gebhart/patrepeval huggingface dataset:
Trastuzumab-Resistant HER2-Driven Breast Cancer Cells Are Sensitive to Epigallocatechin-3 Gallate (2007)

Overexpression of the epidermal growth factor receptor family member HER2 is found in approximately 30% of breast cancers and is a target for immunotherapy. Trastuzumab, a humanized monoclonal antibody against HER2, is cytostatic when added alone and highly successful in clinical settings when used in combination with other chemotherapeutic agents. Unfortunately, HER2 tumors in patients develop resistance to trastuzumab or metastasize to the brain, which is inaccessible to antibody therapy. Previously, we showed that the green tea polyphenol epigallocatechin-3 gallate (EGCG) inhibits growth and transformed phenotype of Her-2/neu-driven mouse mammary tumor cells. The different modes of action of EGCG and trastuzumab led us to hypothesize that EGCG will inhibit HER2-driven breast cancer cells resistant to trastuzumab. We studied trastuzumab-resistant BT474 human breast cancer cells, isolated by chronic trastuzumab exposure, and JIMT-1 breast cancer cells, derived from a pleural effusion in a patient who displayed clinical resistance to trastuzumab therapy. EGCG treatment caused a dose-dependent decrease in growth and cellular ATP production, and apoptosis at high concentrations. Akt activity was suppressed by EGCG leading to the induction of FOXO3a and target cyclin-dependent kinase inhibitor p27Kip1 levels. Thus, EGCG in combination with trastuzumab may provide a novel strategy for treatment of HER2-overexpressing breast cancers, given that EGCG can cross the blood-brain barrier.
DATS - Data Containers for Web Applications (2018)

Data containers enable users to control access to their data while untrusted applications compute on it. However, they require replicating an application inside each container - compromising functionality, programmability, and performance. We propose DATS - a system to run web applications that retains application usability and efficiency through a mix of hardware capability enhanced containers and the introduction of two new primitives modeled after the popular model-view-controller (MVC) pattern. (1) DATS introduces a templating language to create views that compose data across data containers. (2) DATS uses authenticated storage and confinement to enable an untrusted storage service, such as memcached and deduplication, to operate on plain-text data across containers. These two primitives act as robust declassifiers that allow DATS to enforce non-interference across containers, taking large applications out of the trusted computing base (TCB). We showcase eight different web applications including Gitlab and a Slack-like chat, significantly improve the worst-case overheads due to application replication, and demonstrate usable performance for common-case usage.
Efficient Computing Budget Allocation for Simulation-Based Optimization With Stochastic Simulation Time (2012)

The dynamics of many systems nowadays follow not only physical laws but also man-made rules. These systems are known as discrete event dynamic systems and their performances can be accurately evaluated only through simulations. Existing studies on simulation-based optimization (SBO) usually assume deterministic simulation time for each replication. However, in many applications such as evacuation, smoke detection, and territory exploration, the simulation time is stochastic due to the randomness in the system behavior. We consider the computing budget allocation for SBOs with stochastic simulation time in this technical note, which has not been addressed in existing literatures to the author's best knowledge. We make the following major contribution. The relationship between simulation time and performance estimation accuracy is quantified. It is shown that when the asymptotic performance is of interest only the mean value of individual simulation time matters. Then based on the existing optimal computing budget allocation (OCBA) method for deterministic simulation time we develop OCBA for stochastic simulation time (OCBAS), and show that OCBAS is asymptotically optimal. Numerical experiments are used to discuss the impact of the variance of simulation time, the impact of correlated simulation time and performance estimation, and to demonstrate the performance of OCBAS on a smoke detection problem in wireless sensor network. The numerical results also show that OCBA for deterministic simulation time is robust even when the simulation time is stochastic.
High performance ambient processed inverted polymer solar cells through interfacial modification with a fullerene self-assembled monolayer (2008)

The performance of inverted bulk-heterojunction solar cells with zinc oxide nanoparticles as the electron selective contact is compared to those modified with a fullerene self-assembled monolayer (C60-SAM). The devices modified with a C60-SAM show very significant improvement in conversion efficiencies compared to unmodified devices leading to efficiencies as high as 4.9%. This is due to enhanced electronic coupling of the inorganic/organic interface from the C60-SAM leading to improved fill factor and photocurrent. Furthermore, devices fabricated in an inert environment were compared to those fabricated in ambient showing comparable device performance.
Nanocatalysis in continuous flow: supported iron oxide nanoparticles for the heterogeneous aerobic oxidation of benzyl alcohol (2013)

Investigations on heterogeneous iron catalysis in the selective aerobic oxidation of a primary alcohol are presented. Continuous flow technology was used in combination with an iron oxide nanoparticle catalyst stabilized in a mesoporous aluminosilicate support (“flow nanocatalysis”) as a process intensification tool to maximize catalyst efficiency. Using 5 mol% 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) as a co-catalyst, up to 42% benzyl alcohol as a simple model substrate was selectively converted to benzaldehyde in a single pass of the reactor. Full conversion was achieved by continuous recirculation, simulating an extension of the catalyst bed. ICPMS analysis indicated that the catalyst is highly stable and does not leach under the investigated conditions, providing solid evidence for the participation of a heterogeneous iron species in the catalytic cycle.
An analytical dose‐averaged<scp>LET</scp>calculation algorithm considering the off‐axis<scp>LET</scp>enhancement by secondary protons for spot‐scanning proton therapy (2018)

We confirmed that the dual-LET-kernel model well reproduced the MCS, not only in the homogeneous phantom but also in complex patient geometries. The accuracy of the LET<sub>d</sub> was largely improved from the single-LET-kernel model, especially at the lateral penumbra. The model is expected to be useful, especially for proper recognition of the risk of side effects when the target is next to critical organs.
Effect of pulse error accumulation on dynamical decoupling of the electron spins of phosphorus donors in silicon (2012)

Dynamical decoupling (DD) is an efficient tool for preserving quantum coherence in solid-state spin systems. However, the imperfections of real pulses can ruin the performance of long DD sequences. We investigate the accumulation and compensation of different pulse errors in DD using the electron spins of phosphorus donors in silicon as a test system. We study periodic DD sequences based on spin rotations about two perpendicular axes, and their concatenated and symmetrized versions. We show that pulse errors may quickly destroy some spin states, but maintain other states with high fidelity over long times. Pulse sequences based on spin rotations about $x$ and $y$ axes outperform those based on $x$ and $z$ axes due to the accumulation of pulse errors. Concatenation provides an efficient way to suppress the impact of pulse errors, and can maintain high fidelity for all spin components: pulse errors do not accumulate (to first order) as the concatenation level increases, despite the exponential increase in the number of pulses. A symmetrized DD sequence cancels the first-order pulse errors. Our theoretical model gives a clear qualitative picture of the error accumulation and produces results in quantitative agreement with the experiments.
3D model refinement using surface-parallax (2004)

We present an approach to update and refine coarse 3D models of urban environments from a sequence of intensity images using surface parallax. This generalizes the plane-parallax recovery methods to surface-parallax using arbitrary surfaces. A coarse and potentially incomplete depth map of the scene obtained from a digital elevation map (DEM) is used as a reference surface which is refined and updated using this approach. The reference depth map is used to estimate the camera motion and the motion of the 3D points on the reference surface is compensated. The resulting parallax, which is an epipolar field, is estimated using an adaptive windowing technique and used to obtain the refined depth map.
Balloon-Distension Studies in the Gastrointestinal Tract: Current Role (2006)

Balloon distension is a commonly used technique in visceral organs. Research studies take advantage of this technique for studying organ physiology, e.g. for studying the force-deformation relationship and mechanosensitive receptors in the gastrointestinal wall. Balloon distension is also used for diagnostic purposes, e.g. in the diagnostics of non-cardiac chest pain and for treatment of diseases such as bleeding esophageal varices caused by liver disease and lower esophageal sphincter occlusion caused by achalasia. Balloon distension can be carried out with concomitant measurements of pressure, volume and cross-sectional area alone or in combination. Furthermore, balloon-distension techniques can be combined with various imaging techniques such as B-mode ultrasonography and MRI to obtain three-dimensional geometric data about the three-dimensional surface with subsequent calculation of the tension or stress in the gastrointestinal organs. This article describes balloon-distension techniques, in particular new developments of the impedance planimetric technique including methods for studying gastrointestinal muscle function.
Contextos de subordinación sustantiva: el modo en los verbos de pensamiento, voluntad o deseo y sentimiento. Análisis contrastivo español-italiano (2017)

espanolPor un lado, este trabajo esta centrado en el estudio del modo en determinados contextos de subordinacion sustantiva. Para ello, se estudiara un grupo concreto de verbos que se analizaran con sus correspondientes ejemplos y se vera como actua el modo en este tipo de subordinadas y si existen equivalencias con el italiano. Por otro lado, se estudia los errores de los italofonos en el uso del subjuntivo e indicativo en estos contextos y se intenta explicar las causas que provocan dichos errores. A partir de ello, se desarrollara una aplicacion de la teoria a la didactica de ELE, que nos conducira a crear actividades dentro de un enfoque comunicativo orientado a la accion que le permitan al estudiante italiano mejorar el proceso de aprendizaje de ELE. EnglishOn the one hand, this work focuses on the study of mode in certain contexts in substantive subordination. For this, a specific group of verbs will be discussed with his examples in order to see how the mode acts in this type of subordinate and whether there are equivalences with the Italian mode. On the other hand, mistakes of Italian speakers will be studied in the use of the subjunctive and indicative in these contexts and we will try to explain the causes of such mistakes. From this, an application of the theory will be developed to the teaching of ELE, which leads us to create activities within an action-oriented approach that allows the Italian student improve the ELE learning process.
Coaxial Heterogeneous Structure of TiO<sub>2</sub>Nanotube Arrays with CdS as a Superthin Coating Synthesized via Modified Electrochemical Atomic Layer Deposition (2010)

We report the fabrication and characterization of CdS/TiO(2) nanotube-array coaxial heterogeneous structures. Such structures may potentially be applied in various photocatalytic fields, such as water photocatalytic decomposition and toxic pollutant photocatalytic degradation. Thin films of CdS are conformally deposited onto TiO(2) nanotubes using a modified method of electrochemical atomic layer deposition. We propose that such nanostructured electrodes can overcome the poor absorption and high charge-carrier recombination observed with nanoparticulate films. The practical electrochemical deposition technique promotes the deposition of CdS onto the TiO(2) tube walls while minimizing deposition at the tube entrances, thus preventing pore clogging. The coaxial heterogeneous structure prepared by the new electrochemical process significantly enhances CdS/TiO(2) and CdS/electrolyte contact areas and reduces the distance that holes and electrons must travel to reach the electrolyte or underlying conducting substrate. This results in enhanced photon absorption and photocurrent generation. The detailed synthesis process and the surface morphology, structure, elemental analysis, and photoelectrochemical properties of the resulting films with the CdS/TiO(2) nanotube-array coaxial heterogeneous structure are discussed. In comparison with a pure TiO(2) nanotube array, a 5-fold enhancement in photoactivity was observed using the coaxial heterogeneous structure. This methodology may be useful in designing multijunction semiconductor materials for coating of highly structured substrates.
Applications of Alternative Nucleases in the Age of CRISPR/Cas9 (2017)

Breakthroughs in the development of programmable site-specific nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases (MNs), and most recently, the clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (including Cas9) have greatly enabled and accelerated genome editing. By targeting double-strand breaks to user-defined locations, the rates of DNA repair events are greatly enhanced relative to un-catalyzed events at the same sites. However, the underlying biology of each genome-editing nuclease influences the targeting potential, the spectrum of off-target cleavages, the ease-of-use, and the types of recombination events at targeted double-strand breaks. No single genome-editing nuclease is optimized for all possible applications. Here, we focus on the diversity of nuclease domains available for genome editing, highlighting biochemical properties and the potential applications that are best suited to each domain.
Sensitivity of Silicon Photomultipliers to Direct Gamma Ray Irradiation (2019)

Silicon photomultipliers (SiPMs) from various manufacturers are shown to be sensitive to gamma-ray ionizing radiation without being coupled to a scintillator. Survey measurements of units from Hamamatsu, SENSL, and KETEK are shown, followed by detailed measurements of units from SENSL. Pulseheight spectroscopy of gamma-ray-induced signals reveals large pulses in excess of 16 microcells excited per event and as large as ~100 excited microcells. We review other examples of direct excitation by ionizing radiation found in the literature and surmise the effect that is related to the scattered charged particles (electrons) passing through the SiPM. We demonstrate that this direct sensitivity extends to cosmic-ray secondaries by a triple-coincidence experiment. The precise signal producing mechanism is unclear. The signal may be due to light producing processes, such as Čerenkov or scintillation in the optical windows, or charged particle ionization in the microcell layer, which may induce avalanches in microcells along the particle track. Possible applications and avenues for future study are suggested.
Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals (2012)

Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14,500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001). Furthermore, analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter-remarkable difference in promoter activity in the 'quadruplex-destabilized' versus 'quadruplex-intact' promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.
Performance of AlGaAs/GaAs quantum wire lasers fabricated on sub-/spl mu/m-pitch gratings: in both distributed feedback- and wire-directions (2000)

Summary form only given. With the rapid progress of modern technologies in epitaxial growth and lithography, many challenges for sophisticated optoelectronic devices, incorporating low-dimensional structures inside for example, have been increasingly attempted. One of those is the effort to materialize quantum wire (QWR) gain coupled (GC) distributed feedback (DFB) lasers, in which a purely periodic-gain structure is expected to offer a high yield, single mode emission without facet coatings or quarter-wave-shifted gratings, high immunity from feedback and low chirp under high speed modulation. In the presentation, challenging work on the successful fabrication of the so-called one-step QWR GC-DFB lasers in directions perpendicular to the wire axis is targeted along with a high-density of QWR array lasers in directions parallel to the wire.
Collaborative filtering for music recommender system (2017)

Nowadays recommender systems is a software that is used as an important tool of e-commerce, which helps to analyze users' tastes and provide them with lists of products that they would like to prefer. This paper is an investigation of using collaborative filtering techniques for a music recommender system. Collaborative filtering is the technology that focuses on the relationships between users and between items to make a prediction. The goal of the recommender system is to compute a scoring function that aggregates the result of computing similarities between users and between items. We focus on the reviewing two strategies of collaborative filtering: user-based and item-based recommendations. For experimental purpose we explore different metrics to measure the similarity of users and items such as Euclidean distance, cosine metric, Pearson correlation and others. Finally, we compare different evaluations metrics that represent the effectiveness of the recommender system.
Gas assisted thin-film evaporation from confined spaces (2011)

A novel cooling mechanism based on evaporation of thin liquid films is presented for thermal management of confined heat sources, such as microprocessor hotspots. The underlying idea involves utilization of thin nanoporous membranes for maintaining microscopically thin liquid films by capillary action, while providing a pathway for the vapor generated due to evaporation at the liquid-vapor interface. The vapor generated by evaporation is continuously removed by using a dry sweeping gas keeping the membrane outlet dry. This thesis presents a detailed theoretical, computational and experimental investigation of the heat and mass transfer mechanisms that result in dissipating heat.\n\nPerformance analysis of this cooling mechanism demonstrates heat fluxes over 600W/cm2 for sufficiently thin membrane and film thicknesses (~1-5µm) and by using air jet impingement for advection of vapor from the membrane surface. Based on the results from this performance analysis, a monolithic micro-fluidic device is designed and fabricated incorporating micro and nanoscale features. This MEMS/NEMS device serves multiple functionalities of hotspot simulation, temperature sensing, and evaporative cooling. Subsequent experimental investigations using this microfluidic device demonstrate heat fluxes in excess of 600W/cm2 at 90 C using water as the evaporating coolant.\n\nIn order to further enhance the device performance, a comprehensive theoretical and computational analysis of heat and mass transfer at micro and nanoscales is carried out. Since the coolant is confined using a nanoporous membrane, a detailed study of evaporation inside a nanoscale cylindrical pore is performed. The continuum analysis of water confined within a cylindrical nanopore determines the effect of electrostatic interaction and Van der Waals forces in addition to capillarity on the interfacial transport characteristics during evaporation. The detailed analysis demonstrates that the effective thermal resistance offered by the interface is negligible in comparison to the thermal resistance due to the thin film and vapor advection. In order to determine the factors limiting the performance of the MEMS device on a micro-scale, a device-level detailed computational analysis of heat and mass transfer is carried out, which is supported by experimental investigation. Identifying the contribution of various simultaneously occurring cooling mechanisms at different operating conditions, this analysis proposes utilization of hydrophilic membranes for maintaining very thin liquid films and further enhancement in vapor advection at the membrane outlet to achieve higher heat fluxes.
DNA-binding properties of FOXP3 transcription factor (2017)

FOXP3, a lineage-specific forkhead (FKH) transcription factor, plays essential roles in the development and function of regulatory T cells. However, the DNA-binding properties of FOXP3 are not well understood. In this study, FOXP3 fragments containing different domains were purified, and their DNA-binding properties were investigated using electrophoretic mobility shift assay and isothermal titration calorimetry (ITC). Both the FKH and leucine-zipper domains were required for optimal DNA binding for FOXP3. FOXP3 protein not only binds with DNA sequences containing one FKH consensus sequence, but also binds with DNA sequences with two direct repeats of consensus sequences separated by three-nucleotides (DRE3). Our results shed lights on the mechanisms by which FOXP3 recognizes cognate DNA elements, and would facilitate further structural and functional studies of FOXP3.