4,055 research outputs found

    Regret Bounds and Experimental Design for Estimate-then-Optimize

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    In practical applications, data is used to make decisions in two steps: estimation and optimization. First, a machine learning model estimates parameters for a structural model relating decisions to outcomes. Second, a decision is chosen to optimize the structural model's predicted outcome as if its parameters were correctly estimated. Due to its flexibility and simple implementation, this ``estimate-then-optimize'' approach is often used for data-driven decision-making. Errors in the estimation step can lead estimate-then-optimize to sub-optimal decisions that result in regret, i.e., a difference in value between the decision made and the best decision available with knowledge of the structural model's parameters. We provide a novel bound on this regret for smooth and unconstrained optimization problems. Using this bound, in settings where estimated parameters are linear transformations of sub-Gaussian random vectors, we provide a general procedure for experimental design to minimize the regret resulting from estimate-then-optimize. We demonstrate our approach on simple examples and a pandemic control application

    Accelerated Alternating Descent Methods for Dykstra-like problems

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    International audienceThis paper extends recent results by the first author and T. Pock (ICG, TU Graz, Austria) on the acceleration of alternating minimization techniques for quadratic plus nonsmooth objectives depending on two variables. We discuss here the strongly convex situation, and how ‘fast’ methods can be derived by adapting the overrelaxation strategy of Nesterov for projected gradient descent. We also investigate slightly more general alternating descent methods, where several descent steps in each variable are alternatively performed

    Penning traps with unitary architecture for storage of highly charged ions

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    Penning traps are made extremely compact by embedding rare-earth permanent magnets in the electrode structure. Axially-oriented NdFeB magnets are used in unitary architectures that couple the electric and magnetic components into an integrated structure. We have constructed a two- magnet Penning trap with radial access to enable the use of laser or atomic beams, as well as the collection of light. An experimental apparatus equipped with ion optics is installed at the NIST electron beam ion trap (EBIT) facility, constrained to fit within 1 meter at the end of a horizontal beamline for transporting highly charged ions. Highly charged ions of neon and argon, extracted with initial energies up to 4000 eV per unit charge, are captured and stored to study the confinement properties of a one-magnet trap and a two-magnet trap. Design considerations and some test results are discussed

    Post-radiation sarcoma of the neck treated with re-irradiation followed by wide excision

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    BACKGROUND: Post-radiation sarcoma (PRS) is an uncommon disease manifesting as sarcoma in a previously irradiated field, usually with a latent period of 5 years or more. Literature is limited to small series. Optimal management of this disease is unclear. Positive margins are common following attempted curative surgery and outcomes are poor. Radiotherapy is hardly used and its effect on PRS is not known. We described a case of PRS treated with preoperative radiotherapy followed by margin-negative wide excision. CASE PRESENTATION: The 59-year-old patient presented with a mass in the left supraclavicular fossa and numbness in the arm, six years following radical irradiation of the head and neck for nasopharyngeal carcinoma. Open biopsy showed pleomorphic spindle cell sarcoma. She was treated with pre-operative hyperfractionated radiotherapy followed by margin-negative wide excision and nerve grafting. Cumulative radiation dose to the supraclavicular fossa was 98 Gy. Histological examination of the post-irradiation tumor specimens showed evidence of significant tumor response to re-irradiation. The patient remained free of disease five years after surgery with excellent functional outcome. CONCLUSION: Role of radiotherapy in PRS is uncertain. We described a case that was successfully managed with preoperative radiotherapy and margin-negative wide excision in terms of tumor control and functional outcomes. The impact of radiotherapy was demonstrated in the post-irradiation resected specimen. Further investigation using re-irradiation and surgery in PRS is warranted

    Appropriately differentiated ARPE-19 cells regain phenotype and gene expression profiles similar to those of native RPE cells.

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    PurposeThe RPE cell line ARPE-19 provides a dependable and widely used alternative to native RPE. However, replication of the native RPE phenotype becomes more difficult because these cells lose their specialized phenotype after multiple passages. Compounding this problem is the widespread use of ARPE-19 cells in an undifferentiated state to attempt to model RPE functions. We wished to determine whether suitable culture conditions and differentiation could restore the RPE-appropriate expression of genes and proteins to ARPE-19, along with a functional and morphological phenotype resembling native RPE. We compared the transcriptome of ARPE-19 cells kept in long-term culture with those of primary and other human RPE cells to assess the former's inherent plasticity relative to the latter.MethodsARPE-19 cells at passages 9 to 12 grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum were differentiated for up to 4 months. Immunocytochemistry was performed on ARPE-19 cells grown on filters. Total RNA extracted from ARPE-19 cells cultured for either 4 days or 4 months was used for RNA sequencing (RNA-Seq) analysis using a 2 × 50 bp paired end protocol. The RNA-Seq data were analyzed to identify the affected pathways and recognize shared ontological classification among differentially expressed genes. RPE-specific mRNAs and miRNAs were assessed with quantitative real-time (RT)-PCR, and proteins with western blotting.ResultsARPE-19 cells grown for 4 months developed the classic native RPE phenotype with heavy pigmentation. RPE-expressed genes, including RPE65, RDH5, and RDH10, as well as miR-204/211, were greatly increased in the ARPE-19 cells maintained at confluence for 4 months. The RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of the genes in the differentiated ARPE-19 cells. Of the 16,757 genes with detectable signals, nearly 1,681 genes were upregulated, and 1,629 genes were downregulated with a fold change of 2.5 or more differences between 4 months and 4 days of culture. Gene Ontology analysis showed that the upregulated genes were associated with visual cycle, phagocytosis, pigment synthesis, cell differentiation, and RPE-related transcription factors. The majority of the downregulated genes play a role in cell cycle and proliferation.ConclusionsThe ARPE-19 cells cultured for 4 months developed a phenotype characteristic of native RPE and expressed proteins, mRNAs, and miRNAs characteristic of the RPE. Comparison of the ARPE-19 RNA-Seq data set with that of primary human fetal RPE, embryonic stem cell-derived RPE, and native RPE revealed an important overall similar expression ratio among all the models and native tissue. However, none of the cultured models reached the absolute values in the native tissue. The results of this study demonstrate that low-passage ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured and differentiated
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