gebhart/patrepeval huggingface dataset:
Activity‐Based Sensing of Ascorbate by Using Copper‐Mediated Oxidative Bond Cleavage (2020)

Ascorbate is an important biological reductant and enzyme cofactor. Although direct detection through ascorbate-mediated reduction is possible, this approach suffers from poor selectivity due to the wide range of cellular reducing agents. To overcome this limitation, we leverage reduction potential of ascorbate to mediate a copper-mediated oxidative bond cleavage of ether-caged fluorophores. The copper(II) complexes supported by a {bis(2-pyridylmethyl)}benzylamine or a {bis(2-pyridylmethyl)}(2-methoxybenzyl)amine ligand were identified as an ascorbate responsive unit and their reaction with ascorbate yields a copper-based oxidant that enables rapid benzylic oxidation and the release of an ether-caged dye (coumarin or fluorescein). The copper-mediated bond cleavage is specific to ascorbate and the trigger can be readily derivatized for tuning photophysical properties of the probes. The probes were successfully applied for the fluorometric detection of ascorbate in commercial food samples, human plasma, and serum, and within live cells by using confocal microscopy and flow cytometry.
Ultra-linear chirp generation via VCO tuning predistortion (2002)

The multiple signal dynamic range and frequency resolution of wide bandwidth compressive receivers (CR), two key parameters of surveillance systems, have historically been limited by swept local oscillator (SLO) performance. Noise, spurious signals, and nonlinear frequency-time slopes in the SLO have been the cause of these limitations. This paper describes a technique to generate an SLO for a CR application which improves the multiple signal dynamic range by 15 dB over previous techniques at a much lower cost, and with less complexity. This technique for high speed linear chirp generation also has applications in FMCW or pulse compression radar systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design and Application of Highly Responsive Fluorescence Resonance Energy Transfer Biosensors for Detection of Sugar in Living<i>Saccharomyces cerevisiae</i>Cells (2007)

A protein sensor with a highly responsive fluorescence resonance energy transfer (FRET) signal for sensing sugars in living Saccharomyces cerevisiae cells was developed by combinatorial engineering of the domain linker and the binding protein moiety. Although FRET sensors based on microbial binding proteins have previously been created for visualizing various sugars in vivo, such sensors are limited due to a weak signal intensity and a narrow dynamic range. In the present study, the length and composition of the linker moiety of a FRET-based sensor consisting of CFP-linker(1)-maltose-binding protein-linker(2)-YFP were redesigned, which resulted in a 10-fold-higher signal intensity. Molecular modeling of the composite linker moieties, including the connecting peptide and terminal regions of the flanking proteins, suggested that an ordered helical structure was preferable for tighter coupling of the conformational change of the binding proteins to the FRET response. When the binding site residue Trp62 of the maltose-binding protein was diversified by saturation mutagenesis, the Leu mutant exhibited an increased binding constant (82 microM) accompanied by further improvement in the signal intensity. Finally, the maltose sensor with optimized linkers was redesigned to create a sugar sensor with a new specificity and a wide dynamic range. When the optimized maltose sensors were employed as in vivo sensors, highly responsive FRET images were generated from real-time analysis of maltose uptake of Saccharomyces cerevisiae (baker's yeast).
Heat Shock Protein 27 Increases after Androgen Ablation and Plays a Cytoprotective Role in Hormone-Refractory Prostate Cancer (2004)

Heat shock protein 27 (Hsp27) is a chaperone implicated as an independent predictor of clinical outcome in prostate cancer. Our aim was to characterize changes in Hsp27 after androgen withdrawal and during androgen-independent progression in prostate xenografts and human prostate cancer to assess the functional significance of these changes using antisense inhibition of Hsp27. A tissue microarray was used to measure changes in Hsp27 protein expression in 232 specimens from hormone naive and posthormone-treated cancers. Hsp27 expression was low or absent in untreated human prostate cancers but increased beginning 4 weeks after androgen-ablation to become uniformly highly expressed in androgen-independent tumors. Androgen-independent human prostate cancer PC-3 cells express higher levels of Hsp27 mRNA in vitro and in vivo, compared with androgen-sensitive LNCaP cells. Phosphorothioate Hsp27 antisense oligonucleotides (ASOs) and small interference RNA potently inhibit Hsp27 expression, with increased caspase-3 cleavage and PC3 cell apoptosis and 87% decreased PC3 cell growth. Hsp27 ASO and small interference RNA also enhanced paclitaxel chemosensitivity in vitro, whereas in vivo, systemic administration of Hsp27 ASO in athymic mice decreased PC-3 tumor progression and also significantly enhanced paclitaxel chemosensitivity. These findings suggest that increased levels of Hsp27 after androgen withdrawal provide a cytoprotective role during development of androgen independence and that ASO-induced silencing can enhance apoptosis and delay tumor progression.
Surface Acoustic Waves (SAW)-Based Biosensing for Quantification of Cell Growth in 2D and 3D Cultures (2015)

Detection and quantification of cell viability and growth in two-dimensional (2D) and three-dimensional (3D) cell cultures commonly involve harvesting of cells and therefore requires a parallel set-up of several replicates for time-lapse or dose-response studies. Thus, developing a non-invasive and touch-free detection of cell growth in longitudinal studies of 3D tumor spheroid cultures or of stem cell regeneration remains a major unmet need. Since surface acoustic waves (SAWs) permit mass loading-based biosensing and have been touted due to their many advantages including low cost, small size and ease of assembly, we examined the potential of SAW-biosensing to detect and quantify cell growth. Herein, we demonstrate that a shear horizontal-surface acoustic waves (SH-SAW) device comprising two pairs of resonators consisting of interdigital transducers and reflecting fingers can be used to quantify mass loading by the cells in suspension as well as within a 3D cell culture platform. A 3D COMSOL model was built to simulate the mass loading response of increasing concentrations of cells in suspension in the polydimethylsiloxane (PDMS) well in order to predict the characteristics and optimize the design of the SH-SAW biosensor. The simulated relative frequency shift from the two oscillatory circuit systems (one of which functions as control) were found to be concordant to experimental data generated with RAW264.7 macrophage and A549 cancer cells. In addition, results showed that SAW measurements per se did not affect viability of cells. Further, SH-SAW biosensing was applied to A549 cells cultured on a 3D electrospun nanofiber scaffold that generate tumor spheroids (tumoroids) and the results showed the device's ability to detect changes in tumor spheroid growth over the course of eight days. Taken together, these results demonstrate the use of SH-SAW device for detection and quantification of cell growth changes over time in 2D suspension cultures and in 3D cell culture models, which may have potential applications in both longitudinal 3D cell cultures in cancer biology and in regenerative medicine.
Gas-coupled laser acoustic detection at ultrasonic and audio frequencies (1998)

Airborne acoustic waves have been detected by a laser-beam deflection technique in both the ultrasonic and audio frequency ranges. For ultrasonic applications, a probe beam is directed parallel to the surface of a sample. Ultrasonic waves in the solid are detected when an acoustic wave is radiated from the surface into the ambient air, where the density variations cause a beam deflection. Gas-coupled laser acoustic detection (GCLAD) has been used to record well-resolved through-transmission and surface-acoustic wave forms in various materials. GCLAD has also been incorporated into a C-scanning system where it has been used to image subsurface flaws in graphite/polymer composite panels. Because the laser beam is not reflected from the sample surface, the technique is not dependent upon the surface optical properties of the material under investigation. It is particularly useful for testing graphite/polymer composites and other materials with rough surfaces. The beam-deflection technique has been tested quantitatively in the kHz frequency range by passing a probe beam through a cylindrical resonator. The acoustic spectrum of the resonator was measured from 4 to 13.5 kHz by scanning the frequency of a source and recording the acoustic field with both a microphone and the beam-deflection system. The acoustic fields of the lower-frequency modes are well known and enable both qualitative and quantitative tests of the beam-deflection technique. Measurements on the lowest-frequency plane-wave mode were used for absolute calibration of the microphone. The noise level of the beam-deflection measurements at 4.3 kHz was found to be 0.05 nrad (rms), corresponding to an acoustic pressure of 0.005 Pa (rms).
Functional validation of programmable architectures (2004)

Validation of programmable architectures, consisting of processor cores, coprocessors, and memory subsystems, is one of the major bottlenecks in current system-on-chip design methodology. A critical challenge in validation of such systems is the lack of a golden reference model. Traditional validation techniques employ different reference models depending on the abstraction level and verification task (e.g., functional simulation or property checking), resulting in potential inconsistencies between multiple reference models. This paper presents a validation methodology that uses an architecture description language (ADL) based specification as a golden reference model for validation of programmable architectures, and generation of executable models such as simulators and hardware prototypes. We present a validation framework that uses the generated hardware as a reference model to verify the hand-written implementation using a combination of symbolic simulation and equivalence checking. We also present functional coverage based test generation techniques for validation of pipelined processor architectures. Finally, the generated simulator and hardware models are also used for early exploration of programmable architectures.
A 24-Channel 300 Gb/s 8.2 pJ/bit Full-Duplex Fiber-Coupled Optical Transceiver Module Based on a Single “Holey” CMOS IC (2010)

24-channel 850-nm VCSEL and PD arrays are flip-chip soldered to 90-nm CMOS “holey” 48-channel 12.5-Gb/s/channel transceiver chip, featuring through-substrate holes for optical I/O. Aggregate 300-Gb/s bi-drectional data rate is highest reported for single-chip transceiver modules.
A Novel Early Diagnosis System for Mild Cognitive Impairment Based on Local Region Analysis: A Pilot Study (2018)

Alzheimer's disease (AD) is an irreversible neurodegenerative disorder that accounts for 60-70% of cases of dementia in the elderly. An early diagnosis of AD is usually hampered for many reasons including the variable clinical and pathological features exhibited among affected individuals. This paper presents a computer-aided diagnosis (CAD) system with the primary goal of improving the accuracy, specificity, and sensitivity of diagnosis. In this system, PiB-PET scans, which were obtained from the ADNI database, underwent five essential stages. First, the scans were standardized and de-noised. Second, an Automated Anatomical Labeling (AAL) atlas was utilized to partition the brain into 116 regions or labels that served for local (region-based) diagnosis. Third, scale-invariant Laplacian of Gaussian (LoG) was used, per brain label, to detect the discriminant features. Fourth, the regions' features were analyzed using a general linear model in the form of a two-sample <i>t</i>-test. Fifth, the support vector machines (SVM) and their probabilistic variant (pSVM) were constructed to provide local, followed by global diagnosis. The system was evaluated on scans of normal control (NC) vs. mild cognitive impairment (MCI) (19 NC and 65 MCI scans). The proposed system showed superior accuracy, specificity, and sensitivity as compared to other related work.
Polarization stabilizing for diode-pumped passively Q-switched Nd:YAG microchip lasers (2006)

We have demonstrated the new way of the polarization stabilizing in the passively Q-switched laser by using a [110]-cut Cr4+:YAG crystal. The 355-nm ultra-violet light was generated with 32 % conversion efficiency from 1064 nm.
Automatic lesion border selection in dermoscopy images using morphology and color features (2019)

The performance of the classifier-based automatic skin lesion finder is found to be better than any single algorithm used in this research.
Router-assistance for receiver access control in PIM-SM (2002)

The current work looks closer at the problem of receiver access control within the Protocol Independent Multicast (PIM) protocol-specifically PIM Sparse Mode-and proposes a practical solution to this problem for PIM-SM. The proposed solution has a number of benefits. The approach adheres to the basic IP multicast model and maintains the "anonymous-receiver" principle of the model, thereby maintaining the scalability of the original model. In accordance to the basic model, PIM routers in the domain need not maintain or propagate any host identification information. The solution makes use of the authentication-key arrangement of the PIM Working Group (IETF) and adheres to it. Finally, the distributed decision-making approach adopted allows routers (other than the RP) to decide whether or not a new branch of the distribution tree is to be created towards a given receiver thereby relieving the RP from being the sole decision-point and making the overall solution scalable.
Comparison of processing speed of typical wavefront reconstructionmethods for lateral shearing interferometry (2020)

Lateral shearing interferometry is widely applied in wavefront sensing, optical components testing, and defect inspection. The procedure of reconstructing the wavefront is the most specific difference between lateral shearing interferometry and other classical methods such as the Fizeau and Twyman interferometers. The speed and accuracy are two main features to evaluate the performance of one wavefront reconstruction method. In this work, optimized procedures for three typical wavefront reconstruction methods-the iterative FFT wavefront reconstruction method (FFT method), the partial differential least-squares method (LSQ method), and the difference Zernike polynomial fitting method (DZF method)-are designed. The calculation speeds of the three wavefront reconstruction methods are evaluated with different GPUs and CPUs. According to the test results, the DZF method is the fastest method both in the GPUs and CPUs. The shortest processing times of the DZF, FFT, and LSQ methods are 100, 449, and 494 ms, respectively, with the wavefront size of 1024×1024<i>p</i><i>i</i><i>x</i><i>e</i><i>l</i><i>s</i>. The calculation speeds of the FFT method and the LSQ method are similar in the CPUs, and the FFT method is faster in the GPUs. The relationship between the consumed time and the wavefront size is an exponential function in the CPUs and a power function in the GPUs. Generally speaking, GPUs' processing speeds are faster than CPUs'. But CPUs can be faster than GPUs when the test wavefront sizes are smaller than 64×64<i>p</i><i>i</i><i>x</i><i>e</i><i>l</i><i>s</i>. Besides, the differences between the consumed times of different CPUs are relatively smaller than those of the GPUs.
Amplifying TLR2 signals in Tumor-specific T cells Lowers the Activation Threshold to a Weakly Immunogenic Tumor Antigen and Enhances Antitumor Activity (41.50) (2009)

Abstract Although toll-like receptor (TLR) agonists are primarily believed to potentiate T cell responses by activating antigen-presenting cells, we recently demonstrated that TLR2 engagement on CD8 T cells enhanced proliferation and increased the production of several effector molecules. Here, we examined the antitumor activity of TLR2-stimulated pmel CD8 T cells, which recognize the weakly immunogenic melanoma tumor antigen gp100. TLR2 engagement on pmel T cells but not TLR2-/-pmel or MyD88-/-pmel cells reduced the activation threshold up to 100-fold as measured by IFN-γ, granzyme B, perforin and IL-2 production and cytolytic activity. Adoptive T cell transfer of pmel T cells in wild type or MyD88 knockout mice and injection with TLR2 ligand improved the antitumor activity against an established melanoma tumor as compared with mice treated with TLR2-/-pmel or MyD88-/-pmel T cells and TLR2 ligand. Furthermore, TLR2-ligated T cells persisted longer than did control T cells. Overexpressing TLR2 in pmel T cells improved effector responses above that of T cells expressing wild type levels of TLR2. These data highlight an important and physiologically relevant role for activating TLR2-MyD88 signals within T cells and could enhance immunotherapeutic approaches to treat cancer patients by augmenting T cell responses to weakly immunogenic TAs. Supported by a NIH (1P20 RR021970) and the Louisiana Cancer Research Consortium.
Deducing historical correlations for realistic stochastic forecasting of intermittent energy sources (2017)

Intermittent generation, such as wind and solar, are popularizing stochastic simulation of power grids. Stochastic forecasts of these uncertainties are typically characterized by their marginal distributions. However, dependencies between forecasts also influence the grid significantly, but their specification is not straightforward. We propose Correlated Sampling (CS), a novel, purely data-driven technique that deduces spatial and temporal correlations from historical measurements, and samples stochastic forecasts from provided marginal distributions while imposing these correlations. By incorporating correlations between (potentially many) intermittent injections, CS greatly improves peak demand predictions, congestion analysis, spinning reserve optimization, power quality, etcetera, which will save utilities huge costs. In an experiment, CS computes confidence intervals (CIs) of demand aggregated over multiple substations. These CIs are either 3 times as narrow or 2 times as accurate as the CIs of two ‘naive’ techniques that omit estimating correlations. This shows that CS enables much more realistic power system analyses.
Small-molecule inhibitor of intestinal anion exchanger SLC26A3 for treatment of hyperoxaluria and nephrolithiasis (2022)

Nephrolithiasis is a common and recurrent disease affecting 9% of the US population. Hyperoxaluria is major risk factor for calcium oxalate kidney stones, which constitute two-thirds of all kidney stones. SLC26A3 (DRA, downregulated in adenoma) is an anion exchanger of chloride, bicarbonate, and oxalate thought to facilitate intestinal oxalate absorption, as evidenced by approximately 70% reduced urine oxalate excretion in knockout mice. We previously identified a small-molecule SLC26A3 inhibitor (DRAinh-A270) that selectively inhibited SLC26A3-mediated chloride/bicarbonate exchange (IC50 ~ 35 nM) and, as found here, oxalate/chloride exchange (IC50 ~ 60 nM). In colonic closed loops in mice, luminal DRAinh-A270 inhibited oxalate absorption by 70%. Following oral sodium oxalate loading in mice, DRAinh-A270 largely prevented the 2.5-fold increase in urine oxalate/creatinine ratio. In a mouse model of oxalate nephropathy produced by a high-oxalate low-calcium diet, vehicle-treated mice developed marked hyperoxaluria with elevated serum creatinine, renal calcium oxalate crystal deposition, and renal injury, which were largely prevented by DRAinh-A270 (10 mg/kg twice daily). DRAinh-A270 administered over 7 days to healthy mice did not show significant toxicity. Our findings support a major role of SLC26A3 in intestinal oxalate absorption and suggest the therapeutic utility of SLC26A3 inhibition for treatment of hyperoxaluria and prevention of calcium oxalate nephrolithiasis.
Carrier VoIP Security Architecture (2006)

This document describes security architecture for real-time services over IP (RSoIP) architecture. The architecture described here is used to protect AT&T's VoIP infrastructure, hence our liberal use of AT&T VoIP architecture in describing the proposed security architecture. Our VoIP Security architecture describes guidelines and mechanisms designed to safeguard customer data, our VoIP network infrastructure, and voice and multimedia services and applications against internal and external threats including denial-of-service (DoS) and distributed DoS (DDoS) attacks. Our VoIP Security architecture is designed to ensure availability, confidentiality, privacy, and integrity of user information
Novel Class of Zinc-Free Heavy Clear Brines for HPLT Applications (2020)

Abstract In an effort to increase oil production over the past twenty years, the oil industry has moved into deep water for new field developments. During this time, progressively deeper wells containing geopressured reservoirs require the use of high density completion brines. Many of these reservoirs require the use of completion brines above 14.7 ppg. Historically, zinc bromide solutions have been used to provide the required density and true crystallization temperature (TCT) for these reservoirs. However, health, safety, and environmental concerns around zinc bromide have caused operators to seek alternative solutions. The oil and gas industry uses a large amount of heavy brines in the completion of high pressure-low temperature (HPLT) wells, and there are currently very limited options for high density (&gt;14.7 ppg), low TCT fluids that do not contain zinc. One option, cesium formate, is prohibitively expensive, and the other, based on existing halide technology, has a lower density limitation than this new class of clear brine fluid. This paper describes a novel, zinc-free, high-density, low true crystallization temperature brine fluid developed by Albemarle Corporation. We will discuss the testing performed to characterize this new fluid. This new class of brine fluid fills a gap in fluids technology for a fluid suitable for high pressure, low temperature applications at higher densities than previously available. Further, this is accomplished in an environmentally friendly heavy brine fluid that contains no Environmental Protection Agency (EPA) listed materials.