gebhart/patrepeval huggingface dataset:
Abstract 1362: Argonaute 2 controls RAS activation in mouse embryonic fibroblasts (2017)

Abstract The RAS gene family is among the most commonly mutated genes within cancer, and while much research has elucidated the major downstream pathways, including MAPK and PI3K, little progress has been made in successfully targeting mutant RAS in cancer. We recently identified an interaction between the N terminal domain of Argonaute 2 (AGO2), a core component of RNA-induced silencing complex (RISC), and the Switch II domain of KRAS. Furthermore, this interaction was found in all cell lines tested, expressing either wild-type (WT) or mutant KRAS. We found that stable knockdown of AGO2 in KRAS dependent cell lines lead to a decrease in KRAS protein expression with a subsequent decrease in cellular proliferation. Conversely, the overexpression of AGO2 in these cells lead to both an increase in KRAS expression and oncogenesis. In addition, this interaction inhibits the RNAi function of AGO2 by preventing microRNA unwinding in the presence of oncogenic KRAS compared to WT-KRAS. Despite a clear association between mutant KRAS and AGO2 mediating increased KRAS mediated oncogenesis, the precise function of this interaction remains unclear in normal physiology. In order to better assess the endogenous function of the KRAS-AGO2 interaction, we analyzed two mouse embryonic fibroblast cell lines (NIH 3T3 and MEF) with complete knockout of AGO2. Utilizing a Raf-1 RAS binding domain (RBD) pulldown method, we assessed activated WT-RAS levels in AGO2 null NIH 3T3 and MEF cells. We found that knockout of AGO2 lead to an increase in WT RAS-GTP activation compared to normal control cells. Immunoblot analysis also indicates that AGO2 null fibroblasts lead to increase in RAS downstream signaling through the MAPK/ERK and PI3K/AKT pathways. Furthermore, rescue of AGO2 knockout using full length mouse AGO2 decreased wild type RAS activation and its downstream signaling. Taken together, these observations suggest that the AGO2 interaction may suppress WT-KRAS activation, leading to maintenance of RAS-GDP levels. Using RNA-seq, proteome and microRNA analysis, we have begun to identify the pathways that may be involved in RAS activation in AGO2 null cells. Early analyses indicate that AGO2 controls WT-KRAS levels and activity through multiple mechanisms, laying the foundation for a better understanding of the RAS-AGO2 interaction in normal physiology. Citation Format: Ronald F. Siebenaler, Sunita Shankar, Vijaya L. Dommeti, Malay Mody, Arul Chinnaiyan. Argonaute 2 controls RAS activation in mouse embryonic fibroblasts [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 1362. doi:10.1158/1538-7445.AM2017-1362
Sub-to-Supercritical Mixing in Single and Dual Component Systems (2012)

This study compares subcritical and supercritical jet mixing when injected into an atmosphere comprising the same or different species using planar laser induced fluorescence (PLIF). In the first case, the atmosphere consists of the same species as of the jet and hence the entire system is a single component diffusion process. In the second case, the atmosphere comprises an inert gas of a different composition, and hence a binary system. Density distribution is measured and density gradient profiles are inferred from the experimental data. The core lengths have been calculated for both single and dual component cases and a comparison is provided.
Clathrin-coated vesicles contain an ATP-dependent proton pump. (1983)

Clathrin-coated vesicles isolated from calf brain contain an ATP-dependent proton pump. Proton movement was monitored by measuring [14C]methylamine distribution. Addition of Mg2+ and ATP to coated vesicles equilibrated with [14C]methylamine resulted in the generation of a 4- to 5-fold concentration gradient, corresponding to a delta pH of 0.6-0.7 units between the medium and the acidic inside of the coated vesicles. ATP-dependent [14C]methylamine uptake was abolished by the proton ionophore carbonylcyanide p-trifluoromethoxyphenylhydrazone (FCCP) and partially inhibited by the carboxyl reagent N,N'-dicyclohexylcarbodiimide but was unaffected by the Na+, K+-ATPase inhibitors strophanthidin (100 microM) and vanadate (10 microM) and the mitochondrial ATPase inhibitors oligomycin (10 microgram/ml) and aurovertin (1 microgram/ml). GTP, but not the nonhydrolyzable analog 5'-adenylyl imidodiphosphate, could support [14C]methylamine uptake. Dissipation of the membrane potential with K+ and valinomycin resulted in stimulation of [14C]methylamine uptake, whereas both FCCP and valinomycin stimulated the strophanthidin-resistant ATPase activity. These results are consistent with the existence of an electrogenic, ATP-dependent proton pump in clathrin-coated vesicles. This proton pump may play a role in the acidification events that are essential in receptor-mediated endocytosis.
Semiconductor quantum dots II : symposium held November 27-30, 2000, Boston, Massachusetts, U.S.A. (2001)

This book confirms the high level of international interest in understanding and control the properties of semiconductor quantum-dot structures and devices. It highlights the self-assembled (self-forming) type of quantum dots that result from the islanding transition in strained heteroepitaxy of III-V semiconductors. It also features nanocrystals, colloidal dots and biological applications. Technological applications span quantum-dot laser diodes, quantum-dot optical amplifiers, biosensing applications, infrared photodetectors, photovoltaic devices, quantum cellular automata and magnetic semiconductors. It reports the development by researchers at the Johannes Kepler University in Linz of a mid-infrared, vertical cavity surface emitting quantum dot (QD) using the lead salt compounds PbSe and PbEuTe; optical gain and stimulated emission in colloidal quantum dots and the use of quantum dots for optical amplifiers reported by researchers at the National Institute of Standards and Technology in Boulder. Topics include: theory, modeling and simulations; nanocrystals, colloidal dots and biological applications; quantum-dot-based devices and transport studies; carrier dynamics and interactions and energy relaxation and single-dot spectroscopy.
Multi-component nanorods for vaccination applications (2005)

Immune responses from Au/Ni nanorods prepared by electrochemical deposition in alumina templates are evaluated in C57BL/6 mice. When the nanorods are bombarded into skin, they generate a strong CD8 T-cell and antibody response. When pcDNA3 is bound to the Ni segment of the nanorod, it provides a strong immunostimulatory adjuvant effect to the antigen bound on the Au segment.
Video-based automatic and objective endoscopic sinus surgery skill assessment (2020)

There is an increasing need for automatic and objective surgical skill assessment methods to make the surgeon training process more effective. We studied an automatic skill assessment system based on the surgical instrument tip trajectories extracted from cadaveric trans-nasal endoscopic sinus surgery videos. We proposed a tracking algorithm by combining a segmentation-based instrument tip detector and Kalman filter. For surgical skill assessment, we explored four new motion-related metrics. The proposed method has been tested with 10 surgery videos from 4 experts and 5 trainees and shown its potential for the automatic surgical skill assessment.
Semi-analytical solution for the temperature profiles in solid-state laser disks mounted on heat spreaders (2016)

Temperature profiles in pumped solid-state laser disks are generally calculated numerically by using finite-element programs to solve the heat conduction equation in the disk and the heat spreader. Analytical expressions exist for the longitudinal temperature profile in the case of an infinitely thick heat spreader or in the limit of zero thickness of the disk. We are presenting a simplified, semi-analytical method to calculate the three-dimensional temperature profiles for any disk or heat spreader dimensions by solving the heat conduction equation using Hankel transforms. This method allows for straightforward optimization of the cooling properties of heat-sink-mounted solid-state and semiconductor disk lasers.
Atomic Layer Control of Thin Film Growth Using Binary Reaction Sequence Chemistry (1997)

Abstract : Our research is focusing on the atomic layer control of thin film growth. Our goal is to deposit films with precise control of thickness and conformality on both flat and high aspect ratio structures. Atomic layer control of growth is crucial for many technologies that require nanoscale deposition techniques to fabricate ultrathin and conformal films with thicknesses from 10-100 A. Examples of these films are ultrathin gate oxides, high dielectric constant films, conformal transparent conducting layers and ultrathin diffusion barriers.
High operating temperature plasmonic detectors (2022)

We demonstrate high operating temperature plasmonic infrared detectors, with sub-diffractive absorber thicknesses. Our detectors operate at 230 K with substantially better performance than commercial detectors at the same operating temperature.
Direct observation of local ferroelectric phase transitions in BaxSr1−xTiO3 thin films (2000)

The temperature dependence of the local ferroelectric polarization of BaxSr1−xTiO3 thin films is measured with submicrometer resolution using confocal scanning optical microscopy. The local ferroelectric hysteresis loop changes shape and disappears as the temperature is increased over a narrow range of temperatures (ΔT∼10 K). The local Curie temperature TC(x,y) varies significantly with position, and the distribution of TC is consistent with the broad temperature dependence of the dielectric permittivity measured through conventional methods. These results directly confirm the hypothesis that the ferroelectric phase transition in these materials is inhomogeneously broadened.
Active Flow Channel Matrix using Electro-conjugate Fluid for ^|^mu;TAS Application (2012)

We propose a novel droplet transporting method for Micro Total Analysis System (μTAS), which we call an active flow channel matrix, using an electro-conjugate fluid (ECF). The ECF is a kind of dielectric and functional fluid, which generates a powerful flow (ECF flow) when subjected to high DC voltage. We introduced the ECF in this study to a droplet transporting system on a chip, that is, we developed a 2×2 channel matrix, which is filled with the ECE, and put tiny electrode pairs in each channel in order to induce channel flow. With the proposed active flow channel matrix, a water droplet put into the channel may move in any direction according to the channel flow generated by the ECF flow. According to this concept, we developed a prototype of the active flow channel matrix, and confirmed our concept by experiments. A 0.5 ml blue-colored water droplet could move along the channel by the ECF flow in either direction with velocity of up to 6.30 mm/s. Namely we may possibly transport the water droplet to any positions along the channels.
Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation (2013)

Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are key drivers of blood and lymph vessel formation in development, but also in several pathological processes. VEGF-C signaling through VEGFR-3 promotes lymphangiogenesis, which is a clinically relevant target for treating lymphatic insufficiency and for blocking tumor angiogenesis and metastasis. The extracellular domain of VEGFRs consists of seven Ig homology domains; domains 1-3 (D1-3) are responsible for ligand binding, and the membrane-proximal domains 4-7 (D4-7) are involved in structural rearrangements essential for receptor dimerization and activation. Here we analyzed the crystal structures of VEGF-C in complex with VEGFR-3 domains D1-2 and of the VEGFR-3 D4-5 homodimer. The structures revealed a conserved ligand-binding interface in D2 and a unique mechanism for VEGFR dimerization and activation, with homotypic interactions in D5. Mutation of the conserved residues mediating the D5 interaction (Thr446 and Lys516) and the D7 interaction (Arg737) compromised VEGF-C induced VEGFR-3 activation. A thermodynamic analysis of VEGFR-3 deletion mutants showed that D3, D4-5, and D6-7 all contribute to ligand binding. A structural model of the VEGF-C/VEGFR-3 D1-7 complex derived from small-angle X-ray scattering data is consistent with the homotypic interactions in D5 and D7. Taken together, our data show that ligand-dependent homotypic interactions in D5 and D7 are essential for VEGFR activation, opening promising possibilities for the design of VEGFR-specific drugs.
Is corneal arcus an independent predictor of incident cardiovascular disease? (2017)

Purpose To examine the longitudinal relationship between baseline corneal arcus ( CA ) and incident CVD in ethnic Indian and Malay adults in Singapore. Methods This was a population‐based cohort study of Malays and Indians aged 40–80 years, with baseline and 6‐year follow‐up visits conducted between 2004–09 and 2010–15, respectively (follow‐up response rate 73.9%). Baseline CA was assessed by ophthalmologists using slit‐lamp biomicroscopy. The main outcome was self‐reported incident CVD , defined as myocardial infarction, angina pectoris or stroke. Multivariable logistic regression models assessed independent associations between baseline CA and incident CVD , adjusting for traditional CVD risk factors including age, gender, cholesterol (total, and HDL cholesterol), hypertension, diabetes and smoking status. We further conducted gender stratified analyses to identify possible effect modifications. Results Of the total 3637 participants (overall mean ( SD ) age; 56 years. (9), 46% male) with available follow‐up data and no baseline history of CVD , 208 (5.72%) incident CVD cases were reported. CA was found to be independently associated with incident CVD (odds ratio [95% confidence interval]: 1.52 [1.07–2.16]) in adjusted models. After gender stratification, associations between CA and incident CVD were found only in men (1.73 [1.12–2.67]) and not in women (1.05 [0.56–1.97]). Conclusions CA is associated with incident CVD , independent of traditional CVD risk factors, in ethnic Malay and Indian men. Our finding suggests that male persons with CA should be targeted for CVD risk reduction programs.
Real-Time Local Contrast Enhancement Algorithm for Video Cameras with Built-in Noise and Artifact Suppression (2008)

For real-time imaging with digital video cameras, visibility of details is very important to ensure user confidence. Many complex scenes require local contrast improvements that should bring details to the best possible visibility. However, local enhancement methods mainly suffer from ringing artifacts and over-emphasizing noise. We present a multi-window real-time high-frequency enhancement scheme, in which gain is a non-linear function of the detail energy. Our algorithm controls perceived sharpness, ringing artifacts (contrast) and noise, resulting in a good balance between visibility of details and nondisturbance of artifacts. The new scheme can be successfully applied to any class of video system that would benefit from contrast improvement.
Effective Laboratory Method of Chromite Content Estimation in Reclaimed Sands (2016)

Abstract The paper presents an original method of measuring the actual chromite content in the circulating moulding sand of foundry. This type of material is applied for production of moulds. This is the case of foundry which most frequently perform heavy casting in which for the construction of chemical hardening mould is used, both the quartz sand and chromite sand. After the dry reclamation of used moulding sand, both types of sands are mixed in various ratios resulting that in reclaimed sand silos, the layers of varying content of chromite in mixture are observed. For chromite recuperation from the circulating moulding sand there are applied the appropriate installations equipped with separate elements generating locally strong magnetic field. The knowledge of the current ratio of chromite and quartz sand allows to optimize the settings of installation and control of the separation efficiency. The arduous and time-consuming method of determining the content of chromite using bromoform liquid requires operational powers and precautions during using this toxic liquid. It was developed and tested the new, uncomplicated gravimetric laboratory method using powerful permanent magnets (neodymium). The method is used in the production conditions of casting for current inspection of chromite quantity in used sand in reclamation plant.
Investigation of Organosulfur Adsorption Pathways from Liquid Fuels onto Ag/TiOx–Al2O3 Adsorbents at Ambient Conditions (2013)

The adsorption mechanisms for aliphatic and aromatic sulfur compounds onto Ag/TiOx–Al2O3 (10 wt % Ag; Ti/Al = 1:4.4 by weight) adsorbent were investigated in this paper. The mesoporous mixed-oxide-supported silver adsorbent demonstrated promising sulfur adsorption capacities (∼10 mg of S/g of adsorbents) from liquid hydrocarbon fuels [JP5, JP8, and off-road diesel (ORD)]. However, its performance was significantly hindered by the presence of non-sulfur aromatics. In situ infrared (IR) spectra of TiOx–Al2O3 and Ag/TiOx–Al2O3 samples treated with various model fuels revealed dissociative chemisorption pathways for different sulfur species. The aliphatic (1-butanethiol and diethyl sulfide) and aromatic (thiophene, benzothiophene, dibenzothiophene, and 4,6-dimethyldibenzothiophene) sulfur compounds underwent dissociative and reactive adsorption on the surface acid sites at room temperature. The surface hydroxyl groups adsorbed the sulfur aromatics primarily via hydrogen bonding (3100–3400 cm–1), and possible dissociated products were saturated/partially saturated aliphatic compounds. The presence of non-sulfur aromatics (benzene) reduced the sulfur adsorption capacity (∼18% for Ag/TiOx–Al2O3) because of its competitive adsorption on the adsorbent via π interactions.
Source coding for a simple multi-hop network (2005)

We derive the rate-distortion region for source coding on a simple multi-hop network with side information. The result represents the first complete solution to a multi-hop source coding problem. The proof technique combines ideas from Wyner-Ziv coding and coding with unreliable side information
User engagement (2012)

In the online world, user engagement refers to the quality of the user experience that emphasizes the positive aspects of the interaction with a web application and, in particular, the phenomena associated with wanting to use that application longer and frequently. This definition is motivated by the observation that successful web applications are not just used, but they are engaged with. Users invest time, attention, and emotion into them.
Method for the synthesis of CrO2 at ambient pressure and temperature (2003)

In this article, we report the synthesis of metastable chromium dioxide at ambient temperature and pressure. The formulation of this method is based on the fact that the CrO2 particles used in magnetic recording tapes are chemically unstable and react with the organic binder, leading to a disproportionate reaction that produces nonmagnetic Cr(III)OOH and H2Cr(VI)O4 compounds. This suggests that it is also possible to synthesize CrO2 by reacting Cr(III) with Cr(VI) under appropriate conditions. Thus, metastable chromium dioxide (CrO2) powder was synthesized by mechanically grinding a mixture of CrO3 and Cr(OH)3 to induce a solid–solid reaction at atmospheric temperature and pressure. The characteristics of the product obtained after mechanical grinding of the above mixture depended on parameters such as the preparation conditions for the starting material Cr(OH)3, the grinding time, the rotational speed of the mill and the mole ratio of CrO3 and Cr(OH)3. An x-ray diffraction pattern of the product obtained under optimum conditions was in excellent agreement with the profile of CrO2. Furthermore, the powder was strongly ferromagnetic, with saturation magnetization of 63 emu/g in an applied field of 1 T.
Supplementary Methods from Loss of Neural Cell Adhesion Molecule Induces Tumor Metastasis by Up-regulating Lymphangiogenesis (2023)

Supplementary Methods from Loss of Neural Cell Adhesion Molecule Induces Tumor Metastasis by Up-regulating Lymphangiogenesis
Using a Novel Computer Technology for Tailoring Targeted and Chemotherapeutic Drug Schedules to the Individual Patient (2006)

Introduction: Over the last three decades, mathematical approaches have been employed in the attempt to improve the pharmaco-therapeutic rationale in oncology (e.g., Agur, Arnon, Schechter, 1988, 1992; Ubezio, Tagliabue, Schechter, Agur, 1994). To aid in tailoring drug treatments to individual patients, a predictive biosimulation technology was constructed, comprising computer-implemented mathematical models of physiological, pathological and pharmacological processes in a patient's body (denoted Virtual Cancer Patient, or VCP). The VCP was validated by accurately retrieving clinical outcomes in chemotherapy-treated breast cancer patients. Using this tool, in vivo effects of targeted drug therapy on tumor progression were predicted, such as the low efficacy of long-term monotherapy that inhibits the vascular endothelial growth factor (VEGF) receptor, and the higher prospects of a combined therapy, inhibiting both VEGF and the plateletderived growth factor (PDGF; Arakelyan, Vainstein, Agur, 2002a,b). The validated VCP served for identifying a new regimen involving a once weekly application of low docetaxel doses, which is expected to significantly improve efficacy/toxicity ratio in breast cancer patients. The aim of the present work was to test the efficacy of the suggested regimen in a mesenchymal chondrosarcoma (MCS) disease model, validated in xenografts, and to put forward improved regimens of chemotherapy and targeted drug combinations for a specific MCS patient. Materials & Methods: The validated disease model was calibrated by growth curves and histopathological results of untreated human tumor xenografts, derived from a lung metastasis of a MCS patient. The xenograft model was then scaled to a human MCS model, based on a gene expression analysis. Published data and in vitro proliferation assays of the patient's tumor cells served for modeling pharmacokinetics and