594 research outputs found

    Annealing schedule from population dynamics

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    We introduce a dynamical annealing schedule for population-based optimization algorithms with mutation. On the basis of a statistical mechanics formulation of the population dynamics, the mutation rate adapts to a value maximizing expected rewards at each time step. Thereby, the mutation rate is eliminated as a free parameter from the algorithm.Comment: 6 pages RevTeX, 4 figures PostScript; to be published in Phys. Rev.

    Crossing the Communication Chasm: Challenges and Opportunities in Transitions of Care from the Hospital to the Primary Care Clinic

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    Background Transitions of care from specialty and acute settings to primary care abound. Compared to the continuity in end-of-shift handoffs, care transitions involve provider communication between practices and facilities with their own cultures and bureaucracies. Using the transition from acute care to outpatient primary care for stroke/transient ischemic attack (TIA) patients as a case study, this qualitative research explored communication practices and institutional arrangements among clinical providers responsible for longitudinal management of hypertension. In this study, researchers investigated the barriers and facilitators of effective communication between acute stroke/TIA inpatient and primary care providers at a Veterans Affairs Medical Center. Methods A multidisciplinary team conducted consensus-based coding and thematic analysis of semistructured interviews with 21 clinical providers (9 with primary responsibilities for inpatient care and 12 with primary responsibilities in outpatient, primary care). Results Thematic analysis of responses identified three factors that influenced communication between clinical providers: (1) consistent, concise but complete medication and treatment plans; (2) reliable, standardized discharge documentation; (3) use of multiple modes of communication. Participants identified cultural barriers, including challenges with rotating providers at a teaching hospital and local discharge practices. Conclusion Ambiguity about who is being handed off to and time pressures in the acute setting may lead inpatient providers to give lower priority to discharge communication, leaving outpatient providers with low-quality information. While electronic templates have standardized key components of discharge documentation, improvement opportunities remain. Increased awareness of the challenges and opportunities on each side of the care transfer could foster communication practices that systematically account for the information needs of inpatient and outpatient providers

    Development of an acute and chronic ecotoxicity assay using lux -marked Rhizobium leguminosarum biovar trifolii

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    A soil isolate of Rhizobium leguminosarum bv. trifolii was marked with a lux CDABE gene cassette to enable the expression of bioluminescence. The suitability of the bacterium as a soil pollution biosensor was assessed using acute and chronic assays. Bacterial bioluminescence responded sensitively to the metals studied, The order of sensitivity was found to be Cd > Ni = Zn > Cu for the acute test and Cd > Ni = Zn = Cu for the chronic test. The sensitive response of the biosensor highlighted its potential for use as an indicator of soil pollution

    OscoNet: Inferring oscillatory gene networks

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    Background: Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experiments is a challenging task due to the lack of time information. Oscope is a recently proposed method to identify co-oscillatory gene pairs using single-cell RNA-seq data. Although promising, the current implementation of Oscope does not provide a principled statistical criterion for selecting oscillatory genes. Results: We improve the optimisation scheme underlying Oscope and provide a wellcalibrated non-parametric hypothesis test to select oscillatory genes at a given FDR threshold. We evaluate performance on synthetic data and three real datasets and show that our approach is more sensitive than the original Oscope formulation, discovering larger sets of known oscillators while avoiding the need for less interpretable thresholds. We also describe how our proposed pseudo-time estimation method is more accurate in recovering the true cell order for each gene cluster while requiring substantially less computation time than the extended nearest insertion approach. Conclusions: OscoNet is a robust and versatile approach to detect oscillatory gene networks from snapshot single-cell data addressing many of the limitations of the original Oscope method

    Globally optimal parameters for on-line learning in multilayer neural networks

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    We present a framework for calculating globally optimal parameters, within a given time frame, for on-line learning in multilayer neural networks. We demonstrate the capability of this method by computing optimal learning rates in typical learning scenarios. A similar treatment allows one to determine the relevance of related training algorithms based on modifications to the basic gradient descent rule as well as to compare different training methods
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