NLM at ImageCLEF 2017 caption task

This paper describes the participation of the U.S. National Library of Medicine (NLM) in the ImageCLEF 2017 caption task. We proposed different machine learning methods using training subsets that we selected from the provided data as well as retrieval methods using external data. For the concept detection subtask, we used Convolutional Neural Networks (CNNs) and Binary Relevance using decision trees for multi-label classification. We also proposed a retrieval-based approach using Open-i image search engine and MetaMapLite to recognize relevant terms and associated Concept Unique Identifiers (CUIs). For the caption prediction subtask, we used the recognized CUIs and the UMLS to generate the captions. We also applied Open-i to retrieve similar images and their captions. We submitted ten runs for the concept detection subtask and six runs for the caption prediction subtask. CNNs provided good results with regards to the size of the selected subsets and the limited number of CUIs used for training. Using the CUIs recognized by the CNNs, our UMLS-based method for caption prediction obtained good results with 0.2247 mean BLUE score. In both subtasks, the best results were achieved using retrieval-based approaches outperforming all submitted runs by all the participants with 0.1718 mean F1 score in the concept detection subtask and 0.5634 mean BLUE score in the caption prediction subtask

Reporting Framework for Arterial-Level Traffic Signal Performance Measures Estimated from Connected Vehicle Trajectory Data

Traffic signal performance measures based on connected vehicle (CV) trajectory data can provide practitioners actionable information on the operational state of their systems. Agencies need visualization tools that can enable them to quickly assess arterial-level performance by time-of-day (TOD) to identify challenges and opportunities. This document presents a framework to report four signal performance measures over a corridor for all relevant movements, including traditional Highway Capacity Manual (HCM) level of service (LOS), arrivals on green (AOG), split failures (SF), and downstream blockage (DSB). The reporting framework can provide up to 3,072 performance data points per intersection since it provides information for eight different movements and four performance measures for every 15-minute period over 24 hours. To demonstrate implementation, 14 reports displaying performance estimations for 12 corridors, located in 11 different states, are presented. This reporting approach can facilitate the determination of possible mitigation strategies by contrasting operational conditions between movements by TOD

Two-Photon Spectroscopy Between States of Opposite Parities

Magnetic- and electric-dipole two-photon absorption (MED-TPA), recently introduced as a new spectroscopic technique for studying transitions between states of opposite parities, is investigated from a theoretical point of view. A new approximation, referred to as {\it weak quasi-closure approximation}, is used together with symmetry adaptation techniques to calculate the transition amplitude between states having well-defined symmetry properties. Selection rules for MED-TPA are derived and compared to selection rules for parity-forbidden electric-dipole two-photon absorption (ED-TPA).Comment: 7 pages, Revtex File, to be published in Physical Review

Next Generation Traffic Signal Performance Measures: Leveraging Connected Vehicle Data

High-resolution connected vehicle (CV) trajectory and event data has recently become commercially available. With over 500 billion vehicle position records generated each month in the United States, these data sets provide unique opportunities to build on and expand previous advances on traffic signal performance measures and safety evaluation. This report is a synthesis of research focused on the development of CV-based performance measures. A discussion is provided on data requirements, such as acquisition, storage, and access. Subsequently, techniques to reference vehicle trajectories to relevant roadways and movements are presented. This allows for performance analyses that can range from the movement- to the system-level. A comprehensive suite of methodologies to evaluate signal performance using vehicle trajectories is then provided. Finally, uses of CV hard-braking and hard-acceleration event data to assess safety and driver behavior are discussed. To evaluate scalability and test the proposed techniques, performance measures for over 4,700 traffic signals were estimated using more than 910 million vehicle trajectories and 14 billion GPS points in all 50 states and Washington, D.C. The contents of this report will help the industry transition towards a hybrid blend of detector- and CV-based signal performance measures with rigorously defined performance measures that have been peer-reviewed by both academics and industry leaders

Sum Rules for Multi-Photon Spectroscopy of Ions in Finite Symmetry

Models describing one- and two-photon transitions for ions in crystalline environments are unified and extended to the case of parity-allowed and parity- forbidden p-photon transitions. The number of independent parameters for characterizing the polarization dependence is shown to depend on an ensemble of properties and rules which combine symmetry considerations and physical models.Comment: 16 pages, Tex fil

Tissue factor-positive monocytes in children with sickle cell disease: correlation with biomarkers of haemolysis

Tissue Factor (TF) initiates thrombin generation, and whole blood TF (WBTF) is elevated in sickle cell disease (SCD). We sought to identify the presence of TF-positive monocytes in SCD and their relationship with the other coagulation markers including WBTF, microparticle-associated TF, thrombin-antithrombin (TAT) complexes and D-dimer. Whether major SCD-related pathobiological processes, including haemolysis, inflammation and endothelial activation, contribute to the coagulation abnormalities was also studied. The cohort comprised children with SCD (18 HbSS, 12 HbSC, mean age 3.6 years). We demonstrated elevated levels of TF-positive monocytes in HbSS, which correlated with WBTF, TAT and D-Dimer (p=0.02 to p=0.0003). While TF-positive monocytes, WBTF, TAT and D-dimer correlated with several biomarkers of haemolysis, inflammation and endothelial activation in univariate analyses, in multiple regression models the haemolytic markers (reticulocytes and lactate dehydrogenase) contributed exclusively to the association with all four coagulant markers evaluated. The demonstration that haemolysis is the predominant operative pathology in the associated perturbations of coagulation in HbSS at a young age provides additional evidence for the early use of therapeutic agents, such as hydroxycarbamide to reduce the haemolytic component of this disease

The S4–S5 Linker Acts as a Signal Integrator for hERG K+ Channel Activation and Deactivation Gating

Human ether-à-go-go-related gene (hERG) K+ channels have unusual gating kinetics. Characterised by slow activation/deactivation but rapid inactivation/recovery from inactivation, the unique gating kinetics underlie the central role hERG channels play in cardiac repolarisation. The slow activation and deactivation kinetics are regulated in part by the S4–S5 linker, which couples movement of the voltage sensor domain to opening of the activation gate at the distal end of the inner helix of the pore domain. It has also been suggested that cytosolic domains may interact with the S4–S5 linker to regulate activation and deactivation kinetics. Here, we show that the solution structure of a peptide corresponding to the S4–S5 linker of hERG contains an amphipathic helix. The effects of mutations at the majority of residues in the S4–S5 linker of hERG were consistent with the previously identified role in coupling voltage sensor movement to the activation gate. However, mutations to Ser543, Tyr545, Gly546 and Ala548 had more complex phenotypes indicating that these residues are involved in additional interactions. We propose a model in which the S4–S5 linker, in addition to coupling VSD movement to the activation gate, also contributes to interactions that stabilise the closed state and a separate set of interactions that stabilise the open state. The S4–S5 linker therefore acts as a signal integrator and plays a crucial role in the slow deactivation kinetics of the channel

A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient

<p>Abstract</p> <p>Background</p> <p>An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry). Typically this estimation is done under a static point of view. Therefore, the fluxes so obtained are only valid while the environmental conditions and the cell state remain stable. However, estimating the evolution over time of the metabolic fluxes is valuable to investigate the dynamic behaviour of an organism and also to monitor industrial processes. Although Metabolic Flux Analysis can be successively applied with this aim, this approach has two drawbacks: i) sometimes it cannot be used because there is a lack of measurable fluxes, and ii) the uncertainty of experimental measurements cannot be considered. The Flux Balance Analysis could be used instead, but the assumption of optimal behaviour of the organism brings other difficulties.</p> <p>Results</p> <p>We propose a procedure to estimate the evolution of the metabolic fluxes that is structured as follows: 1) measure the concentrations of extracellular species and biomass, 2) convert this data to measured fluxes and 3) estimate the non-measured fluxes using the Flux Spectrum Approach, a variant of Metabolic Flux Analysis that overcomes the difficulties mentioned above without assuming optimal behaviour. We apply the procedure to a real problem taken from the literature: estimate the metabolic fluxes during a cultivation of CHO cells in batch mode. We show that it provides a reliable and rich estimation of the non-measured fluxes, thanks to considering measurements uncertainty and reversibility constraints. We also demonstrate that this procedure can estimate the non-measured fluxes even when there is a lack of measurable species. In addition, it offers a new method to deal with inconsistency.</p> <p>Conclusion</p> <p>This work introduces a procedure to estimate time-varying metabolic fluxes that copes with the insufficiency of measured species and with its intrinsic uncertainty. The procedure can be used as an off-line analysis of previously collected data, providing an insight into the dynamic behaviour of the organism. It can be also profitable to the on-line monitoring of a running process, mitigating the traditional lack of reliable on-line sensors in industrial environments.</p