Fast Penalized Regression and Cross Validation for Tall Data with the oem Package

A large body of research has focused on theory and computation for variable selection techniques for high dimensional data. There has been substantially less work in the big "tall" data paradigm, where the number of variables may be large, but the number of observations is much larger. The orthogonalizing expectation maximization (OEM) algorithm is one approach for computation of penalized models which excels in the big tall data regime. The oem package is an efficient implementation of the OEM algorithm which provides a multitude of computation routines with a focus on big tall data, such as a function for out-of-memory computation, for large-scale parallel computation of penalized regression models. Furthermore, in this paper we propose a specialized implementation of the OEM algorithm for cross validation, dramatically reducing the computing time for cross validation over a naive implementation

ATP hydrolysis tunes specificity of a AAA+ protease

In bacteria, AAA+ proteases such as Lon and ClpXP degrade substrates with exquisite specificity. These machines capture the energy of ATP hydrolysis to power unfolding and degradation of target substrates. Here, we show that a mutation in the ATP binding site of ClpX shifts protease specificity to promote degradation of normally Lon-restricted substrates. However, this ClpX mutant is worse at degrading ClpXP targets, suggesting an optimal balance in substrate preference for a given protease that is easy to alter. In vitro, wild-type ClpXP also degrades Lon-restricted substrates more readily when ATP levels are reduced, similar to the shifted specificity of mutant ClpXP, which has altered ATP hydrolysis kinetics. Based on these results, we suggest that the rates of ATP hydrolysis not only power substrate unfolding and degradation, but also tune protease specificity. We consider various models for this effect based on emerging structures of AAA+ machines showing conformationally distinct states

Adaptive Display Frequency Control for Power Savings

This publication describes systems and techniques directed at adaptive display frequency control for power savings. In aspects, a display manager can adjust a base frequency and/or a driving frequency of display panel circuitry based on determining a number of operating conditions, including an ambient light condition, a current base frequency and driving frequency, a user interaction with the display, and/or a display brightness. Responsive to determining one or more of these conditions, the display manager can implement a base frequency and a driving frequency that can reduce power consumption and eliminate display artifacts commonly associated with automatic driving frequency transition

The Essential Role of ClpXP in Caulobacter crescentus Requires Species Constrained Substrate Specificity

The ClpXP protease is a highly conserved AAA+ degradation machine that is present throughout bacteria and in eukaryotic organelles. ClpXP is essential in some bacteria, such as Caulobacter crescentus, but dispensible in others, such as Escherichia coli. In Caulobacter, ClpXP normally degrades the SocB toxin and increased levels of SocB result in cell death. ClpX can be deleted in cells lacking this toxin, but these ΔclpX strains are still profoundly deficient in morphology and growth supporting the existence of additional important functions for ClpXP. In this work, we characterize aspects of ClpX crucial for its cellular function. Specifically, we show that although the E. coli ClpX functions with the Caulobacter ClpP in vitro, this variant cannot complement wildtype activity in vivo. Chimeric studies suggest that the N-terminal domain of ClpX plays a crucial, species-specific role in maintaining normal growth. We find that one defect of Caulobacter lacking the proper species of ClpX is the failure to properly proteolytically process the replication clamp loader subunit DnaX. Consistent with this, growth of ΔclpX cells is improved upon expression of a shortened form of DnaX in trans. This work reveals that a broadly conserved protease can acquire highly specific functions in different species and further reinforces the critical nature of the N-domain of ClpX in substrate choice

Electron tomography at 2.4 {\AA} resolution

Transmission electron microscopy (TEM) is a powerful imaging tool that has found broad application in materials science, nanoscience and biology(1-3). With the introduction of aberration-corrected electron lenses, both the spatial resolution and image quality in TEM have been significantly improved(4,5) and resolution below 0.5 {\AA} has been demonstrated(6). To reveal the 3D structure of thin samples, electron tomography is the method of choice(7-11), with resolutions of ~1 nm^3 currently achievable(10,11). Recently, discrete tomography has been used to generate a 3D atomic reconstruction of a silver nanoparticle 2-3 nm in diameter(12), but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of a ~10 nm gold nanoparticle at 2.4 {\AA} resolution. While we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified at three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply-twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic scale resolution(13-15), but also to improve the spatial resolution and image quality in other tomography fields(7,9,16-20).Comment: 27 pages, 17 figure

EGF-Induced EMT and Invasiveness in Serous Borderline Ovarian Tumor Cells: A Possible Step in the Transition to Low-Grade Serous Carcinoma Cells?

In high-grade ovarian cancer cultures, it has been shown that epidermal growth factor (EGF) induces cell invasion by activating an epithelial-mesenchymal transition (EMT). However, the effect of EGF on serous borderline ovarian tumors (SBOT) and low-grade serous carcinomas (LGC) cell invasion remains unknown. Here, we show that EGF receptor (EGFR) was expressed, that EGF treatment increased cell migration and invasion in two cultured SBOT cell lines, SBOT3.1 and SV40 large T antigen-infected SBOT cells (SBOT4-LT), and in two cultured LGC cell lines, MPSC1 and SV40 LT/ST-immortalized LGC cells (ILGC). However, EGF induced down-regulation of E-cadherin and concurrent up-regulation of N-cadherin in SBOT cells but not in LGC cells. In SBOT cells, the expression of the transcriptional repressors of E-cadherin, Snail, Slug and ZEB1 were increased by EGF treatment. Treatment with EGF led to the activation of the downstream ERK1/2 and PI3K/Akt. The MEK1 inhibitor PD98059 diminished the EGF-induced cadherin switch and the up-regulation of Snail, Slug and ZEB1 and the EGF-mediated increase in SBOT cell migration and invasion. The PI3K inhibitor LY294002 had similar effects, but it could not block the EGF-induced up-regulation of N-cadherin and ZEB1. This study demonstrates that EGF induces SBOT cell migration and invasion by activating EMT, which involves the activation of the ERK1/2 and PI3K/Akt pathways and, subsequently, Snail, Slug and ZEB1 expression. Moreover, our results suggest that there are EMT-independent mechanisms that mediate the EGF-induced LGC cell migration and invasion