gebhart/patrepeval huggingface dataset:
Molecular characteristics of non-small cell lung cancer (NSCLC) patients sensitive to gefitinib (2004)

7025 Background: Gefitinib (Iressa), a small molecule inhibitor of the epidermal growth factor receptor tyrosine kinase (EGFR-TK), induces objective regressions in 9–18% of NSCLC patients. Bronchioloalveolar histology and smoking history may predict response to gefitinib (Shah, NT, Proc ASCO 2003). Molecular studies to date have not shown any correlation between EGFR status and sensitivity to gefitinib (Bailey LR, Proc AACR 2003). To determine molecular characteristics predictive of sensitivity, we undertook selected analyses in gefitinib-sensitive and –refractory patients. Methods: Unstained slides or pathology blocks were collected on an IRB-approved protocol from 54 of 139 consecutive NSCLC patients treated at MSKCC with single agent gefitinib from 09/98 –11/02. Immunohistochemistry was performed on anonymized samples for total EGFR, the putative target of gefitinib; HER2/NEU, an EGFR family member whose co-expression may predict poorer outcome in NSCLC; phospho-AKT, an activated downstream signaling molecule that may confer resistance to gefitinib; and p53, a tumor suppressor gene frequently altered in NSCLC. Staining was graded by 2 pathologists blinded to clinical variables and outcomes. Results: The status of EGFR, HER2, p-AKT, and p53 are given in the table below. Among 20 patients whose tumors were EGFR(+) and HER2(+), 9 were gefitinib-sensitive; by contrast, only 1 of 8 patients whose tumors were negative for both markers was sensitive (p=0.19). Conclusions: We found no relationship between total EGFR, p-AKT or p53 and sensitivity to gefitinib. HER2 expression (63%) was higher than that usually reported in NSCLC. The high percentage (80%) of HER2-positive tumors among gefitinib-sensitive patients warrants confirmation in a larger series, and strategies to block concurrently both EGFR and HER2 may be clinically useful. Studies on p-EGFR, p-MAPK, and PTEN are in progress. Author Disclosure Employment or Leadership Consultant or Advisory Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration AstraZeneca AstraZeneca AstraZeneca Telek AstraZeneca
Numerical analysis of antenna fields using multipole expansions (2006)

A new systematic approach is described which can be used to efficiently obtain the frequency- and time-domain multipole amplitudes of the electromagnetic field due to an arbitrary linear antenna. In particular, the method is perfectly fitted for the finite-difference time-domain (FDTD) method, which is first used to obtain the time-domain multipole amplitudes of the antenna driven by a wide-band signal. Though the time-domain representation is valid in the far-field only, a single numerically performed Fourier transform leads to the frequency-domain multipole amplitudes valid for the entire spectrum of the input impulse and at any point outside a minimum sphere which contains all radiating elements.
Precision Lattice Constants from X-Ray Powder Photographs (1935)

A very general method is given for the calculation of lattice constants from powder photographs in which there is taken into account the various systematic errors inevitable in such photographs, including radius errors, film shrinkage, absorption, eccentricity and finite slit height. While the solution of the data is made by least squares, it is not at all laborious and is much simpler than the various methods, both analytical and graphical, which have previously been proposed. Examples are given of cubic, hexagonal and orthorhombic structures solved in this way using data from Debye and focusing cameras, extension to other structures and cameras being made evident. In effect, powder cameras become absolute instruments, independent of calibrating substances, and dependent only on the value of the x-ray wavelength.
Synthesis of (.+-.)-methyl epijasmonate and (.+-.)-methyl cucurbate. (1987)

A novel synthesis of (±)-methyl epijasomonate (2) and the first synthesis of (±)-methyl cucurbate (4) were achieved starting from 2-allylcyclohexane-1, 3-dione (8). The synthetic epimer 2 had a stronger jasmin flavor than the trans-isomer 1 with 95% purity.
The Digital Marauder's Map: A New Threat to Location Privacy (2009)

"The Marauder's Map" is a magical map in J. K. Rowling's fantasy series, "Harry Potter and the Prisoner of Azkaban". It shows all moving objects within the boundary of the "Hogwarts School of Witchcraft and Wizardry". In this paper, we introduce a similar attack to location privacy in wireless networks. Our system, namely the digital Marauder's map, can reveal the locations of WiFi-enabled mobile devices within the coverage area of a single high-gain antenna. The digital Marauder's map is built solely with off-the-shelf wireless equipments, and features a mobile design that can be quickly deployed to a new location and instantly used without training. We present a comprehensive set of theoretical analysis and experimental results which demonstrate the coverage and localization accuracy of the digital Marauder's map.
Silver metallization for advanced interconnects (1999)

Silver metal has the highest room-temperature electrical conductivity of any substance; however, it has found limited acceptance in the electronic industry (e.g., silver filled epoxy) due to the high rate of metal corrosion and migration causing dendrites and electrical failures. With decreasing transistor feature sizes, device-operating voltages have scaled down considerably. In this paper, the reliability of silver and potential benefits of silver metallization are discussed in terms of future trends in microelectronic interconnections. Experimental data supports existing reliability models indicating that electrochemical migration failure modes may not be operative at low voltages. Silver metal corrosion and migration are studied under accelerated test conditions to obtain a qualitative understanding of the failure mechanism.
Role of tyrosine‐80 in the stability of kanamycin nucleotidyltransferase analyzed by site‐directed mutagenesis (1988)

A thermostable mutant of kanamycin nucleotidyltransferase (KNTase) with a single amino acid replacement of Asp at position 80 by Tyr has been isolated by a novel screening method in a previous study [Matsumura, M. & Aiba, S. (1985) J. Biol. Chem. 260, 15298-15303]. To elucidate the role of Tyr80 in stabilizing the enzyme, the KNTase gene was modified by site-directed mutagenesis so that the codon for Asp80 of the wild type was replaced by that for Ser, Thr, Ala, Val, Leu, Phe and Trp, respectively. The eight mutant KNTases including Tyr80 were all purified, as well as the wild-type enzyme. The heat-inactivation rate constants were determined at 58 degrees C and the half-life values were found to be correlated with the hydrophobicity of the amino acid residues replaced at the unique position. The Gibbs energy change of unfolding in water of KNTase assessed from urea denaturation (25 degrees C, pH 7.0) was also found to be correlated with hydrophobicity. The results suggest that different amino acids at position 80 of KNTase contribute to the stability of the protein by hydrophobic interactions. In the case of tyrosine at position 80 the unusually high stability of the enzyme compared to the Phe80 enzyme suggests that the hydroxyl group also contributes to the conformational stability.
SEEDS: Superpixels Extracted Via Energy-Driven Sampling (2015)

Superpixel algorithms aim to over-segment the image by grouping pixels that belong to the same object. Many state-of-the-art superpixel algorithms rely on minimizing objective functions to enforce color homogeneity. The optimization is accomplished by sophisticated methods that progressively build the superpixels, typically by adding cuts or growing superpixels. As a result, they are computationally too expensive for real-time applications. We introduce a new approach based on a simple hill-climbing optimization. Starting from an initial superpixel partitioning, it continuously refines the superpixels by modifying the boundaries. We define a robust and fast to evaluate energy function, based on enforcing color similarity between the boundaries and the superpixel color histogram. In a series of experiments, we show that we achieve an excellent compromise between accuracy and efficiency. We are able to achieve a performance comparable to the state-of-the-art, but in real-time on a single Intel i7 CPU at 2.8GHz.
Energy-efficient STDP-based learning circuits with memristor synapses (2014)

It is now accepted that the traditional von Neumann architecture, with processor and memory separation, is ill suited to process parallel data streams which a mammalian brain can efficiently handle. Moreover, researchers now envision computing architectures which enable cognitive processing of massive amounts of data by identifying spatio-temporal relationships in real-time and solving complex pattern recognition problems. Memristor cross-point arrays, integrated with standard CMOS technology, are expected to result in massively parallel and low-power Neuromorphic computing architectures. Recently, significant progress has been made in spiking neural networks (SNN) which emulate data processing in the cortical brain. These architectures comprise of a dense network of neurons and the synapses formed between the axons and dendrites. Further, unsupervised or supervised competitive learning schemes are being investigated for global training of the network. In contrast to a software implementation, hardware realization of these networks requires massive circuit overhead for addressing and individually updating network weights. Instead, we employ bio-inspired learning rules such as the spike-timing-dependent plasticity (STDP) to efficiently update the network weights locally. To realize SNNs on a chip, we propose to use densely integrating mixed-signal integrate-andfire neurons (IFNs) and cross-point arrays of memristors in back-end-of-the-line (BEOL) of CMOS chips. Novel IFN circuits have been designed to drive memristive synapses in parallel while maintaining overall power efficiency (<1 pJ/spike/synapse), even at spike rate greater than 10 MHz. We present circuit design details and simulation results of the IFN with memristor synapses, its response to incoming spike trains and STDP learning characterization.
Gold nanoparticle/ZnO nanorod hybrids for enhanced reactive oxygen species generation and photodynamic therapy (2015)

金 nanoparticle (Au NP )@ ZnO nanorod (NR )(Au@ZnO ) 有各种各样的 ZnO 的混血儿: Au 臼齿的比率被开发在光力学的治疗(太平洋夏季时间) 提高反应的氧种类(ROS ) 的产生应用程序。介绍在 Au NP 和 ZnO NR 之间的一个金属 / 半导体 heterostructure 接口调制了电子转移在下面紫外(紫外) 照耀，它戏剧性地在 ZnO 压制了电子洞再结合并且同时在 Au NP 表面与高精力增加了激动的电子的数量。因此， nanohybrid 的 ROS 收益更加独自太古的 Au NP 或 ZnO NR 在那些上被改进并且表明了 1 + 1 > 2 效果。这改进随混血儿的 Au 的比例的增加被加强。结果证明有 ZnO 的 Au@ZnO nanohybrids : 因为他们有在 Au 和 ZnO 之间的最大的接口区域， 20:1 的 Au 比率产生了最高的 ROS 收益，它接着在太平洋夏季时间期间为 HeLa 和 C2C12 房间导致了最低房间生存能力。而且， ROS 产生和房间破坏断然与 nanohybrid 剂量被相关。Au@ZnO 混血儿(20:1， 100 g/mL ) 导致了为 2 min 象 28% 一样在紫外暴露以后低的 HeLa 房间生存能力，它显示了它的有希望的潜力改进太平洋夏季时间的治疗学的功效。
Quality Assessment of DIBR-Synthesized Images by Measuring Local Geometric Distortions and Global Sharpness (2017)

Depth-image-based rendering (DIBR) is a fundamental technique in free viewpoint video, which is widely adopted to synthesize virtual viewpoints. The warping and rendering operations in DIBR generally introduce geometric distortions and sharpness change. The state-of-the-art quality indices are limited in dealing with such images since they are sensitive to geometric changes. In this paper, a new quality model for DIBR-synthesized view images is presented by measuring LOcal Geometric distortions in disoccluded regions and global Sharpness (LOGS). A disoccluded region detection method is first proposed using SIFT-flow-based warping. Then, the sizes and distortion strength of local disoccluded regions are combined to generate a score. Furthermore, a reblurring-based strategy is proposed to quantify the global sharpness. Finally, the overall quality score is calculated by pooling the scores of local disoccluded regions and global sharpness. Experiments on four public DIBR-synthesized image/video databases show the superiority of the proposed metric over the state-of-the-art quality models. The proposed method is further adopted for boosting the performances of existing quality metrics and benchmarking DIBR algorithms, both achieving very promising results.
A Neutron Detector Having Uniform Sensitivity from 10 Kev to 3 Mev (1947)

A neutron detector having approximately uniform sensitivity from 10-kev neutron energy to 3-Mev energy is described. The arrangement, known as a long counter, consists of a paraffin cylinder about 10\ensuremath{''} outer diameter \ifmmode\times\else\texttimes\fi{}12\ensuremath{''} long surrounding a long boron trifluoride proportional counter. Sensitivity curves are given for two of the best arrangements. The response is flat over the above range to about 10 percent.
Synthesis of poly(chitosan‐<i>N</i>‐isopropylacrylamide) complex particles with the method of soapless dispersion polymerization (2003)

Abstract Crosslinked poly(chitosan‐ N ‐isopropylacrylamide) [poly(NIPAAM‐chitosan)] complex particles were successfully synthesized with the method of soapless dispersion polymerization. The anionic initiator ammonium persulfate (APS) and the cationic initiator 2,2′‐azobis(2‐methylpropionamidine) dihydrochloride (AIBA) were used to initiate the copolymerization. The poly(NIPAAM‐chitosan) copolymer particles synthesized with APS as the initiator had a homogeneous morphology, whereas the copolymer particles synthesized with AIBA as the initiator showed a core–shell morphology. In addition, various variables such as the particle size, reaction rate, and ζ potential were taken into account. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2053–2063, 2003
AMD and the alternative complement pathway: genetics and functional implications (2016)

Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses. Here, we review the genetic architecture of AMD, considering the contribution of both common and rare alleles to susceptibility, and we explore the possible mechanistic links between photoreceptor degeneration and the alternative complement pathway, a cascade that has emerged as the most potent genetic driver of this disorder.
Optimal Control of Multi-Level Quantum Systems (2011)

This thesis is concerned with the control of quantum systems. Given a Hamiltonian model of a quantum system, we are interested in finding controls---typically shaped electromagnetic pulses---that steer the evolution of the system toward a desired target operation. For this we employ a numerical optimisation method known as the GRAPE algorithm. For particular experimental systems, we design control schemes that respect constraints of robustness and addressability, and are within the reach of the experimental hardware.

A general procedure is given for specifying a Hamiltonian model of a driven N-level system and converting it to an appropriate rotating frame. This is then applied together with the numerical algorithm to design improved schemes for a six-level system, where laser fields manipulate orbital and hyperfine states of Pr3+. The generation of cluster states in Ising-coupled systems is also studied. We find that, in the ideal case, the solution of evolving only under the coupling Hamiltonian is not time-optimal. This surprising result is in contrast to the known cases for unitary gates. For a symmetrised three-qubit example, we provide a geometrical interpretation of this. Numerically optimised control schemes are then developed for a non-ideal coupling topology, modelling an experimental configuration of trapped ions.

Controls for the implementation of the two-qubit Deutsch and Grover algorithms are designed for a pair of 13C nuclear spins at a nitrogen vacancy center in diamond. These implementations are robust to experimental errors, and found to be reproduced with high accuracy on a VFG-150 pulse generator. We also consider two-qubit gate synthesis in a system of superconducting qubits coupled by microwave resonators known as the cavity grid. We find that the optimised schemes allow two-qubit operations to be performed between an arbitrary qubit pair on the grid with only a small time overhead, with speedups of 2-4 over the existing schemes. The methods applied here are fairly general and can be adapted to a variety of other physical systems and tasks.
Cytology (1992)

Exfoliative cytology is a relatively sensitive, highly specific technique for the detection and diagnosis of bladder cancer, and for monitoring conservative treatment. Cytologic diagnosis is based on cellular changes in DNA content, chromatin structure, and metabolic activities which are characteristic of cancer cells and can be recognized in desquamated isolated cells or cell clusters. The cytologic techniques are most effective in identifying low stage flat or papillary carcinoma, but not cytologically benign papillomas or ulcerating invasive cancers that do not easily shed cancer cells. With the growing number of pathologists who, in recent years, have become skilled cytopathologists, urinary tract cytology has developed into an essential diagnostic tool for the urologist.
Presence and detection of carbonates on the Martian surface (2001)

The messages we receive from Mars about the presence of carbonates are quite contradictory. On the one hand, images of the planet clearly show the signatures of past bodies of standing water, where the accumulation of sedimentary deposits should have occurred. On the other hand, the apparent absence of carbonates in the homogeneous fines covering the Martian surface raises the question: where could carbonates hide now? In this paper we discuss the subject and demonstrate that a proposed destruction mechanism, the photodecomposition caused by UV radiation, cannot account alone for the “missing” carbonates. By means of simulations we show that the difficulties in detecting the carbonates can be ascribed to the low temperatures of the emitting zones, observed up to now. Finally, we derive the minimum amount of such minerals that could possibly be detected in future observations of Mars, and we compare the results of simulations with observed spectra.
Quantum Clusters of Gold Exhibiting FRET (2008)

Fluorescence resonance energy transfer between the metal core and the ligand in Au25SG18 (SG-glutathione thiolate) is demonstrated using dansyl chromophores attached to the cluster core through glutathione linkers. The dansyl chromophore functionalization of the cluster has been carried out by two different routes. Efficient energy transfer from the dansyl donor to the Au25 core is manifested by way of the reduced lifetime of the excited state of the former and drastic quenching of its fluorescence. The donor−acceptor separation observed in the two synthetic routes reflects the asymmetry in the ligand binding on the cluster core, which is in agreement with the recent theoretical and experimental results on the structure of Au25.
The Human Immunodeficiency Virus Type 1 (HIV-1) Vpu Protein Interferes with an Early Step in the Biosynthesis of Major Histocompatibility Complex (MHC) Class I Molecules (1997)

The human immunodeficiency virus type 1 (HIV-1) vpu gene encodes a small integral membrane phosphoprotein with two established functions: degradation of the viral coreceptor CD4 in the endoplasmic reticulum (ER) and augmentation of virus particle release from the plasma membrane of HIV-1-infected cells. We show here that Vpu is also largely responsible for the previously observed decrease in the expression of major histocompatibility complex (MHC) class I molecules on the surface of HIV-1-infected cells. Cells infected with HIV-1 isolates that fail to express Vpu, or that express genetically modified forms of Vpu that no longer induce CD4 degradation, exhibit little downregulation of MHC class I molecules. The effect of Vpu on class I biogenesis was analyzed in more detail using a Vpu-expressing recombinant vaccinia virus (VV). VV-expressed Vpu induces the rapid loss of newly synthesized endogenous or VV-expressed class I heavy chains in the ER, detectable either biochemically or by reduced cell surface expression. This effect is of similar rapidity and magnitude as the VV-expressed Vpu-induced degradation of CD4. Vpu had no discernible effects on cell surface expression of VV-expressed mouse CD54, demonstrating the selectivity of its effects on CD4 and class I heavy chains. VV-expressed Vpu does not detectably affect class I molecules that have been exported from the ER. The detrimental effects of Vpu on class I molecules could be distinguished from those caused by VV-expressed herpes virus protein ICP47, which acts by decreasing the supply of cytosolic peptides to class I molecules, indicating that Vpu functions in a distinct manner from ICP47. Based on these findings, we propose that Vpu-induced downregulation of class I molecules may be an important factor in the evolutionary selection of the HIV-1-specific vpu gene by contributing to the inability of CD8+ T cells to eradicate HIV-1 from infected individuals.
Impact of High Pressure and Pulsed Electric Fields on Bioactive Compounds and Antioxidant Activity of Orange Juice in Comparison with Traditional Thermal Processing (2005)

Bioactive compounds (vitamin C, carotenoids, and flavanones) and DPPH* radical scavenging capacity (RSC) were measured in orange juice (OJ) subjected to different technologies. High pressure (HP) (400 MPa/40 degrees C/1 min), pulsed electric fields (PEF) (35 kVcm(-1)/750 micros), low pasteurization (LPT) (70 degrees C/30 s), high pasteurization (HPT) (90 degrees C/1 min), HPT plus freezing (HPT+F) (-38 degrees C/15 min), and freezing (F) were studied. Among the treatments assayed, even though the losses in total vitamin C were < 9%, treatments with the higher temperatures tended to show the higher decrease in the content of both forms of vitamin C. HP treatment led to an increased (P < 0.05) carotenoid release (53.88%) and vitamin A value (38.74%). PEF treatment did not modify individual or total carotenoids content. Traditional thermal treatments did not exert any effect on total carotenoid content or vitamin A value. With regard to individual carotenoid extraction, HPT and HPT+F led to different releases of carotenoids. With respect to flavanones, HP treatment led to increased (P < 0.05) naringenin (20.16%) and hesperetin (39.88%) contents, whereas PEF treatment did not modify flavanone content. In general, pasteurization and freezing process led to a diminished (P < 0.05) naringenin content (16.04%), with no modification in hesperetin. HP and PEF treatments did not modify DPPH* RSC. In the case of traditional thermal technologies, HPT treatment showed a decrease (P < 0.05) in RSC (6.56%), whereas LPT, HPT+F, and F treatments did not modify RSC. Vitamin C modulated RSC, in terms of antioxidant concentration (EC50) and kinetics (AE = 1/EC50TEC50), in the treated and untreated OJ. In summary, HP and PEF technologies were more effective than HPT treatment in preserving bioactive compounds and RSC of freshly squeezed orange juice.