gebhart/patrepeval huggingface dataset:
Phosphorylation and Activation of Phospholipase D1 by Protein Kinase C in Vivo:  Determination of Multiple Phosphorylation Sites (1999)

Protein kinase C (PKC) is an important regulator of phospholipase D1 (PLD1). Currently there is some controversy about a phosphorylation-dependent or -independent mechanism of the activation of PLD1 by PKC. To solve this problem, we examined whether PLD1 is phosphorylated by PKC in vivo. For the first time, we have now identified multiple basal phophopeptides and multiple phorbol myristate acetate (PMA) induced phosphopeptides of endogenous PLD1 in 3Y1 cells as well as of transiently expressed PLD1 in COS-7 cells. Down regulation or inhibition of PKC greatly attenuated the PMA-induced phosphorylation as well as the activation of PLD1. In the presence of PMA, purified PLD1 from rat brain was also found to be phosphorylated by PKCalpha in vitro at multiple sites generating seven distinct tryptic phosphopeptides. Four phosphopeptides generated in vivo and in vitro correlated well with each other, suggesting direct phosphorylation of PLD1 by PKCalpha in the cells. Serine 2, threonine 147, and serine 561 were identified as phosphorylation sites, and by mutation of these residues to alanine these residues were proven to be specific phosphorylation sites in vivo. Interestingly, threonine 147 is located in the PX domain and serine 561 is in the negative regulatory "loop" region of PLD1. Mutation of serine 2, threonine 147, or serine 561 significantly reduced PMA-induced PLD1 activity. These results strongly suggest that phosphorylation plays a pivotal role in PLD1 regulation in vivo.
Abstract 393: Predicting DNA accessibility in the pan-cancer tumor genome using RNA-Seq, WGS, and deep learning (2017)

Abstract DNA accessibility, chromatin regulation, and genome methylation are key drivers of cancer transcription. However, there is much left to be understood about the functional implications of sequence-level data to the regulation of gene expression, especially when it comes to the noncoding genome. Recently [Kelley, D., Snoek, J., and Rinn, J., Genome Res. 2016] trained neural networks to effectively predict DNA accessibility in multiple cell types. These models make it possible to explore the impact of mutations on the predicted accessibility and thus directly link one aspect of the gene regulation puzzle all the way down to the sequence level. We present a model with improved performance on the original dataset of 164 ENCODE and Roadmap Epigenomics Consortium sample types, and then extend the method to provide predictions on any sample with RNA-Seq data without need of DNase-seq for the sample. We first demonstrate that with several model and algorithmic changes we improve performance across 164 cell types from a mean AUC of 0.895 to a mean AUC of 0.910. Unfortunately current accessibility models require DNase-seq for each new cell type. Models for detecting transcription factor binding sites, which rely on ChIP-seq for training data, also share this issue. In order to generalize sequence-based predictive models to apply to unseen cell types without requiring re-training we investigate using RNA-Seq as a proxy signature of cell type. The model aims to capture the interdependence of gene expression levels that characterize a cell with the regulatory logic in which sequence-level signatures are combined to determine accessibility without restriction to cell type. We explore the model’s performance when applied to held-out cell types in the ENCODE and Roadmap Epigenomics Consortium data as well as data from the TCGA Pan-Cancer initiative. We look for the impact of non-coding changes in whole-genome sequencing data in TCGA samples, and report on predicted differences in DNA accessibility across cancer subtypes. Citation Format: Kamil Wnuk, Jeremi Sudol, Shahrooz Rabizadeh, Patrick Soon-Shiong, Christopher Szeto, Charles Vaske. Predicting DNA accessibility in the pan-cancer tumor genome using RNA-Seq, WGS, and deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 393. doi:10.1158/1538-7445.AM2017-393
Estimate on the uncertainty of predicting radiated emission from near-field scan caused by insufficient or inaccurate near-field data: Evaluation of the needed step size, phase accuracy and the need for all surfaces in the Huygens' box (2012)

Near-field scan on a Huygens' box can be used in order to predict the maximal radiated emission from a Printed Circuit Board. The significance of step size and phase accuracy, and the importance of a full Huygens' box are investigated by simulation of two different models with two different numerical methods. The prediction of maximal radiated emission is quite robust but the results also show that a full scan on all six surfaces is probably needed.
Full Organic Aqueous Battery Based on TEMPO Small Molecule with Millimeter-Thick Electrodes (2019)

Thick electrodes with sodium and even anion intercalation organic compounds integrated in a neutral-pH aqueous battery offer unique advantages in terms of round trip efficiency, environmental impact, and scalability for off- or on-grid renewable energy storage. Herein, we report the first anion-rocking chair/dual-ion organic battery. The latter reaches 35 Wh/kgmaterials at a C/8 rate. It shows remarkable cyclability and coulombic efficiency in a cheap and neutral NaClO4 electrolyte pouch cell with highly loaded millimeter-thick electrodes (5 mAh/cm2). This achievement is based on a thorough study of a commercial 2,2,6,6-tetramethylpiperidinyl-N-oxyl (TEMPO) (TEMPO) benzene derivative, namely, 4-hydroxy TEMPO benzoate, and its naphthalene analog (4-carboxy TEMPO naphthalate) as positive electrode materials and a bipyridinium–naphthalene oligomer as the negative electrode. Combined UV–vis spectroelectrochemistry and operando X-ray diffraction account for the much improved cyclability of the hydrophobic 4-carboxy TEMPO naphthalate at the expense of a lower specific capacity. This trend is reversed in the case of the 4-hydroxy TEMPO benzoate derivative. Results show that the kinetic limitations of 4-hydroxy TEMPO benzoate are associated with the surrounding composite electrode, whereas inner-grain ionic and/or electronic transports play a decisive role for 4-carboxy TEMPO naphthalate.
MOTILIN AND MIGRATING MYOELECTRIC COMPLEXES IN THE PIG AND THE DOG (1984)

Associations between migrating myoelectric complexes (m.m.c.s) and peak plasma motilin concentrations were confirmed in the dog fasted 18 h and shown not to be present in pigs fasted 3-4 h. Infusions of both natural porcine and synthetic 13-Nle-motilin failed to induce m.m.c.s in the pig. It was confirmed that motilin infusions stimulated the premature appearance of m.m.c.s in the dog whether motilin remained within, or exceeded, its normal plasma values. Immunoneutralization by intravenous administration of rabbit antimotilin serum was without effect on naturally occurring m.m.c.s in the dog and the pig. In the dog, antimotilin serum blocked production of m.m.c.s by exogenous motilin for 7-10 d post-immunoneutralization. It is suggested that there are both: (i) species differences in associations of m.m.c.s and plasma motilin concentration, and (ii) an independence of m.m.c.s from plasma motilin even in the dog in which normally exogenous motilin can produce m.m.c.s.
Ellipsometric measurements of molecular-beam-epitaxy-grown semiconductor multilayer thicknesses: A comparative study (1987)

Variable angle of incidence spectroscopic ellipsometry, cross-sectional transmission electron microscopy, and Rutherford backscattering are used to measure heterojunction layer thicknesses in the same AlGaAs/GaAs sample. All three techniques yield the same thickness values within error limits. Two additional samples were implanted with 750-keV Ga ions to fluences of 5×1015 and 1016 cm−2, respectively, and results of diagnostics measurements by the three techniques compared. The three techniques are found to complement each other in providing useful information.
Fiber Bragg gratings in few-mode highly birefringent microstructured optical fibers for sensing applications (2012)

In this paper we present the results of theoretical characterization of a few-mode birefringent microstructured fiber dedicated for fiber Bragg grating (FBG) inscription. The spectral characteristics of FBGs written (with a nanosecond and femtosecond laser Talbot interferometer setups) in the core region of the investigated fiber are presented and discussed. We compare the experimental results of the polarimetric strain sensitivity with our previously reported data, outlining perspectives for developing a highly sensitive (with strain sensitivity of second order mode two orders of magnitude higher in comparison to fundamental mode), temperature independent, FBG based strain transducer.
Correction to: Efficacy of canakinumab as first-line biologic agent in adult-onset Still’s disease (2019)

Following publication of the original article [1], the authors reported an error in the spelling of Lorenzo Dagna's name.
Flavonoid-Induced Morphological Modifications of Endothelial Cells Through Microtubule Stabilization (2009)

Flavonoids are common components of the human diet and appear to be of interest in cancer prevention or therapy, but their structure-activity relationships (SAR) remain poorly defined. In this study, were compared 24 flavonoids for their cytotoxicity on cancer cells (B16 and Lewis lung) and their morphological effect on endothelial cells (EC) that could predict antiangiogenic activity. Ten flavonoids presented inhibitory concentrations for 50% of cancer cells (IC50, 48 h) below 50 microM: rhamnetin, 3',4'-dihydroxyflavone, luteolin, 3-hydroxyflavone, acacetin, apigenin, quercetin, baicalein, fisetin, and galangin. Important SAR for cytotoxicity included the C2-C3 double bond and 3',4'-dihydroxylation. Concerning the morphological effects on EC, only fisetin, quercetin, kaempferol, apigenin, and morin could induce the formation of cell extensions and filopodias at noncytotoxic concentrations. The SAR for morphologic activity differed from cytotoxicity and involved hydroxylation at C-7 and C-4'. Fisetin, the most active agent, presented cell morphology that was distinct compared to colchicine, combretastatin A-4, docetaxel, and cytochalasin D. Resistance to cold depolymerization and a 2.4-fold increase in acetylated alpha-tubulin demonstrated that fisetin was a microtubule stabilizer. In conclusion, this study disclosed several SAR that could guide the choice or the rational synthesis of improved flavonoids for cancer prevention or therapy.
On the outage probability of a class of signaling schemes for multiple antennas (2003)

The concept of outage probability is appropriate for delay-constrained transmission over quasi-static channels since it serves as a useful lower bound for the frame error probability. In this work, we characterize a rich class of schemes, each member of which exhibits an identical asymptotic (in SNR) outage probability decay, given by maximum spatial diversity available in the system. The class includes several commonly used spatial power allocation and beamforming schemes, derived for varying amount of channel information at the transmitter and the receiver.
BlueRendezvous: Simple Pairing for Mobile Devices (2006)

A major user experience challenge for Smartphones and other mobile devices is to find ways that allow users to dynamically interconnect devices in a quick, simple, and intuitive manner. BlueRendezvous is a prototype application for the SmartPhone that greatly simplifies the Bluetooth discovery process. BlueRendezvous also makes it extremely simple to connect devices in different ways or for different purposes. For example, users can employ the same basic mechanism for mutual sharing of contact information, one-way sharing of images, or establishing a longer-term relationship between devices. This document presents currently implemented scenarios as well as alternative embodiments, extensions, and design scenarios that we have invented.
One-channel time-reversal in chaotic cavities: Experimental results (1999)

Experiments are presented that show the feasibility of reconstructing a point source using acoustic time-reversal with a single transmitter/receiver. The propagation medium is a closed 2-D silicon cavity with chaotic ray dynamics and negligible absorption. Injection of a short pulse at one point yields a long signal at a second one; by reversing a part of this signal, we obtain a focus at the initial injection point. The characterization of the focus was observed by scanning with an optical interferometer and by measuring the signal at the focal spot. With circular converging wavefronts, the reconstructed focus was excellent (corresponding to an aperture of 360°), but not perfect. The increase in quality of the focus with growing length of the reversed signal is described by a statistical ray model. Despite the irreversibility in classical chaos (due to strong sensitivity to initial conditions), the underlying chaotic ray dynamics is useful in this case.
Gas Cluster Ion Beam Processing for Si Photonics (2007)

Gas cluster ion beam (GCIB) process is applied for surface smoothing of one dimensional photonic band gap structure. After argon GCIB irradiations, hillocks on the Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> surface were preferentially removed and smooth surface was realized. Reflectance spectra of PBG structure after Ar-GCIB irradiation was much closer to that of the theoretical line than that of the as-deposited sample. GCIB process will be a candidate for precise pattern formation which is required for Si micro photonics.
Monomer Reactivities and Kinetics in Radical Copolymerization of Hydroxystyrene Derivatives and tert-Butyl (Meth)acrylate (2000)

Monomer reactivity ratios in radical copolymerization of 4-hydroxystyrene derivatives with tert-butyl acrylate and methacrylate have been determined by nonlinear regression as well as by the Kelen−Tüdös graphic method. The hydroxystyrene derivatives employed in the study included 4- and 3-hydroxystyrenes, 4- and 3-acetoxystyrenes, and 4-tert-butoxycarbonyloxystyrene. The electron-rich 4-hydroxystyrene is unique as its copolymerization with the electron-deficient acrylate monomers is more alternating. The simulation of the copolymerization on the basis of the reactivity ratios has been shown to fully describe the copolymerization behavior and copolymer structures. The kinetics of radical copolymerization of 4-acetoxystyrene with tert-butyl (meth)acrylate has been studied in detail using a gas chromatographic procedure and also by in situ 1H NMR spectroscopy. The kinetics behavior has shown an excellent agreement with the computer simulation of the copolymerization using the reactivity ratio values determined on the basis of the terminal model.
Viral Clearance and Inflammatory Response Patterns in Adults Hospitalized for Pandemic 2009 Influenza A(H1N1) Virus Pneumonia (2010)

In severe 2009 H1N1 pneumonia, viral clearance is slow with treatment, particularly in the lower respiratory tract. A more sustained antiviral regime appears warranted.
InGaN-Based Solar Cells and High-Performance Broadband Optical Coatings for Ultrahigh Efficiency Hybrid Multijunction Device Designs (2013)

Efficiencies exceeding 40% have already been achieved with GaAs-based multijunction (MJ) solar cells. In this talk, we will discuss the unique advantages and challenges of fabricating hybrid InGaN-GaAs MJ cells for ultrahigh efficiency device designs.
SU‐E‐I‐87: Calibrating Cherenkov Emission to Match Superficial Dose in Tissue (2015)

Purpose: Through Monte Carlo simulations and phantom studies, the dominant factors affecting the calibration of superficial Cherenkov intensity to absolute surface dose was investigated, including tissue optical properties, curvatures, beam properties and imaging angle. Methods: The phasespace files for the TrueBeam system from Varian were used in GAMOS (a GEANT4 based Monte Carlo simulation toolkit) to simulate surface emission Cherenkov signals and the correlated deposited dose. The parameters examined were: i) different tissue optical properties (skin color from light to dark), ii) beam types (X‐ray and electron beam), iii) beam energies, iv) thickness of tissues (2.5 cm to 20 cm), v) SSD (80 cm to 120 cm), vi) field sizes (0.5×0.5 cm2 to 20×20 cm2), vii) entrance/exit sides, viii) curvatures (cylinders with diameters from 2.5 cm to 20cm) and ix) imaging angles (0 to 90 degrees). In a specific case, for any Cherenkov photon emitted from the surface, the original position and direction, final position and direction and energy were recorded. Similar experimental measurements were taken in a range of the most pertinent parameters using tissue phantoms. Results: Combining the dose distribution and sampling sensitivity of Cherenkov emission, quantitatively accurate calibration factors (the amount of radiation dose represented by a single Cherenkov photon) were calculated. The data showed relatively large dependence upon different optical properties, curvature, entrance/exit and beam types. For a diffusive surface, the calibration factor was insensitive to imaging angles smaller than 60 degrees. Normalization with the reflectance image was experimentally validated as a simple and accurate method for calibrations of different optical properties. Conclusion: This study sheds light on how and to what extent different conditions affect the calibration from Cherenkov intensity to absolute superficial dose and provides practical solutions to allow quantitative Cherenkov imaging to be used as a dose surrogate for imaging.
Controlling chaos in high dimensions: Theory and experiment (1996)

The main contribution of this work is the development of a high-dimensional chaos control method that is effective, robust against noise, and easy to implement in experiment. Assuming no knowledge of the model equations, the method achieves control by stabilizing a desired unstable periodic orbit with any number of unstable directions, using small time-dependent perturbations of a single system parameter. Specifically, our major results are as follows. First, we derive explicit control laws for time series produced by discrete maps. Second, we show how to apply this control law to continuous-time problems by introducing straightforward ways to extract from a continuous-time series a discrete time series that measures the dynamics of some Poincar\'e map of the original system. Third, we illustrate our approach with two examples of high-dimensional ordinary differential equations, one autonomous and the other periodically driven. Fourth, we present the result on our successful control of chaos in a high-dimensional experimental system, demonstrating the viability of the method in practical applications.
Plants and Environmental Sensors for Smart Agriculture, an Overview (2020)

Smart agriculture is a fast-growing research field. From one side, the increase of the human population is always demanding more food production. On the other side, the consciousness of the importance of diet quality requires a more controlled and higher quality production, both in terms of nutrition factors and lower use of pesticides. Thus, it is straightforward to apply the progress in electronics and sensors technology for reaching these different objectives. In this paper, we present an overview of the sensors applied for smart agriculture. Two different categories are presented: sensors for evaluating plant health and fruit conditions and sensors used to monitor the environmental condition where the plants are growing.
Implementation of optical interconnections for VLSI (1987)

Primitives for broadcast communication that have been integrated with the Amoeba distributed operating system are introduced. The semantics of the broadcast primitives are simple and easy to understand, but are still powerful. The proposed primitives, for example, guarantee global ordering of broadcast messages. The proposed primitives are also efficient: a reliable broadcast can be done in just slightly more than two messages, so the performance is comparable to a remote procedure call. In addition, the primitives are flexible; user applications can, for example, trade performance against fault-tolerance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-resolution, high-aspect-ratio iridium–nickel composite nanoimprint molds (2016)

Nanoimprint molds are traditionally made from silicon. Silicon molds suffer from distinct disadvantages as they are brittle, prone to damage, scratch easily, and can only be used in a planar format. This has limited their use in higher throughput systems where flexible molds are required such as in roll-to-roll and roll-to-plate systems. Nickel (Ni) molds, which are now de-rigueur in both batch and roller nanoimprint processes, can be used to address these problems, but fabrication and durability issues limit their availability and effectiveness in production. In this report, the authors introduce a fabrication route that has the potential to overcome the fabrication, quality, and wear problems of Ni molds. The new process relies on atomic layer deposition to form a smooth and high-aspect ratio patterned layer of iridium (Ir) on a Ni substrate. A large area nanohole array mold was fabricated using displacement Talbot lithography to demonstrate this process. The authors show the use of such composite molds via a batch thermal imprinting process to fabricate 70 nm hole arrays onto polycarbonate templates with a ±10% tolerance in diameter between the polycarbonate and the composite mold, and less than 1% of defects.
A Human Genome-Wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α–XBP1 Activation (2018)

Activation of the unfolded protein response (UPR) signaling pathways is linked to multiple human diseases, including cancer. The inositol-requiring kinase 1α (IRE1α)-X-box binding protein 1 (XBP1) pathway is the most evolutionarily conserved of the three major signaling branches of the UPR. Here, we performed a genome-wide siRNA screen to obtain a systematic assessment of genes integrated in the IRE1α-XBP1 axis. We monitored the expression of an XBP1-luciferase chimeric protein in which luciferase was fused in-frame with the spliced (active) form of XBP1. Using cells expressing this reporter construct, we identified 162 genes for which siRNA inhibition resulted in alteration in XBP1 splicing. These genes express diverse types of proteins modulating a wide range of cellular processes. Pathway analysis identified a set of genes implicated in the pathogenesis of breast cancer. Several genes, including <i>BCL10, GCLM</i>, and <i>IGF1R</i>, correlated with worse relapse-free survival (RFS) in an analysis of patients with triple-negative breast cancer (TNBC). However, in this cohort of 1,908 patients, only high GCLM expression correlated with worse RFS in both TNBC and non-TNBC patients. Altogether, our study revealed unidentified roles of novel pathways regulating the UPR, and these findings may serve as a paradigm for exploring novel therapeutic opportunities based on modulating the UPR.<b>Implications:</b> Genome-wide RNAi screen identifies novel genes/pathways that modulate IRE1α-XBP1 signaling in human tumor cells and leads to the development of improved therapeutic approaches targeting the UPR.<b>Visual Overview:</b> http://mcr.aacrjournals.org/content/molcanres/16/5/745/F1.large.jpg <i>Mol Cancer Res; 16(5); 745-53. ©2018 AACR</i>.