gebhart/patrepeval huggingface dataset:
Data from Antitumor Activity of the Glutaminase Inhibitor CB-839 in Triple-Negative Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Glutamine serves as an important source of energy and building blocks for many tumor cells. The first step in glutamine utilization is its conversion to glutamate by the mitochondrial enzyme glutaminase. CB-839 is a potent, selective, and orally bioavailable inhibitor of both splice variants of glutaminase (&lt;i&gt;KGA&lt;/i&gt; and &lt;i&gt;GAC&lt;/i&gt;). CB-839 had antiproliferative activity in a triple-negative breast cancer (TNBC) cell line, HCC-1806, that was associated with a marked decrease in glutamine consumption, glutamate production, oxygen consumption, and the steady-state levels of glutathione and several tricarboxylic acid cycle intermediates. In contrast, no antiproliferative activity was observed in an estrogen receptor–positive cell line, T47D, and only modest effects on glutamine consumption and downstream metabolites were observed. Across a panel of breast cancer cell lines, GAC protein expression and glutaminase activity were elevated in the majority of TNBC cell lines relative to receptor positive cells. Furthermore, the TNBC subtype displayed the greatest sensitivity to CB-839 treatment and this sensitivity was correlated with (i) dependence on extracellular glutamine for growth, (ii) intracellular glutamate and glutamine levels, and (iii) &lt;i&gt;GAC&lt;/i&gt; (but not &lt;i&gt;KGA&lt;/i&gt;) expression, a potential biomarker for sensitivity. CB-839 displayed significant antitumor activity in two xenograft models: as a single agent in a patient-derived TNBC model and in a basal like HER2&lt;sup&gt;+&lt;/sup&gt; cell line model, JIMT-1, both as a single agent and in combination with paclitaxel. Together, these data provide a strong rationale for the clinical investigation of CB-839 as a targeted therapeutic in patients with TNBC and other glutamine-dependent tumors. &lt;i&gt;Mol Cancer Ther; 13(4); 890–901. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Attenuation of natural killer cell functions by capsaicin through a direct and TRPV1-independent mechanism (2014)

The assessment of the biological activity of capsaicin, the compound responsible for the spicy flavor of chili pepper, produced controversial results, showing either carcinogenicity or cancer prevention. The innate immune system plays a pivotal role in cancer pathology and prevention; yet, the effect of capsaicin on natural killer (NK) cells, which function in cancer surveillance, is unclear. This study found that capsaicin inhibited NK cell-mediated cytotoxicity and cytokine production (interferon-γ and tumor necrosis factor-α). Capsaicin impaired the cytotoxicity of NK cells, thereby inhibiting lysis of standard target cells and gastric cancer cells by modulating calcium mobilization in NK cells. Capsaicin also induced apoptosis in gastric cancer cells, but that effect required higher concentrations and longer exposure times than those required to trigger NK cell dysfunction. Furthermore, capsaicin inhibited the cytotoxicity of isolated NK cells and of an NK cell line, suggesting a direct effect on NK cells. Antagonists of transient receptor potential vanilloid subfamily member 1 (TRPV1), a cognate capsaicin receptor, or deficiency in TRPV1 expression failed to prevent the defects induced by capsaicin in NK cells expressing functional TRPV1. Thus, the mechanism of action of capsaicin on NK cells is largely independent of TRPV1. Taken together, capsaicin may have chemotherapeutic potential but may impair NK cell function, which plays a central role in tumor surveillance.
Supplementary Tables 5 - 10 from High-Throughput Detection of Clinically Relevant Mutations in Archived Tumor Samples by Multiplexed PCR and Next-Generation Sequencing (2023)

&lt;p&gt;XLSX file - 602KB, Supplementary Table 5. Cancer cell lines analyzed in this study. Supplementary Table 6. Tumor tissues analyzed in this study. Supplementary Table 7. List of 340 well characterized hotspot mutations interrogated by the amplicon libraries in this study. Variants also assayed by asPCR are indicated. Supplementary Table 8. Variants detected in 66 cancer cell lines, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 9. Variants detected in 73 FFPE endometrial tumor tissues, after applying post-processing filters. Note that indels and predicted deleterious SNVs are reported for all interrogated genes and transcripts. Supplementary Table 10. For cell line data, concordance with COSMIC somatic mutation annotation.&lt;/p&gt;
Cable condition monitoring for nuclear power plants (2012)

Analysis and Measurement Services (AMS) Corporation has been conducting two research projects focused on understanding cable aging and developing cable condition monitoring technologies for nuclear power plants. The goal of the first project is to develop a cable aging management program to correlate the aged condition of a cable with condition monitoring techniques that can identify and locate aging in the cable's polymer material as well as faults that may occur in the conductor. This project involves laboratory experiments using low and medium voltage cable types typically installed in nuclear power plants. The second project is focused on development of an integrated cable condition monitoring system for nuclear facilities. This system integrates a number of cable testing and cable condition monitoring techniques, such as time domain reflectometry (TDR), frequency domain reflectometry (FDR), inductance, capacitance, resistance (LCR), reverse TDR (RTDR), voltage, waveform acquisition, current-to-voltage (IV) for testing of nuclear instrumentation sensors, and insulation resistance (IR). The purpose of the project is to combine all proven technologies into one system to detect and pinpoint problems in cable circuits as well as cable insulation, shield, or jacket material.
Effective reduction of threshold voltage variability and standby leakage using advanced co-implantation and laser anneal for low power applications (2008)

We have successfully reduced threshold voltage variation by combination of co-implantation and laser spike anneal on 45 nm low power SoC platform with conventional poly-Si/SiON gate stack. Doping profiles of CMOSFET channel is modulated through co-implantation of diffusion suppressor. We have explored the possibility of cluster carbon doping in order to minimize junction leakage degradation. Systematic junction profile design for n- and pFET enables us to reduce random dopant variation significantly without compromising standby leakage, drive current and gate oxide integrity, which finally contributes to RO ~5% performance improvement at equivalent Iddq and ensures high yield of SRAM array by reducing beta and gamma ratio variation.
Image coding based on a morphological representation of wavelet data (1999)

In this paper, an experimental study of the statistical properties of wavelet coefficients of image data is presented, as well as the design of two different morphology-based image coding algorithms that make use of these statistics. A salient feature of the proposed methods is that, by a simple change of quantizers, the same basic algorithm yields high performance embedded or fixed rate coders. Another important feature is that the shape information of morphological sets used in this coder is encoded implicitly by the values of wavelet coefficients, thus avoiding the use of explicit and rate expensive shape descriptors. These proposed algorithms, while achieving nearly the same objective performance of state-of-the-art zerotree based methods, are able to produce reconstructions of a somewhat superior perceptual quality, due to a property of joint compression and noise reduction they exhibit.
Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening (2016)

The expanding number of crystal structures of G protein-coupled receptors (GPCRs) has increased the knowledge on receptor function and their ability to recognize ligands. Although structure-based virtual screening has been quite successful on GPCRs, scores obtained by docking are typically not indicative for ligand affinity. Methods capturing interactions between protein and ligand in a more explicit manner, such as interaction fingerprints (IFPs), have been applied as an addition or alternative to docking. Originally IFPs captured the interactions of amino acid residues with ligands with specific definitions for the various interaction types. More complex IFPs now capture atom-atom interactions, such as in SYBYL, or fragment-fragment co-occurrences such as in SPLIF. Overall, most of the IFPs have been studied in comparison with docking in retrospective studies. For GPCRs it remains unclear which IFP should be used, if at all, and in what manner. Thus, the performance between five different IFPs was compared on five different representative GPCRs, including several extensions of the original implementations,. Results show that the more detailed IFPs, SYBYL and SPLIF, perform better than the other IFPs (Deng, Credo, and Elements). SPLIF was further tuned based on the number of poses, fingerprint similarity coefficient, and using an ensemble of structures. Enrichments were obtained that were significantly higher than initial enrichments and those obtained by 2D-similarity. With the increase in available crystal structures for GPCRs, and given that IFPs such as SPLIF enhance enrichment in virtual screens, it is anticipated that IFPs will be used in conjunction with docking, especially for GPCRs with a large binding pocket.
Human Tumor Mutants in PI3K p110&alpha; Subunit (2006)

The PI3K-Akt pathway is frequently upregulated in human tumors. Recently, somatic mutations of PIK3CA, encoding p110alpha catalytic subunit of Class IA PI3Ks, have been found in various cancers. The two most common types of p110alpha mutants, those in the helical and kinase domains, have been shown to be very potent in Akt activation and oncogenic transformation by several groups. Notably these common mutations may not enhance recruitment of p110alpha to the plasma membrane where its substrates are located. We have investigated the effect of membrane localization on common PIK3CA tumor mutants via myristoylation. In addition we have studied a third class of less frequent mutants in the p85-binding domain, in an attempt to gain insight into p85's inhibitory effect on p110alpha. This article briefly reviews and extends the literature on mutant forms of p110alpha.
Morphological Changes in Yeasts as a Result of the Action of 5-Fluorocytosine (1977)

The mode of action of 5-fluorocytosine on Candida albicans and Saccharomyces cerevisiae was studied with special reference to morphology and ultrastructure. Shortly after contact of yeast cells with 10 mug of 5-fluorocytosine per ml, marked enlargement of the cells occurred. The initial increase in cell size was almost the same with both yeast strains. As incubation proceeded, further increase in cell volume continued with C. albicans, whereas no further change in cell volume was observed with S. cerevisiae. An electron microscope examination of C. albicans cells after exposure to the drug revealed characteristic changes, consisting of an enlarged nucleus and a thin cell wall. The morphological changes were exactly comparable to those reported with inhibitors of deoxyribonucleic acid synthesis in mammalian cells and some bacteria.
In-Stationary Tapped Delay Line Channel Modeling and Simulation (2020)

An essential tool in the performance analysis of communication systems is a tractable and accurate propagation channel model. The aim of this paper is to discuss the implementation of tapped delay line channel model for vehicle to infrastructure channels and devise a generator to produce a channel impulse response based on an already derived model parameters from measurement data. The root-mean square delay spread is used for a model validation between simulated and collected data on the basis of how well they agree. The analysis investigates correlation coefficient among taps persistence, as well as, modeling persistence process. The results illustrate that only few taps are essential to regenerate accurately the delay spread.
Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X (2022)

Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression, and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using machine learning classifiers trained to distinguish disease-associated from dispensable genes, we classify 247 genes, including 115 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.
Seeds: physiology of development and germination J. D. Bewley and M. Black, xv + 445 pp. Second Edition. Plenum Press, New York, London, 1994. ISBN 0-306-44747-9 (hardbound) $75.00. ISBN 0-306-44748-7 (paperback) $39.50 (1995)

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A novel control strategy for fast tracking of photovoltaic maximum power point voltage (2010)

A novel method to track and control the maximum power point (MPP) of the photovoltaic system is proposed in this paper. Using a microprocessor, the proportional and integral (PI) controller for the system is implemented. Linear control methods can be used due to the linearization block that is implemented in the microprocessor. The closed-loop control proposed is robust and provides fast tracking and control of the system MPP. This would enable the use of numerical methods to calculate the MPP. Unlike the conventional Perturb and Observe (P and O) methods and Incremental Conductance (IncCon) methods, the operating point of the system would not oscillate around the MPP. Efficiency of the system is also increased by replacing the diode with an active switching element.
A<inf>1</inf> mode Lamb wave on thin LiTaO<inf>3</inf> for high frequency acoustic devices (2016)

The Lamb waves and horizontal shear waves' propagation in LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> thin plate is investigated as a function of Euler angles. Both velocity and electromechanical coupling factor largely depend on the plate's thickness. Around (0°, 30°, 0°), LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> thin plate has a high velocity and a suitable coupling factor for a high frequency filter. Authors fabricated A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mode Lamb wave resonators in (0°, 39°, 0°) LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> 's thin plate. Lamb waves' velocities and leaky Lamb wave' velocities were measured by network analyzer and ultrasonic microscopy. Measured velocities correspond to the ones calculated by FEM. Velocities higher than 20,000 m/s were obtained. It is then shown that A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> mode Lamb wave close to (0°, 30°, 0°) LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> thin plate is suitable for high frequency devices.
Angular dependence of bulk fluorescence noise in supercritical angle fluorescence (Conference Presentation) (2018)

Supercritical angle fluorescence (SAF) is a near-field collection method that has surface sensitivities similar to or better than near-field excitation techniques like TIRF and waveguide based excitation. SAF is emitted by fluorophores that are a few hundred nanometers away from an interface, above the critical angle, into the higher index material. SAF decreases exponentially with increasing distance from the interface and is therefore more sensitive to molecules near the surface. Although a lot of research has used SAF for biosensing and microscopy, the angular dependence of SAF on both the surface and bulk fluorescence contributions hasn’t been experimentally studied. We present a method that measures the surface selectivity of SAF in the presence of bulk fluorophores. Two different fluorophores were used. One was bound to the surface and the other was suspended in the bulk. The spectrum was measured at discrete points in the back focal plane (BFP) and the contribution of the two fluorophores was extracted from it. The results of the experiment show the highest signal-to-noise ratio in the region just above the critical angle of 61.31º because of the higher signal intensity. However, for experiments where bulk exclusion is important, we observe the highest signal-to-bulk ratio at angles above 68˚ for a glass-water interface. Understanding the angular dependence on the sensitivity of a SAF biosensor enables tuning the collection angles towards specific applications and could lead to the creation of smaller, more sensitive devices.
Highly Porous TiO2 Anatase Optical Thin Films with Cubic Mesostructure Stabilized at 700 °C (2003)

TiO2 optical thin films stable to 700 °C, exhibiting 35% volume porosity, more than 100 m2·g-1 in surface area, fully nanocrystalline anatase framework, and organized mesostructure (cubic Im3m derived), have been stabilized by careful delayed rapid crystallization (DRC) thermal treatments. In-situ time-resolved SAXS and WAXS investigations were simultaneously performed during such treatments. They revealed that a slow and progressive heating to a temperature just below that of the formation of anatase (Tc ≈ 400 °C), followed by a long pretreatment at this temperature, stabilizes the amorphous network. A following rapid increase of temperature up to temperatures as high as typically 700 °C, followed by a short residence time at this high temperature, provokes the homogeneous formation of crystalline small nanoparticles and the total elimination of organic residues. The crystallization is accompanied by matter migration through diffusing sintering and pore merging along the [111] directions of the cubic structure, leading to a novel grid-like mesostructure with open porosity. This DRC treatment allows the preparation of highly porous and crystalline anatase films, with thermal stability 200 °C higher than previously reported, that are ideal for energy transfer applications. This emphasizes the role of the treatment method to stabilize transition metal oxide mesoporous materials over extended crystallization at high temperatures. These films exhibit excellent long time stability below 500 °C.
Comparison of 6‐31G*‐based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules (1993)

Abstract A comparison between Miertus–Scrocco–Tomasi (MST) SCRF and free energy perturbation (FEP) estimates of the free energy of hydration of eight small neutral molecules is presented. In both cases, the 6‐31G* molecular electrostatic potential is used to describe the electrostatic properties of the molecules. The results demonstrate the ability of both methodologies to provide useful theoretical estimates of the total free energy of hydration; the average errors are only 1.5 kcal/mol (FEP) and 0.8 kcal/mol (MST/SCRF). The largest errors in the FEP and MST/SCRF results are less than 1.5 kcal/mol for all molecules except acetic acid, where the FEP method overestimates the free energy of hydration by 3.3 kcal/mol. © John Wiley &amp; Sons, Inc.
Carboxylic Acid Containing Direct Thrombin Inhibitors for the Treatment of Thromboembolic Diseases (2016)

Many direct thrombin inhibitors possessing a carboxylic acid pharmacophore have been approved for the treatment of thromboembolic disease. This chapter talks about the history, synthesis, mode of action, and the structure-activity relationship of carboxylic acid containing direct thrombin inhibitors. Direct inhibition of thrombin was originally observed with the biological peptide hirudin, a component of leech saliva, which facilitates feeding. The synthesis of melagatran (3) commenced with a hydrogenation to convert phenylglycine 9 into the cyclohexylglycine 10. Amide coupling with methyl (S) 2-azetidinecarboxylate 11 easily provided dipeptide 12. Upon injury to a vessel wall, a tissue factor can be exposed on the surface of the compromised endothelium. The interaction of tissue factor with plasma factor VII activates the corresponding coagulation cascade pathway. Through this cascade, thrombin is produced in a stepwise manner through activation of a series of proenzymes.
Wavelength-Tunable Laser for Signal Remodulation in WDM Access Networks Using DPSK Downlink and OOK Uplink (2009)

In this investigation, a simple wavelength-tunable laser based on a Fabry-Perot laser diode (FP-LD) and an erbium-doped fiber amplifier to serve as a downlink signal in a colorless wavelength-division-multiplexed passive optical network (PON) is proposed and experimentally demonstrated. The tuning range of the proposed laser is between 1529.48 and 1560.72 nm, and the output performance of proposed laser is discussed. Colorless operation is implemented by using an FP-LD and a reflective semiconductor optical amplifier in each optical network unit for uplink signal remodulation, respectively. In addition, error-free data signal remodulation using 10-Gb/s downlink differential phase-shift keying and 2.5-Gb/s uplink on-off keying is achieved in a 25-km reach PON.
Surface Reaction of C60with Atomic Hydrogen: Formation of a Protecting Hydrocarbon Layer (2005)

Abstract The interaction of a single domain C60/InP(0 0 1)‐(2×4) film during exposure to atomic hydrogen was investigated. At low hydrogen dosing, a high reactivity of the C60 molecules was detected. Presumably, the cracking of fullerene cages follows from a fast destruction of the molecular order. High dosing leads, by chemical modification, to the formation of a stable coverage of hydrocarbons, which is promising for future technological applications.
In-situ demonstration of radio-frequency enhanced chlorinated hydrocarbon remediation (1994)

This paper discusses the results of a successful demonstration of radio frequency (RF) heating for enhanced chlorinated hydrocarbon remediation at the M-Area Seepage Basin of the Department of Energy`s Savannah River Site. RF heating was integrated with soil vapor extraction (SVE) to enhance the release of residual volatile chlorinated hydrocarbons which are concentrated in low permeable clay lenses in the unsaturated zone. Participants in this effort consisted of the Westinghouse Savannah River Technology Center; the Westinghouse Science and Technology Center (Pittsburgh, PA); and KAI Technologies, Inc. which provided the RF technology. Additionally, a better understanding of RF heating technology is gained through a description of the RF heating system.