue in the positive and negative envelope slopes. Weights were also larger for modulations cycles near the waveform onset. Weights estimated for the concomitant interaural level cue were positive for the positive envelope slope and negative for the negative slope, consistent with exclusive use of time cues.We thank Virginia M. Richards and Bruce G. Berg for helpful discussions. We also thank Brian C. J. Moore and an anonymous reviewer for their insightful comments on an earlier draft of the manuscript. Work supported by grants from the National Science Council, Taiwan NSC 98-2410-H-008-081-MY3 and NIH R01DC009659

Early Atomic Models - From Mechanical to Quantum (1904-1913)

A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J. J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic {\alpha}-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their scattering eventually allowed him to infer the existence of an atomic nucleus. Niels Bohr was particularly troubled by the radiative instability inherent to any mechanical atom, and succeeded in 1913 where others had failed in the prediction of emission spectra, by making two bold hypotheses that were in contradiction to the laws of classical physics, but necessary in order to account for experimental facts.Comment: 58 Pages + References, 8 Figures. Accepted for publication in the European Physical Journal H (Historical Perspectives on Contemporary Physics). V2 - minor typos corrected and a footnote added to p.2