gebhart/patrepeval huggingface dataset:
Optical properties of two-layer one-dimensional magneto-plasmonic crystals (2010)

This paper discusses the optical properties of magneto-plasmonic crystals, which are one-dimensional metallic gratings deposited on a uniform magnetic dielectric layer. All possible cases of the orientation of the magnetization are investigated. The resonance features in the spectra of magnetooptic effects are explained in terms of the excitation of the intrinsic waves of the system: surface plasmon–polaritons and quasi-waveguide modes of the dielectric layer.
A new rate-based switch algorithm for ABR traffic to achieve max-min fairness with analytical approximation and delay adjustment (2002)

A new rate-based switch mechanism for ABR traffic in ATM networks, which aims to rapidly achieve max-min fairness allocation, is proposed. Simulation results show that the proposed scheme can out-perform both CAPC and ERICA in terms of response times and peak queue lengths. An analytical approximation of the performance is also introduced and its accuracy is found to be close to the simulation results. A variant of the proposed scheme is presented for handling the problem of different source-to-bottleneck separations. By using this scheme, the peak queue lengths at the switches can further be reduced without any degradation in throughput.
High-temperature resistivity of Cr-doped epitaxial GaP (1982)

Epitaxial layers of Cr-doped GaP have been grown by metalorganic chemical vapor deposition. The layers were characterized by capacitance and current-voltage (I-V) measurements on Schottky-barrier structures, and by I-V measurements on layers with alloyed ‘‘quasi-ohmic’’ contacts. A high degree of compensation was achieved, and resistivities of up to 106 Ω cm were measured. The temperature dependence of the resistivity was measured up to 475 °C, and analysis of the results indicates two high-temperature activated processes, with activation energies of 0.13 and about 1.0 eV. This material may be useful in GaP high-temperature device technology.
Data from Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival (2023)

&lt;div&gt;Abstract&lt;p&gt;Prognosis of triple-negative breast cancer (TNBC) remains poor. To identify shared and selective vulnerabilities of basal-like TNBC, the most common TNBC subtype, a directed siRNA lethality screen was performed in 7 human breast cancer cell lines, focusing on 154 previously identified dependency genes of 1 TNBC line. Thirty common dependency genes were identified, including multiple proteasome and RNA splicing genes, especially those associated with the U4/U6.U5 tri-snRNP complex (e.g., &lt;i&gt;PRPF8, PRPF38A&lt;/i&gt;). &lt;i&gt;PRPF8&lt;/i&gt; or &lt;i&gt;PRPF38A&lt;/i&gt; knockdown or the splicing modulator E7107 led to widespread intronic retention and altered splicing of transcripts involved in multiple basal-like TNBC dependencies, including protein homeostasis, mitosis, and apoptosis. E7107 treatment suppressed the growth of basal-A TNBC cell line and patient-derived basal-like TNBC xenografts at a well-tolerated dose. The antitumor response was enhanced by adding the proteasome inhibitor bortezomib. Thus, inhibiting both splicing and the proteasome might be an effective approach for treating basal-like TNBC. &lt;i&gt;Mol Cancer Ther; 16(12); 2849–61. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Platinum silicide as electrode material of microfabricated quantum electron tunneling transducers (2010)

The platinum silicide is proposed as electrode material for electrostatically controlled MEMS/NEMS, in our case - for nanoelectromechanical sensors based on quantum electron tunneling. The process flow of device fabrication is presented and reasons to use platinum silicide as metallization material are described. In this paper we also demonstrate the use of conductive atomic force micoscopy (AFM) in spreading resistance imaging mode for inspection of topography and electrical properties of platinum silicide surface. The goal of this study is to define the platinum silicide films structural and electrical properties variation after thermal processing (conventional operation in CMOS process flow) and to correct the process flow parameters as may be required. Both AFM-inspection operations of pre- and post-thermal processed test structures are performed. The experimental results are presented.
Mutagenesis of the Novel <i>Hericium erinaceus</i> Ribonuclease, RNase He1, Reveals Critical Responsible Residues for Enzyme Stability and Activity (2014)

Here, we determined the sequence of a cDNA encoding a guanylic acid-specific ribonuclease (RNase He1) from Hericium erinaceus that exhibits high sequence identity (59%) with RNase Po1, an enzyme with anti-cancer activity and which is found in Pleurotus ostreatus. RNase He1 and RNase Po1 have similar structures and heat stabilities; hence, RNase He1 may also have potential as an anti-cancer agent. Therefore, we initiated structure-function studies to further characterize the enzyme. Based on the RNase Po1 structure, RNase He1 is predicted to form 3 disulfide bonds involving Cys7-Cys98, Cys5-Cys83, and Cys47-Cys81 linkages. The Cys5Ala mutant exhibited no RNase activity, whereas the Cys81Ala mutant retained RNase activity, but had reduced heat stability. Therefore, the Cys5-Cys83 bond in RNase He1 is essential for the structure of the RNase active site region. Similarly, the Cys47-Cys81 bond helps maintain the conformational stability of the active site region, and may contribute to the greater heat stability of RNase He1.
Vacancy Diffusion in NaAlH4 and Na3AlH6 (2011)

In recent years there has been considerable interest in sodium alanate as a prototypical complex hydride for solid-state hydrogen storage. Much effort has gone into understanding the rate-limiting processes in its hydrogen release and absorption reactions. The diffusion of metal species has been suggested as a possible kinetic bottleneck in Ti-doped materials. In this paper, we outline an approach for calculating the diffusivity of defects in complicated lattices using a combination of first-principles density-functional theory calculations and stochastic kinetic Monte Carlo methods. We apply this methodology to the diffusion of metal defects in NaAlH4 and Na3AlH6 that have been predicted to exist in large concentrations. We find that of the metal defects that exist in the largest concentrations, a neutral AlH3 vacancy is the most mobile in NaAlH4 (ΔHmig = 0.34 eV, D0 = 1.30 × 10–2 cm2/s, and DT=400K = 7.55 × 10–7 cm2/s) and that a negatively charged Na vacancy is the most mobile in Na3AlH6 (ΔHmig = 0.33 eV, D0 = 6.67 × 10–3 cm2/s, and DT=400K = 4.96 × 10–7 cm2/s). At T = 400 K, the calculated diffusion rates are an order of magnitude lower for charged AlH4 vacancies in NaAlH4 (ΔH = 0.44 eV, D0 = 1.41 × 10–2 cm2/s, and DT=400K = 3.92 × 10–8 cm2/s) and charged Na vacancies in NaAlH4 (ΔH = 0.43 eV, D0 = 2.96 × 10–3 cm2/s, and DT=400K = 1.19 × 10–8 cm2/s). This information is necessary for understanding the kinetics of mass transport during the hydrogen release and absorption reactions of NaAlH4.
Supplementary Figure from Immunoprevention of HER-2/<b><i>neu</i></b> Transgenic Mammary Carcinoma through an Interleukin 12-Engineered Allogeneic Cell Vaccine (2023)

&lt;p&gt;Microarray cluster analysis&lt;/p&gt;
On tokamak ignition equilibria and thermal stability (1980)

Tokamak ignition equilibria and their stability are examined in a radially dependent model with empirical (Alcator) scaling for the energy confinement time. The empirical energy loss term corresponds to a diffusion operator, whose stationary eigenfunctions are the ignition equilibria. The dispersion relation for fluctuations around these equilibria is then derived, yielding the threshold for thermal instability. The instability growth rate is non-linearly enhanced by broadening of the temperature profile, which broadening is itself caused by an increase in temperature. Saturation of the instability occurs at a lower temperature than that indicated by zero-dimensional considerations. The model system appears to have no built-in saturation mechanism, other than the D-T reaction slow-down.
Asservissement visuel à partir de droites et auto-étalonnage pince-caméra (1999)

L'utilisation de droites en asservissement visuel pose, contrairement au cas des points, un probleme de representation. Nous y avons repondu en nous basant sur les coordonnees de Plucker d'une droite, ce qui nous a permis d'introduire la notion d'alignement en coordonnees de Plucker binormees. Grâce a ces dernieres, nous avons defini deux lois de commande voisines qui realisent le nouvel alignement ; sont explicites et partiellement decouplees entre rotation et translation ; melangent informations 2D et 3D ; et enfin, ne necessitent pas d'estimation de profondeur. Nous avons exhibe des resultats de convergence de ces lois et caracterise leurs singularites. Nous avons ensuite applique ces lois au positionnement d'une camera face a un triedre orthogonal. Cette configuration ne permet pas d'observer la profondeur. Pour compenser ce manque, nous avons adjoint un pointeur laser non etalonne a la camera. En reformulant le probleme d'etalonnage pince-camera par un systeme purement lineaire, nous avons produit une analyse algebrique du systeme et une classification des mouvements d'etalonnage. Les procedures classiques sont contraignantes puisqu'elles necessitent l'observation d'une mire et/ou l'interruption de la tâche effectuee par le robot. Afin de lever ces contraintes, nous avons adapte notre methode lineaire pour proposer une methode d'auto-etalonnage, qui se passe de mire, et une methode d'etalonnage en ligne, qui n'interrompt pas la tâche.
Measuring real-time blood viscosity with a ventricular assist device (2019)

Ventricular assist devices assist in blood circulation and form a crucial component of artificial hearts. While it is important to measure parameters such as the flow rate, pressure head and viscosity of the blood, implanting additional devices to do such measurements is inadvisable. To this end, we demonstrate the adaptation of a ventricular assist device for the purpose of measuring blood viscosity. Such an approach eliminates the need for additional dedicated viscometers in artificial hearts. In the proposed method, the blood viscosity is measured by applying radial vibrational excitation to the impeller in a ventricular assist device using its magnetic levitation system. During the measurement, blood is exposed to a combination of a low shear rate (≈100/s) generated by the radial vibration of the impeller and a high shear rate (>10,000/s) generated by the impeller's rotation. The apparent viscosity of blood depends on the shear rate, so we determined which shear rate was the dominant one in the proposed method. The measurement results showed that the viscosity measured by the proposed method was in good agreement with the reference viscosity measured with a high shear rate. The mean absolute deviation in the measurements using the proposed method and those obtained using a concentric cylindrical viscometer at a high shear rate was 0.12 mPa s for four samples of porcine blood, with viscosities ranging from 2.32 to 2.75 mPa s.
Quantitative metabolomic and lipidomic profiling reveals aberrant amino acid metabolism in type 2 diabetes (2012)

Type 2 diabetes (T2DM) is a multi-factorial disease with a complex pathogenic mechanism; however a complete understanding of precise biochemical alterations accompanying the onset and progression of T2DM is lacking. Using a combination of untargeted and targeted metabolomic profiling approach we were able to delineate significantly altered metabolites in the diabetic (T2DM) group. Our results indicate significant perturbations in amino acid metabolism, TCA cycle and glycerol-phospholipid metabolism possibly impacting the overall glucose homeostasis in T2DM. A systems approach offers promise towards identification of clinically relevant markers of T2DM and novel molecular targets to foster drug discovery for effective therapeutic development for diabetes.
Resonant multiphoton optogalvanic detection of atomic hydrogen in flames (1982)

Atomic hydrogen has been studied in an atmospheric-pressure hydrogen-air flame by using resonant multiphoton optogalvanic spectroscopy. This technique offers excellent spatial and temporal resolution, with an estimated sensitivity at the 1-part-in-10(6) level. This experiment represents the first reported direct, in situ optical detection of the extremely important hydrogen radical in a combustion environment.
Remarkable Reactivity Difference in Oxygen-Substituted versus Non-Oxygen-Substituted Bromoalkynes in Cu(I)-Catalyzed Cross-Coupling Reactions:  Total Synthesis of (−)-S-18-Hydroxyminquartynoic Acid (2003)

The conjugated tetraacetylenic natural product (S)-18-hydroxyminquartynoic acid (2) is synthesized in five linear steps and 17.7% overall yield from commercially available 1,2,5,6-O-diisopropylidene mannitol. The key step is a one-pot three-component Cadiot-Chodkiewicz reaction affording the tetrayne unit. The oxygen-substituted bromoalkyne 10 was found to react at a much faster rate than the non-oxygen-substituted bromoalkyne 6 in the key step. The undesired symmetric cross-coupling by 10 generates a symmetric tetrayne intermediate, which undergoes a nucleophilic addition by 1 equiv of ethylamine. This side reaction is suppressed by controlling the order and rate of addition of each component and by reducing the amount of ethylamine.
Re: Reconstitution of Experimental Neurogenic Bladder Dysfunction Using Skeletal Muscle-Derived Multipotent Stem Cells (2011)

No AccessJournal of UrologyInvestigative Urology1 Jan 2011Re: Reconstitution of Experimental Neurogenic Bladder Dysfunction Using Skeletal Muscle-Derived Multipotent Stem Cells Anthony AtalaM.D. Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(11)60069-4AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Reconstitution of Experimental Neurogenic Bladder Dysfunction Using Skeletal Muscle-Derived Multipotent Stem Cells." The Journal of Urology, 185(1), p. 353 © 2011 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 185Issue 1January 2011Page: 353 Advertisement Copyright & Permissions© 2011 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF DownloadLoading ...
Cytochemical classification of nonpalpable breast carcinoma. (1983)

A stereotaxic needle biopsy technique makes it possible to obtain diagnostic cytologic material from nonpalpable breast lesions down to sizes of 2 to 3 mm in diameter. Considering the high correlation between the type of DNA distribution pattern and patient survival demonstrated in palpable breast carcinomas, cytophotometric DNA measurements were performed on smear preparations from nonpalpable tumors. In a series of 30 consecutive nonpalpable breast carcinomas, the same types of DNA profiles as shown in palpable tumors were found. This indicates that malignancy grading of breast carcinomas by cytochemical means can be performed on stereotaxic needle biopsy material and that an improved prognostic evaluation may be expected by the use of the methods described. This should result in a better therapeutic approach to patients with nonpalpable breast tumors.
Deterministic Hardness Amplification via Local GMD Decoding. (2007)

We study the average-case hardness of the class NP against deterministic polynomial time algorithms. We prove that there exists some constant μ > 0 such that if there is some language in NP for which no deterministic polynomial time algorithm can decide L correctly on a 1 − (log n) fraction of inputs of length n, then there is a language L in NP for which no deterministic polynomial time algorithm can decide L correctly on a 3/4+(logn) fraction of inputs of length n. In coding theoretic terms, we give a construction of a monotone code that can be uniquely decoded up to error rate 1 4 by a deterministic local decoder.
Controlled fusion burning and current drive in a degenerate plasma (2006)

Summary form only given. In a Fermi-degenerate plasma, the rates of electron physical processes, such as collision, bremsstrahlung, inverse bremsstrahlung and Compton scattering, are much reduced due to the Fermi-Dirac statistics. Especially, ion-electron couplings (ion-electron collision and electron-ion collision) are vastly reduced. We use this fact about reduced ion-electron coupling in addressing two well-known plasma physics problems: advanced fuel burning and current drive. We show how, in a degenerate plasma, changes in the power balance for fusion make feasible regimes where aneutronic fuel can be ignited. For electron-based current drive mechanisms, the current drive efficiency is higher than n the classical prediction by more than a factor of 6 in a degenerate hydrogen plasma, mainly because the electron-electron collisions do not quickly slow down fast electrons. Moreover, electrons much faster than thermal speeds are more readily excited without exciting thermal electrons. In ion- based mechanisms of current drive, the efficiency is likewise enhanced due to the degeneracy effects, since the electron stopping power on slow ion beams is significantly reduced
Exposure of surfactant protein A to ozone in vitro and in vivo impairs its interactions with alveolar cells (1992)

This study focused on the question of whether exposure of surfactant protein A (SP-A) to ozone affected properties of this protein that may be involved in regulating alveolar type II cell and alveolar macrophage functions. In vitro exposure of human or canine SP-A to ozone reduced the ability of this protein to inhibit phorbol-ester induced secretion of [3H]phosphatidylcholine by alveolar type II cells in culture. Ozone-exposed human SP-A showed a decreased ability to enhance phagocytosis of herpes simplex virus and to stimulate superoxide anion production by alveolar macrophages. Experiments with elastase showed that ozone-exposed canine SP-A was more susceptible to proteolysis. A conformational change of the protein could underlie this phenomenon. Surfactant isolated from ozone-exposed rats (0.4 ppm ozone for 12 h) was also less able to stimulate superoxide anion production by alveolar macrophages than surfactant from control rats, which suggested that SP-A in vivo was also susceptible to ozone. The results of this study suggest that SP-A-alveolar cell interactions can be inhibited by ozone exposure, which may contribute to the toxicity of ozone in the lungs.
Abstract 799: Aberrant mitochondrial protein involvement through early PDAC initiation and progression using multiplexed DNA-PAINT and correlative histology (2019)

Abstract Prior to pancreatic ductal adenocarcinoma (PDAC), pancreatic acini cells change their morphology through pancreatic intraepithelial neoplasia (PanIN) stages, becoming increasingly dysplastic as stroma and tissue hypoxia increase. This increasing hypoxia forms a cancer promoting microenvironment, wherein we propose metabolic changes trigger aberrant mitochondrial networks form healthy tissue. We developed tissue superresolution imaging to directly quantify structural mitochondrial response through patient histology, whereby DNA-PAINT can provide super-resolution detail decoupled from photo bleaching to visualize mitochondria through tissue layers. Expanding from preliminary data, target mitochondrial dynamics proteins’ organization will also be correlated to PanIN stages. Introduction: Early oncogene involvement in PDAC progression links to metabolic and mitochondrial regulatory changes. Typically nutrient deprivation and hypoxia trigger cell death from increased reactive oxygen species production and organelle damage which trigger apoptosis, yet these prolonged effects can be cancer promoting when less severe. Mitochondrial dynamics and proteins related to mitochondrial fission and fusion can reduce apoptotic signaling, enhance aerobic glycolysis, and increase ROS to allow cancer progression. Materials and Methods: Adapting from previous proof of concept, mitochondria (TOM20) within formalin-fixed paraffin embedded (FFPE) tissue sections were imaged with stochastic optical reconstruction microscopy (STORM). In brief: cadaver healthy pancreas FFPE tissue samples underwent deparafinization, antigen retrieval, indirect immuno-labeling with AlexaFluor647, TIRF illumination with a 60x objective was used for data collection, whereby data processing was conducted using the open-source FIJI and custom MATLAB software. Results and Discussion: Preliminary data shows proof of principle that both STORM and DNA-PAINT can be correlated to histological staining of human pancreas. Conclusions: Superresolution imaging reveals ultrastructural details of mitochondria in FFPE patient samples not resolved via conventional fluorescence imaging. Through quantitative feature analysis, we would be able to correlate aberrant mitochondria structure and abundance to PDAC progression. Acknowledgements: Funding provided by the Cancer Early Detection Advanced Research (CEDAR) Center of OHSU Knight Cancer Institute. Citation Format: Matthew J. Rames, Fehmi Civitci, Ting Zheng, Josiah Wagner, Jason Link, Xiaolin Nan. Aberrant mitochondrial protein involvement through early PDAC initiation and progression using multiplexed DNA-PAINT and correlative histology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 799.
Design of a 5-phase permanent magnet brushless DC motor for automobiles (2003)

Permanent magnet (PM) brushless DC motors (BDCM) have been increasingly used in automobiles due to their light weight, small size, high efficiency, high reliability, variable speed operation and good dynamic performance. This paper presents the design and development of a 5-phase BDCM for automobiles. Both the analytical method and finite element method (FEM) were used. The analytical method based on generalized electrical machine theory was applied to the preliminary design of the BDCM in conjunction with the empirical method. The model of the BDCM, along with those of the motor controller and load, was developed for simulation studies. The FEM was used to calculate electromagnetic torque due to PM-current interaction, torque ripple due to reluctance variation of teeth and slots, average airgap flux density, maximum flux densities in the rotor and stator, self-inductances, mutual inductances, and back-emf waveforms. A range of geometrical variations was investigated by the authors for the BDCM design. The 5-phase BDCM was developed based on the design and has been in mass production for automobiles. The test waveforms are presented in this paper to offer a comparison with those obtained using the analytical and FEM methods.