gebhart/patrepeval huggingface dataset:
Laminated Sand-Shale Formation Evaluation Using Azimuthal LWD Resistivity (2009)

Abstract Intervals of thinly bedded hydrocarbon-bearing sands and laminar clay cannot be fully evaluated with conventional log measurements and interpretation techniques. This is because the laminar nature of the clay component suppresses the logged deep resistivity measurements and results in calculated values of water saturation that are artificially high. This formation evaluation challenge is already widely recognized by the industry and addressed by an interpretation solution that uses simultaneous measurements of horizontal and vertical resistivity, available from the new generation of wireline induction-resistivity tools. A newly deployed logging-while-drilling (LWD) sensor now provides equivalent measurements of azimuthal resistivity; this technology was deployed for the first time for the formation evaluation of thinly bedded sands in Trinidad's Dolphin Field. This tool provides multiple depths of investigation and 32 azimuthal resistivity measurements. Horizontal and vertical resistivity are extracted from the multi-spacing and multi-frequency azimuthal data using fast and robust inversion algorithms. The results were validated with a back-to-back run with an equivalent wireline service. An interpretation methodology is presented that sets out the equations used for the mathematical solution of these data. The Thomas-Stieber method is used to partition the calculated clay volume into its laminated, structural, and dispersed components and to calculate the effective and total porosity of the sand fraction of the reservoir. The corresponding true resistivity of the laminated sand fraction is derived from the quadratic solution of horizontal and vertical resistivity and the laminar clay volume. The water saturation of the sand fraction is calculated using the Archie Equation and subsequently volumetrically weighted to provide the total water saturation. The Thomas-Stieber parameters are also used to calculate the formation averages. The high angle, high step-out wells drilled in this phase of field development have calculated hydrocarbon pore volumes of up to 33% greater than historic, near-vertical wells logged with conventional resistivity tools only. The results of the thin bed interpretation are observed to be sensitive to both borehole deviation and the stratigraphic interval.
Sepsis, Signals, and Surgical Sequelae (A Hypothesis) (1990)

Cytokines, products of the bodies on cells, are the major signals that orchestrate the host's response to bacterial infection. Those signals generated following infection include interleukins 1, 2, and 6, interferon gamma, and tumor necrosis factor (or cachectin). Tumor necrosis factor is the only cytokine, to date, that has been shown to fulfill Koch's postulates and, thus, be casually related to host responses. Host responses to cytokines vary because of alterations in the genetic mechanism that controls cytokine production, because of an alteration in the responsiveness of the reticuloendothelial system at the time of signal induction and because of alterations in cell surface receptors. Only now are techniques evolving that can detect cytokine concentrations or production rates to relate these molecules to varying aspects of human disease. A major therapeutic goal in the future will be directed toward blocking the deleterious effects of cytokines while maintaining their protective or beneficial effects.
A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency (2017)

Antiretroviral therapy for HIV-1 infection/AIDS has significantly extended the life expectancy of HIV-1-infected individuals and reduced HIV-1 transmission at very high rates. However, certain individuals who initially achieve viral suppression to undetectable levels may eventually suffer treatment failure mainly due to adverse effects and the emergence of drug-resistant HIV-1 variants. Here, we report GRL-142, a novel HIV-1 protease inhibitor containing an unprecedented 6-5-5-ring-fused crown-like tetrahydropyranofuran, which has extremely potent activity against all HIV-1 strains examined with IC<sub>50</sub> values of attomolar-to-picomolar concentrations, virtually no effects on cellular growth, extremely high genetic barrier against the emergence of drug-resistant variants, and favorable intracellular and central nervous system penetration. GRL-142 forms optimum polar, van der Waals, and halogen bond interactions with HIV-1 protease and strongly blocks protease dimerization, demonstrating that combined multiple optimizing elements significantly enhance molecular and atomic interactions with a target protein and generate unprecedentedly potent and practically favorable agents.
Specificity of receptor-G protein interactions. Discrimination of Gi subtypes by the D2 dopamine receptor in a reconstituted system. (1990)

The selectivity of D2 dopamine receptor-guanine nucleotide-binding protein (G protein) coupling was studied by reconstitution techniques utilizing purified D2 dopamine receptors from bovine anterior pituitary and resolved G proteins from bovine brain, bovine pituitary, and human erythrocyte. Titration of a fixed receptor concentration with varying G protein concentrations revealed two aspects of receptor-G protein coupling. First, Gi2 appeared to couple selectively with the D2 receptor with approximately 10-fold higher affinity than any other tested Gi subtype. Second, the G proteins differed in the maximal receptor-mediated agonist stimulation of the intrinsic GTPase activity. Gi2 appeared to be maximally stimulated by agonist-receptor complex with turnover numbers of approximately 2 min-1. The other Gi subtypes, Gi1 and Gi3, could be only partially activated, resulting in maximal rates of GTPase of approximately 1 min-1. Agonist-stimulated GTPase activity was not detected in preparations containing Go from bovine brain. The differences in maximal agonist-stimulated GTPase rates observed among the Gi subtypes could be explained by differences in agonist-promoted guanyl nucleotide exchange. Both guanosine 5'-3-O-(thio)triphosphate (GTP gamma S) binding and GDP release parameters were enhanced 2-fold for the Gi2 subtype over the other Gi subtypes. These results suggest that even though several types of pertussis toxin substrate may exist in most tissues, a receptor may interact discretely with G proteins, thereby dictating signal transduction mechanisms.
Optical Metasurfaces: Progress and Applications (2018)

A metasurface is an artificial nanostructured interface that has subwavelength thickness and that manipulates light by spatially arranged meta-atoms—fundamental building blocks of the metasurface. Those meta-atoms, usually consisting of plasmonic or dielectric nanoantennas, can directly change light properties such as phase, amplitude, and polarization. As a derivative of three-dimensional (3D) metamaterials, metasurfaces have been emerging to tackle some of the critical challenges rooted in traditional metamaterials, such as high resistive loss from resonant plasmonic components and fabrication requirements for making 3D nanostructures. In the past few years, metasurfaces have achieved groundbreaking progress, providing unparalleled control of light, including constructing arbitrary wave fronts and realizing active and nonlinear optical effects. This article provides a systematic review of the current progress in and applications of optical metasurfaces, as well as an overview of metasurface building blocks based on plasmonic resonances, Mie resonance, and the Pancharatnam-Berry phase.
Stable triple helices are formed upon binding of RNA oligonucleotides and their 2'-O-methyl derivatives to double-helical DNA. (1992)

Pyrimidine oligoribonucleotides bind to the major groove of double-helical DNA at homopurine.homopyrimidine sequences. They recognize Watson-Crick base pairs by forming T.A x U and C.G x C base triplets via Hoogsteen hydrogen bonding. The stability of these triple helices is much higher than that of triple helices formed by oligodeoxyribonucleotides as shown by an increase of the temperature at which half-dissociation of the third strand occurs. When the 2'-hydroxyl group of ribose moieties is replaced by 2'-O-methyl substituent, triple helix stability is further increased.
Epicardial differentiation drives fibro-fatty remodeling in arrhythmogenic cardiomyopathy (2021)

Arrhythmogenic cardiomyopathy (ACM) is an inherited disorder often caused by pathogenic variants in desmosomal genes and characterized by progressive fibrotic and fat tissue accumulation in the heart. The cellular origin and responsible molecular mechanisms of fibro-fatty deposits have been a matter of debate, due to limitations in animal models recapitulating this phenotype. Here, we used human-induced pluripotent stem cell (hiPSC)–derived cardiac cultures, single-cell RNA sequencing (scRNA-seq), and explanted human ACM hearts to study the epicardial contribution to fibro-fatty remodeling in ACM. hiPSC-epicardial cells generated from patients with ACM showed spontaneous fibro-fatty cellular differentiation that was absent in isogenic controls. This was further corroborated upon siRNA-mediated targeting of desmosomal genes in hiPSC-epicardial cells generated from healthy donors. scRNA-seq analysis identified the transcription factor TFAP2A (activating enhancer-binding protein 2 alpha) as a key trigger promoting this process. Gain- and loss-of-function studies on hiPSC-epicardial cells and primary adult epicardial-derived cells demonstrated that TFAP2A mediated epicardial differentiation through enhancing epithelial-to-mesenchymal transition (EMT). Furthermore, examination of explanted hearts from patients with ACM revealed epicardial activation and expression of TFAP2A in the subepicardial mesenchyme. These data suggest that TFAP2A-mediated epicardial EMT underlies fibro-fatty remodeling in ACM, a process amenable to therapeutic intervention.
Extensive Large-Scale Study of Error in Samping-Based Distinct Value Estimators for Databases (2016)

The problem of distinct value estimation has many applications. Being a critical component of query optimizers in databases, it also has high commercial impact. Many distinct value estimators have been proposed, using various statistical approaches. However, characterizing the errors incurred by these estimators is an open problem: existing analytical approaches are not powerful enough, and extensive empirical studies at large scale do not exist. We conduct an extensive large-scale empirical study of 11 distinct value estimators from four different approaches to the problem over families of Zipfian distributions whose parameters model real-world applications. Our study is the first that \emph{scales to the size of a billion-rows} that today's large commercial databases have to operate in. This allows us to characterize the error that is encountered in real-world applications of distinct value estimation. By mining the generated data, we show that estimator error depends on a key latent parameter --- the average uniform class size --- that has not been studied previously. This parameter also allows us to unearth error patterns that were previously unknown. Importantly, ours is the first approach that provides a framework for \emph{visualizing the error patterns} in distinct value estimation, facilitating discussion of this problem in enterprise settings. Our characterization of errors can be used for several problems in distinct value estimation, such as the design of hybrid estimators. This work aims at the practitioner and the researcher alike, and addresses questions frequently asked by both audiences.
MRI-based pre-planning in patients with cervical cancer treated with three-dimensional brachytherapy (2011)

MRI-based pre-planning with consecutive CT/MRI data fusion is feasible and safe, with the advantage of increasing the dose to the tumour and decreasing the dose to the organs at risk.
Fire Ant Venom Alkaloid, Isosolenopsin A, a Potent and Selective Inhibitor of Neuronal Nitric Oxide Synthase (2003)

Massive, multiple fire ant, Solenopsis invicta, stings are often treated aggressively, particularly in the elderly, despite limited evidence of systemic toxicity due to the venom. Over 95% of the S. invicta venom is composed of piperidine alkaloid components, whose toxicity, if any, is unknown. To assess a possible pharmacological basis for systemic toxicity, an alkaloid-rich, protein-free methanol extract of the venom from whole ants was assayed for inhibitory activity on the following nitric oxide synthase (NOS) isoforms, rat cerebellar neuronal (nNOS), bovine recombinant endothelial (eNOS), and murine recombinant immunologic (iNOS). Cytosolic NOS activity was determined by measuring the conversion of [(3)H]arginine to [(3)H]citrulline in vitro. Rat nNOS activity was inhibited significantly and in a concentration-dependent manner by the alkaloid-rich venom extract. For nNOS, enzyme activity was inhibited by approximately 50% with 0.33 +/- 0.06 microg of this venom extract, and over 95% inhibition of the three isoforms, nNOS, eNOS, and iNOS, was found with doses of 60 microg in 60 microl reaction mixture. These results indicate that the alkaloid components of S. invicta venom can produce potent inhibition of all three major NOS isoforms. Isosolenopsin A (cis-2-methyl-6-undecylpiperidine), a naturally occurring fire ant piperidine alkaloid, was synthesized and tested for inhibitory activity against the three NOS isoforms. Enzyme activities for nNOS and eNOS were over 95% inhibited with 1000 microM of isosolenopsin A, whereas the activity of iNOS was inhibited by only about 20% at the same concentration. The IC(50) for each of three NOS isoforms was approximately 18 +/- 3.9 microM for nNOS, 156 +/- 10 microM for eNOS, and >1000 microM for iNOS, respectively. Kinetic studies showed isosolenopsin A inhibition to be noncompetitive with L-arginine (K(i) = 19 +/- 2 microM). The potency of isosolenopsin A as an inhibitor of nNOS compares favorably with the inhibitory potency of widely used nNOS inhibitors. Inhibition of NOS isoforms by isosolenopsin A and structurally similar compounds may have toxicological significance with respect to adverse reactions to fire ant stings.
Software-based ultrasound phase rotation beamforming on multi-core DSP (2011)

Phase rotation beamforming (PRBF) is a commonly-used digital receive beamforming technique. However, due to its high computational requirement, it has traditionally been supported by hardwired architectures (e.g., application-specific integrated circuits (ASICs) or more recently field-programmable gate arrays (FPGAs)). In this paper, we investigate the feasibility of supporting software-based PRBF on a multi-core DSP. To alleviate the high computing requirement, the analog front-end (AFE) chips integrating quadrature demodulation in addition to analog-to-digital conversion could be adopted. Under this condition, only delay alignment and phase rotation need to be performed by DSP, substantially reducing the computational load. We implemented the delay alignment and phase rotation modules on a Texas Instruments C6678 DSP with 8 cores. With a sampling rate of 40 MHz and 2∶1 decimation, it takes 200 µs to generate one scanline (2048 samples/scanline) on two cores. With 4 cores, it can support beamforming for 64 channels with 10k scanlines/s, e.g., 200 scanlines/frame and at 50 frames/s. The remaining 4 cores can work on back-end processing tasks and applications, e.g., color Doppler or ultrasound elastography.
SMART TRASH: Study on RFID tags and the recycling industry: Interim Report (D3) SMART 2010/0042 (2012)

Aims to assess the environmental impact of the RFID tags themselves as well as the environmental advantages that the use of RFID can provide to product lifecycle management.
Auto White Balance Using the Coincidence of Chromaticity Histograms (2012)

This paper presents a simple and robust auto white balance algorithm using the coincidence of chromaticity histograms. After analyzing the relationship between the coincidence of the color histogram and color constancy, the overlap area of chromaticity histograms that keep chromaticity of color images but not the effect of luminance existing in the color histogram is employed to estimate the correct illuminant in scenes. When the overlap reaches the maximum, correspondingly the respective gain coefficients of color channels can be derived to achieve the white balance of the camera. Through numerous experiments and evaluations based on the processing of real world images, the proposed coincidence of chromaticity histograms algorithm achieves the outstanding performance comparing to other algorithms. Furthermore, the simplicity, easy implementation and robustness to the luminance make it flexibly apply to the vision system of the autonomous robot running outdoor.
Distinct Roles of Wnt/<i>β</i>-Catenin Signaling in the Pathogenesis of Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis (2017)

Wnt signaling pathways are tightly controlled under a physiological condition, under which they play key roles in many biological functions, including cell fate specification and tissue regeneration. Increasing lines of evidence recently demonstrated that a dysregulated activation of Wnt signaling, particularly the Wnt/<i>β</i>-catenin signaling, was involved in the pathogenesis of chronic pulmonary diseases, such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). In this respect, Wnt signaling interacts with other cellular signaling pathways to regulate the initiation and pathogenic procedures of airway inflammation and remodeling, pulmonary myofibroblast proliferation, epithelial-to-mesenchymal transition (EMT), and development of emphysema. Intriguingly, Wnt/<i>β</i>-catenin signaling is activated in IPF; an inhibition of this signaling leads to an alleviation of pulmonary inflammation and fibrosis in experimental models. Conversely, Wnt/<i>β</i>-catenin signaling is inactivated in COPD tissues, and its reactivation results in an amelioration of airspace enlargement with a restored alveolar epithelial structure and function in emphysema models. These studies thus imply distinct mechanisms of Wnt/<i>β</i>-catenin signaling in the pathogenesis of these two chronic pulmonary diseases, indicating potential targets for COPD and IPF treatments. This review article aims to summarize the involvement and pathogenic roles of Wnt signaling pathways in the COPD and IPF, with a focus on the implication of Wnt/<i>β</i>-catenin signaling as underlying mechanisms and therapeutic targets in these two incurable diseases.
Bacterial Ice Crystal Controlling Proteins (2014)

Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.
Passively actuated spoiler for gust load alleviation (2016)

This paper summarises a conceptual study regarding a passively actuated spoiler for gust load alleviation. The design of such system is intended to limit the use of computers, sensors and actuators to operate the device. The study mainly relies on using Theodorsen’s unsteady flow theory for a typical airfoil section. To cope with the limitations of this type of model for spoiler aerodynamic, corrections are brought from unsteady high fidelity flow simulations by means of transfer functions. The outcome is a 2D aeroelastic model with three degrees of freedom. It describes the spoiler contribution to the overall aeroelastic behaviour of the airfoil in the event of a gust encounter. Results show that the spoiler can help to reduce loads passively, but requires to be retracted with an active system to work properly.
Lab-scale long-term operation of passive multivariable RFID temperature sensors integrated into single-use bioprocess components (2011)

We address the significant need for the monitoring of critical manufacturing parameters in single-use biopharmaceutical manufacturing by developing passive radio-frequency identification (RFID)-based sensors and their integration into single use bioprocess components. Our sensor development approach converts ubiquitous passive 13.56 MHz RFID tags into inductively coupled sensors. In this work, we integrated RFID sensors into single-use bioprocess bags and have tested these sensors for over 570 h for measurements of temperature. The achieved performance accuracy was 0.1 °C when measurements were performed over the 32 - 48 °C temperature range. Developed RFID sensors provide several important features previously unavailable from other single-use sensing technologies such as the same sensor platform for measurements of physical, chemical, and biological parameters; multi-parameter monitoring with individual sensors; and simultaneous digital identification.
A mammalian Mitochondrial RNA Processing Activity Contains Nucleus-Encoded RNA (1987)

Ribonuclease mitochondrial RNA processing, a site-specific endoribonuclease involved in primer RNA metabolism in mammalian mitochondria, requires an RNA component for its activity. On the basis of copurification and selective inactivation with complementary oligonucleotides, a 135-nucleotide RNA species, not encoded in the mitochondrial genome, is identified as the RNA moiety of the endoribonuclease. This finding implies transport of a nucleus-encoded RNA, essential for organelle DNA replication, to the mitochondrial matrix.
Distance-measurement error associated with antenna phase-center displacement in time-reference radio positioning systems (2004)

This paper presents a tutorial discussion of the effects of antenna phase-center displacement on distance determination in time-correlation radio positioning systems. A technique to determine the antenna phase-center displacement as a function of observation angle is reviewed. A simple method to determine the distance error versus observation angle, derived from the antenna phase-center displacement, is then presented. Numerical distance-error predictions, determined directly from antenna phase-center displacement, are presented for a Yagi and a log-periodic antenna used in a commercial UHF radio distance-measurement system. Finally, the measured distance error versus observation angle for these antennas as determined in several field trials is presented, validating the numerical predictions.
Trapping Set Error Correction through Adaptive Informed Dynamic Scheduling Decoding of LDPC Codes (2012)

Recent studies indicate that sequential scheduling of iterative decoding of low-density parity-check codes can provide improved code performance in comparison with the conventional flooding in terms of decoding success rate and convergence speed. In particular, a class of sequential scheduling schemes known as informed dynamic scheduling (IDS) has shown to outperform other sequential scheduling schemes from its capability to correct trapping set errors. In this letter, we present an adaptive IDS scheme which combines and outperforms previously proposed sequential scheduling schemes.