gebhart/patrepeval huggingface dataset:
Structural Analysis of Siah1-Siah-interacting Protein Interactions and Insights into the Assembly of an E3 Ligase Multiprotein Complex (2005)

Siah1 is the central component of a multiprotein E3 ubiquitin ligase complex that targets beta-catenin for destruction in response to p53 activation. The E3 complex comprises, in addition to Siah1, Siah-interacting protein (SIP), the adaptor protein Skp1, and the F-box protein Ebi. Here we show that SIP engages Siah1 by means of two elements, both of which are required for mediating beta-catenin destruction in cells. An N-terminal dimerization domain of SIP sits across the saddle-shaped upper surface of Siah1, with two extended legs packing against the sides of Siah1 by means of a consensus PXAXVXP motif that is common to a family of Siah-binding proteins. The C-terminal domain of SIP, which binds to Skp1, protrudes from the lower surface of Siah1, and we propose that this surface provides the scaffold for bringing substrate and the E2 enzyme into apposition in the functional complex.
Media Gateways in Hybrid Wired and Wireless Media Production (2022)

Professional media production will in the future require more flexibility over where and how its operations are provided, so “effective use” includes operation where there are multiple networks, which could include 5G, wired, cloud-based and home networks. The broadcast industry's adoption of live networked media systems is still relatively immature, and there is not yet a consistent and complete approach to describing architectures and the interfaces required for interoperability. In this paper, the AMWA Network Media Systems Template has been used to build a set of media orchestration and control functions for a professional media production using both 5G and wired (ST 2110 based) media network. In particular, the scenario under consideration comes from the EU Horizon IC-41 Project called 5G-RECORDS (https://www.5g-records.eu/) and is about a multi-camera 5G-enabled broadcast studio. The MOCG (Media Operational Control Gateway) is the component that the partners are developing to control the setup of media resources; it sits on top of the 5G network, to automate and simplify the operational control of broadcast equipment deployed in various locations. In production, this is done through AMWA NMOS APIs. In the 5G network, the use of these APIs needs to be adapted through the introduction of several middleware components decoupling the remote operations from the studio and replicating/emulating NMOS control functions within a 5G environment. This paper gives a detailed description of the wireless studio use-case, the MOCG and the Media Gateway responsible for anchoring the media components within the 5G network and the production studio.
Genetic Control and Evolution of Sesquiterpene Biosynthesis in Lycopersicon esculentum and L. hirsutum (2000)

Rutger S. van der Hoeven, Antonio J. Monforte, David Breeden, Steven D. Tanksley, John C. Steffens, Genetic Control and Evolution of Sesquiterpene Biosynthesis in Lycopersicon esculentum and L. hirsutum, The Plant Cell, Vol. 12, No. 11 (Nov., 2000), pp. 2283-2294
An assessment of alternative wireless access technologies for PCS applications (1993)

The results of studies on three important wireless access technology issues in the personal communications services (PCS) arena are described. They are signal duplexing, multiplexing on the downlink, and channel frequency assignment. Each of these issues was addressed through the comparison of two competing technologies. In the area of duplexing, frequency division duplexing (FDD) was compared to time division duplexing (TDD) with the result that FDD is preferred if appropriate spectrum is available. Multiplexing on the downlink examined time division multiplexing (TDM) versus a burst downlink (TDMA). TDM is preferred for the wide-area local-exchange environment, but in certain indoor, office applications, TDMA may prove advantageous. The two methods of frequency channel assignment investigated are quasi-state autonomous frequency assignment (QSAFA) and dynamic channel assignment (DCA). QSFA is generally preferred, although indoor, multitenent environments with low port loading may benefit from the use of DCA. These analyses assume that the system uses time-division multiple access (TDMA).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations (2020)

Results from single-molecule imaging and phospho-flow cytometry experiments. Content: <strong>"E3 vs XFP Receptor Diffusion statistics.xlsx"</strong><br> The file contains results of average diffusion coefficients obtained from MSD analyses per cell. Average, standard deviation, percent error and number of cells are given. <strong>"FRET Analysis 2DKD_HW.xlsx"</strong><br> The file contains 2DKD data obtained from single molecule FRET experiments. 2DKD results for each cell, as well as average, standard deviation, median, and number of cells are given. <strong>"KD and free energyMH.xlsx"</strong><br> The file contains 2DKD and free energy evaluation obtained from dimerization experiments. <strong>"overview dimerization mean+std dev.xlsx"</strong><br> The file contains dimerization data obtained from colocomotion experiments. Results for each cell, as well as average, standard deviation and number of cells are given. <strong>"steps für co-tracks.xlsx"</strong><br> The file contains the analysis for the minimum trajectory length of for colocomotion analysis. Trajectories of each channel, co-trajectories, as well as dimerization results are given per cell and per trajectory length. <strong>"summary flow cytometry data.xlsx"</strong><br> The file contains results of phospho-flow cytometry experiments.
Feasibility study of the use of the TandemHeart® percutaneous ventricular assist device for treatment of cardiogenic shock (2006)

The TandemHeart PTVA System may be a useful complementary treatment for patients with CGS, especially as a bridge to another treatment. Further study is needed to definitively establish safety and efficacy.
First-principle simulations of electronic structure in semicrystalline polyethylene (2017)

In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (∼0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.
Millimeter-wave sintering of ceramics with applied pressure (2014)

Pressure-free microwave processing of polycrystalline materials has demonstrated rapid, efficient sintering attributed to volumetric heating and microwave-activated mass transport. However, the potential for improved sintering in the nanoparticle regime has often not been realized in part because of the tendency of nanoparticles to form agglomerates that reduce the density of the green compact leading to large pores and excessive grain growth. The application of pressure during sintering, i.e., hot pressing and hot isostatic pressing, has been shown to be an effective sintering method as the stress resulting from an external load can easily exceed the stress caused by surface tension. The application of pressure can result in faster sintering and lower sintering temperature. The current experimental investigations are being carried out in an 83 GHz, 15 kW gyrotron-based materials processing facility with a hydraulic press integrated into the millimeter-wave applicator in order to exert regulated pressure on the samples being heated by the beam. The pressing fixtures are fabricated from refractory ceramic materials with low microwave absorptivity such as alumina and boron nitride. Uniaxial pressures up to 10 MPa have been applied during sintering. Sample temperature is monitored by a two-color pyrometer. The processing environment can be vacuum or special atmosphere. Results of pressure-enhanced sintering of advanced ceramics will be presented showing rapid sintering rates and high final densification. We compare the measured sintering rate with the predictions of a micro-mechanical theory of sintering based on grain-boundary diffusion [1]. The model shows the sintering rate increases with applied load. The ponderomotive microwave effect [2] included in the model also contributes to increasing the sintering rate.
Broadband optical mammography: Breast tissue thickness compensation algorithm (2015)

We present a method to compensate for breast tissue thickness variability in broadband, continuous-wave, parallel plate optical mammography. Tissue thickness information is relevant for the recovery of chromophore concentrations within the breast using continuous-wave, diffusion-based models that assume the breast to be in slab geometry. This method compensates for the discrepancy between the actual phantom or breast shape and the models assumed slab geometry by approximating the thickness of the probed tissue volume. In this work, we applied our tissue thickness compensation algorithm on a breast shaped, homogeneous, tissue-mimicking phantom. Using the thickness found from our algorithm (referred to as our “estimated thickness”) as an input into a continuous-wave, diffusion based model, we recovered the absorption coefficient throughout all scanned pixels in the phantom and found an overall deviation of 12% from the true absorption coefficient. By using the known phantom thickness, we found a strong shape bias within the absorption coefficient recovery and a larger overall deviation of 29%. To test the algorithm on <i>in vivo</i> measurements, we applied this tissue thickness compensation method to a human breast cancer optical mammogram scan. Since the exact thickness of the breast at each pixel is unknown, we compared these results to when a uniform breast thickness is assumed and found a drastic improvement of cancer visualization. This method allows for parallel plate, continuous-wave optical imaging to compensate for the tissue thickness variability at each scanned pixel when modeling the breast data in slab geometry. This compensated thickness is needed as an input to the model in order to accurately map the breast chromophore concentrations and enhance the image contrast of cancer.
Stress migration risk on electromigration reliability in advanced narrow line copper interconnects (2011)

The influence of stress migration (SM) on the electromigration (EM) reliability is studied here for very fine line interconnects, fabricated using the 45-nm Cu/low-κ interconnect process flow. As opposed to the current understanding that SM is not a concern for the narrow metal lines because of limited availability of vacancies for voiding, we found that SM does have serious wear-out effects. The EM lifetime distribution was severely degraded by around 38% for the samples that had been subjected to a 1000-h SM-only test, with a drastic reduction in the slope of the EM lognormal fitting distribution, from 0.548 to 0.193. The current density exponent of Black’s equation for SM+EM stressed samples is ∼1, suggesting that void had already been nucleated because of the SM-only test. The high intrinsic tensile stress in the line is suspected to be responsible for this early void nucleation. In the second part, we developed a Monte Carlo simulation model to estimate the void nucleation and growth time using the EM-only and SM+EM degradation tests. We found that at low percentile failures overall failure time is mainly growth dominated, whereas at high percentile failures overall failure time is nucleation dominated. Stress migration was found to shorten the nucleation time for all the samples.
Biosensing with photonic crystal surfaces (2010)

Photonic crystals (PC) designed to produce narrow bandwidth resonant modes that extend into a surrounding fluid media have resulted in a variety of approaches for measuring the interaction of light with biological material. Label-free optical biosensing, PC-enhanced fluorescence (PCEF), PC-enhanced surface-enhance Raman spectroscopy (PC-SERS), and distributed feedback laser biosensor technology have resulted from the ability to inexpensively produce large-area PC surfaces by methods that include nanoreplica molding in plastic and nanoimprint lithography on glass. This talk will summarize recent research in the Nano Sensors Group at the University of Illinois at Urbana-Champaign in which PC surfaces are used to address a variety of biosensing needs in pharmaceutical high throughput screening, disease diagnostic testing, gene expression analysis, chemical analysis, and point-of-care detection systems. Because PC surfaces can be produced upon inexpensive and flexible plastic substrates, they are inexpensively manufactured by roll-to-roll fabrication methods and incorporated into disposable microplates, cartridges, microscope slides, plastic tubing, and other labware.
Hidden correlation in the CEP noise of mode-locked lasers (2017)

Stabilizing the carrier-envelope phase (CEP) of mode-locked laser sources has made tremendous progress in recent years, enabling the generation of isolated attosecond pulses and precision frequency metrology at the 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-18</sup> uncertainty level. While some laser types can be very well stabilized, other interesting laser materials have proven notoriously difficult or even impossible to be CEP stabilized. The exact mechanisms behind these problems are poorly understood. Here, we present a novel diagnostic method that provides unprecedented insight into the inner workings of noise generating mechanisms in laser oscillators.
Dielectric barrier hollow cathode discharge and its enhanced performance for light source (2005)

We invented the dielectric barrier hollow cathode discharge (DBHCD) configuration as a novel light source and studied on the physical properties of discharge and the possibility of the parallel operation of many holes of the DBHCD without additional impedances such as inductance or capacitance. The electrical characteristics and the photo images of discharges sustained in cavity were investigated. The experimental result showed that the surface discharge mode was transformed into a hollow cathode mode according to a decrease of the pD (operating pressure times hole diameter). The parallel operation of the 13 arrays of DBHCD was also possible without additional impedances for limiting current. We measured the relative IR emission efficiency of the coplanar dielectric barrier discharge (CDBD) and DBHCD to evaluate the enhanced performance as light sources. According to the experiment, the 25 arrays of DBHCD result in 30%-enhanced performance in IR emission efficiency compared with CDBD.
MR angiography using steady‐state free precession (2002)

Contrast-enhanced MR angiography (CE-MRA) using steady-state free precession (SSFP) pulse sequences is described. Using SSFP, vascular structures can be visualized with high signal-to-noise ratio (SNR) at a substantial (delay) time after the initial arterial pass of contrast media. The peak blood SSFP signal was diminished by <20% 30 min after the initial administration of 0.2 mmol/kg of Gd-chelate. The proposed method allows a second opportunity to study arterial or venous structures with high image SNR and high spatial resolution. A mask subtraction scheme using spin echo SSFP-S(-) acquisition is also described to reduce stationary background signal from the delayed SSFP angiography images.
Discovery and functional characterization of a neomorphic PTEN mutation (2015)

Although a variety of genetic alterations have been found across cancer types, the identification and functional characterization of candidate driver genetic lesions in an individual patient and their translation into clinically actionable strategies remain major hurdles. Here, we use whole genome sequencing of a prostate cancer tumor, computational analyses, and experimental validation to identify and predict novel oncogenic activity arising from a point mutation in the phosphatase and tensin homolog (PTEN) tumor suppressor protein. We demonstrate that this mutation (p.A126G) produces an enzymatic gain-of-function in PTEN, shifting its function from a phosphoinositide (PI) 3-phosphatase to a phosphoinositide (PI) 5-phosphatase. Using cellular assays, we demonstrate that this gain-of-function activity shifts cellular phosphoinositide levels, hyperactivates the PI3K/Akt cell proliferation pathway, and exhibits increased cell migration beyond canonical PTEN loss-of-function mutants. These findings suggest that mutationally modified PTEN can actively contribute to well-defined hallmarks of cancer. Lastly, we demonstrate that these effects can be substantially mitigated through chemical PI3K inhibitors. These results demonstrate a new dysfunction paradigm for PTEN cancer biology and suggest a potential framework for the translation of genomic data into actionable clinical strategies for targeted patient therapy.
On Steiner Triple Systems and Perfect Codes. (1999)

Using a computer implementation, we will show that there are perfect codes of length 15, generating Steiner triple systems which have rank 15. We will also show a strong connection between the rank/kernel of a perfect code and its systematics. Finally, we describe a method that will generate a perfect code from a Steiner triple system.
Efficient Macromolecular Crystallization Using Microfluidics and Randomized Design of Screening Reagents (2008)

Microfluidic technologies enable a relatively new approach to macromolecular crystallization, but offer several significant advantages over more traditional techniques. Microfluidic devices provide significant savings in the amount of material required to complete a set of experiments, although recent innovations with vapor diffusion and microbatch methods have also greatly reduced their material requirements. When compared with these other methods, microfluidic approaches still consume 5-100x less material. In addition, comparisons in one set of experiments suggest that microfluidic free-interface diffusion may also offer substantially higher success rates than sitting drop vapor diffusion. Microfluidic methods also provide opportunities for experimental strategies involving testing multiple samples in parallel. When combined with randomized design of screening reagents, microfluidic devices provide a highly efficient method for sampling crystallization space. Commercial microfluidic crystallization chips have been in circulation for a number of years now and stable protocols for their use, tips and tricks, and data on their success and failure are now available.
<title>Millimeter-wave aperture synthesis for remote sensing of the Earth</title> (1998)

Millimeter-wave radiometry of the earth's surface from Low Earth Orbit (LEO) with a resolution of a few km requires antenna apertures several meters across and sub-second scanning times. Fulfilling these requirements with a mechanically scanned real-aperture antenna presents formidable mechanical challenges. An attractive alternative described here is to use synthetic aperture techniques employing a sparse-array of antennas that trade the mechanical complexity of real-aperture imaging for the electrical complexity of synthetic aperture imaging. We present results of an ESA- sponsored study aimed at seeking the optimum technique for high performance synthetic aperture mm-wave radiometry from LEO.
Improved Noise Characterization for Relative Impulse Response Estimation (2018)

Relative Impulse Responses (ReIRs) have several applications in speech enhancement, noise suppression and source localization for multi-channel speech processing in reverberant environments. Noise is usually assumed to be white Gaussian during the estimation of the ReIR between two microphones. We show that the noise in this system identification problem is instead dependent upon the microphone measurements and the ReIR itself. We then present modifications that incorporate this new noise model into three prevalent methods: Least Squares, Non-Stationary Frequency Domain and Sparse Bayesian Learning based approaches. We demonstrated improvements with an experimental study using real-world measurements in various noise environments.
Supplementary Data from Preclinical Evaluation of a Novel SHIP1 Phosphatase Activator for Inhibition of PI3K Signaling in Malignant B Cells (2023)

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27.5 A pixel-pitch-matched ultrasound receiver for 3D photoacoustic imaging with integrated delta-sigma beamformer in 28nm UTBB FDSOI (2017)

A variety of emerging applications in medical ultrasound rely on 3D volumetric imaging, calling for dense 2D transducer arrays with thousands of elements. Due to this high channel count, the traditional per-element cable interface used for 1D arrays is no longer viable. To address this issue, recent work has proven the viability of flip-chip bonding or direct transducer integration. This shifts the burden to a CMOS substrate, which must provide dense signal conditioning and processing before the massively parallel image data can be pushed off chip. A common approach for data reduction is to employ subarray beamforming (BF), which applies delay and sum operations within a group of pixels. To implement such functionality within the tight pixel pitch, prior works have implemented the delays using simple S/H circuits or analog filters, and typically suffer from a combination of issues related to limited delay, coarse delay resolution and limited SNR.
New Y2BaAl4SiO12:Ce3+yellow microcrystal-glass powder phosphor with high thermal emission stability (2016)

New Y<sub>2</sub>BaAl<sub>4</sub>SiO<sub>12</sub>:Ce<sup>3+</sup>microcrystal-glass powder phosphor (emitting at 537 nm under 460 nm excitation) exhibits high thermal emission stability.
SDN/NFV-enabled Security Architecture for Fine-grained Policy Enforcement and Threat Mitigation for Enterprise Networks (2017)

No abstract available.
Causal Analysis of Syntactic Agreement Mechanisms in Neural Language Models (2021)

Matthew Finlayson, Aaron Mueller, Sebastian Gehrmann, Stuart Shieber, Tal Linzen, Yonatan Belinkov. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.