Marina Spivak

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Hygienic behaviour performed by middle!aged worker bees is an important intranidal task in colonies of the honey bee Apis mellifera "L[#[ It comprises detecting diseased brood in the larval and pupal stages and removing all such infected brood\ thereby decreasing the incidence of infection[ Hygienic behaviour consists of two task!components] uncapping cells(More)
Shotgun proteomics coupled with database search software allows the identification of a large number of peptides in a single experiment. However, some existing search algorithms, such as SEQUEST, use score functions that are designed primarily to identify the best peptide for a given spectrum. Consequently, when comparing identifications across spectra, the(More)
To be an effective platform for performance-sensitive realtime systems, commercial-off-the-shelf (COTS) distributed object computing (DOC) middleware must support application quality of service (QoS) requirements end-to-end. However, conventional DOC middleware does not provide this support, which makes it unsuited for applications with stringent latency,(More)
The fast Gauss transform allows for the calculation of the sum of N Gaussians at M points in O(N + M) time. Here, we extend the algorithm to a wider class of kernels, motivated by quadrature issues that arise in using integral equation methods for solving the heat equation on moving domains. In particular, robust high-order product integration methods(More)
Strict control over the scheduling and execution of processor resources is essential for many fixed-priority real-time applications. To facilitate this common requirement, the Real-Time CORBA (RT-CORBA) specification defines standard middleware features that support end-to-end predictability for operations in such applications. One of the most important(More)
We have developed a mathematical approach to the study of dynamical biological networks, based on combining large-scale numerical simulation with nonlinear "dimensionality reduction" methods. Our work was motivated by an interest in the complex organization of the signaling cascade centered on the neuronal phosphoprotein DARPP-32 (dopamine- and(More)
The goal of many shotgun proteomics experiments is to determine the protein complement of a complex biological mixture. For many mixtures, most methodological approaches fall significantly short of this goal. Existing solutions to this problem typically subdivide the task into two stages: first identifying a collection of peptides with a low false discovery(More)
We describe and evaluate two algorithms for Neyman-Pearson (NP) classification problem which has been recently shown to be of a particular importance for bipartite ranking problems. NP classification is a nonconvex problem involving a constraint on false negatives rate. We investigated batch algorithm based on DC programming and stochastic gradient method(More)
Salinity reduces Ca(2+) availability, transport, and mobility to growing regions of the plant and supplemental Ca(2+) is known to reduce salinity damages. This study was undertaken to unravel some of the ameliorative mechanisms of Ca(2+) on salt stress at the cellular and tissue levels. Zea mays L. plants were grown in nutrient solution containing 1 or 80(More)
Determining the three-dimensional structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using “single particle” cryo-electron microscopy (cryo-EM) for this purpose. In cryo-EM, hundreds of thousands of two-dimensional images are obtained of(More)