gebhart/patrepeval huggingface dataset:
Identification of chromosome arm 9p as the most frequent target of homozygous deletions in lung cancer (2005)

Genome scanning at a 1-Mb resolution was undertaken in 29 lung cancer cell lines to clarify the distribution of homozygous (i.e., both allele) deletions along lung cancer genomes, using a high-resolution single nucleotide polymorphism array. Eighteen regions, including two known tumor suppressor loci, CDKN2A at 9p21 and FHIT at 3p14, were found homozygously deleted. Frequencies of deletions at the 18 regions were evaluated by genomic polymerase chain reaction in 78 lung cancer cell lines. Seven regions, 2q24, 3p14, 5q11, 9p21, 9p23, 11q14, and 21q21, were homozygously deleted in two or more cell lines. The CDKN2A locus at 9p21 was most frequently deleted (20/78, 26%), and the deletions were detected exclusively in non-small-cell lung carcinomas (NSCLCs). The PTPRD (protein tyrosine phosphatase receptor type D) locus at 9p23 was the second-most frequently deleted (8/78, 10%), and the deletions were detected in both small-cell lung carcinomas (SCLC) and NSCLC. In addition, the 9p24 region was deleted in a NSCLC. In total, 24 (31%) cell lines carried at least one deletion on chromosome arm 9p, while deletions on the remaining chromosome arms were observed at most in four (5%) cell lines. Deletions at 9p24, 9p23, and 9p21 were not contiguous with one another, and preferential co-occurrence or mutual exclusiveness for the deletions at these three loci was not observed. Thus, it was indicated that 9p is the most frequent target of homozygous deletions in lung cancer, suggesting that the arm contains multiple lung tumor suppressor genes and/or genomic features fragile during lung carcinogenesis.
Blue to True-Blue Phosphorescent IrIII Complexes Bearing a Nonconjugated Ancillary Phosphine Chelate: Strategic Synthesis, Photophysics, and Device Integration (2009)

We report the design and synthesis of Ir(III) complexes functionalized with substituted pyridyl cyclometalate or azolate chromophores, plus one newly designed nonconjugated phosphine chelate, which not only greatly restricts its participation in the lowest-lying electronic transition but also enhances the coordination strength. These two key factors lead to fine-tuning of the phosphorescence chromaticity toward authentic blue and simultaneously suppress, in part, the nonradiative deactivation. This conceptual design presents a novel strategy in achieving heretofore uncommon, high-efficiency blue and true-blue phosphorescence. The fabrication of the organic light-emitting devices (OLEDs) employing phosphorescent dopants [Ir(dfpbpy)(2)(P(wedge)N)] (1b) and [Ir(fppz)(2)(P(wedge)N)] (3) was successfully made, for which the abbreviations (dfpbpy)H, (fppz)H, and (P(wedge)N)H represent 2-(4,6-difluorophenyl)-4-tert-butylpyridine, 3-(trifluoromethyl)-5-(2-pyridyl)pyrazole, and 5-(diphenylphosphinomethyl)-3-(trifluoromethyl)pyrazole, respectively. Of particular interest is the 3-doped OLEDs, which exhibit remarkable maximum efficiencies of 6.9%, 8.1 cd A(-1), and 4.9 lm W(-1), together with a true-blue chromaticity CIE(x,y) = 0.163, with 0.145 recorded at 100 cd m(-2).
IC‐P‐179: IN VIVO TRACKING OF TAU PATHOLOGIES WITH 18F‐PM‐PBB3 (18F‐APN‐1607) PET IN AD AND DIVERSE NON‐AD TAUOPATHIES (2019)

Our previous studies demonstrated 18F-PM-PBB3 (18F-APN-1607) to be a promising PET ligand, with suitable pharmacokinetics, high contrast and minimal parenchymal off-target binding, for quantifying tau pathologies in Alzheimer's disease (AD) and non-AD tauopathy patients. The present study aims to investigate the association between distribution pattern of PM-PBB3 and clinical features in patients with 4-repeat tauopathies. We enrolled 17 patients with 4-repeat tauopathies including clinically diagnosed progressive supranuclear palsy (PSP), corticobasal syndrome (CBS), and one patient with corticobasal degeneration (CBD) confirmed by brain biopsy. Seven AD spectrum patients, two Parkinson's disease (PD) patients, and 15 cognitively healthy controls were also recruited. All participants underwent PET scans with 18F-PM-PBB3 and 11C-PiB for estimating regional tau and amyloid-β loads. We generated parametric images of the standardized uptake value ratio (SUVR) to the cerebellar cortex for PM-PBB3 and PiB to evaluate brain regional tau and amyloid-β loads. We confirmed that all patients with AD spectrum were PiB-positive, while all other participants were PiB-negative. 18F-PM-PBB3 PET showed a characteristic distribution pattern in patients with 4-repeat tauopathies, which was distinct from that observed in AD spectrum patients. Patients with 4-repeat tauopathies showed remarkable uptake of PM-PBB3 especially around subthalamic nucleus, basal ganglia, midbrain including nigra and red nucleus, and dentate nucleus, whereas PD patients did not show any prominent parenchymal uptake of PM-PBB3. Compared with PSP with Richardson syndrome, patients with other PSP-variants including PSP with progressive gait freezing, predominant parkinsonism, ocular motor dysfunction, and CBS/CBD showed relatively milder uptake of PM-PBB3 especially around the midbrain. In contrast, patients with 4-repeat tauopathies presenting behavioral and/or verbal symptoms also presented increased PM-PBB3 uptake in some cortices in addition to the above-mentioned regions. Interestingly, some cognitively healthy elderly showed elevated PM-PBB3 uptake with slight white matter atrophy, which resembled patients with 4-repeat tauopathies in terms of distribution pattern, despite the fact that they were PiB-negative and cognitively normal. Our results support the hypothesis that distribution of PM-PBB3 may reflect clinical manifestations of 4-repeat tauopathies. 18F-PM-PBB3 PET may facilitate better understanding of the pathological basis of, and drug development for 4-repeat tau pathologies.
Acute and chronic changes in adenohypophyseal hormone secretion in sheep during zeranol administration (1983)

The effect of zeranol on circulating plasma concentrations of 5 adenohypophyseal (anterior pituitary gland) hormones was investigated in growing, castrated male sheep in 3 studies: after IM injection of 1 mg of zeranol (acute study), during a 6-week period after subcutaneous implantation of 12 mg of zeranol (chronic study), and during a 4-hour continuous IV infusion of gonadotropin-releasing hormone (Gn-RH) plus thyrotropin releasing hormone (TRH), 10 micrograms/hour. The sheep used in the chronic study (challenge study) were the same animals used in the 6-week implant study. Plasma concentrations of luteinizing hormone (LH), follicle-stimulating hormone (FSH), prolactin (PRL), thyroid-stimulating hormone (TSH), and growth hormone (GH) were measured by specific radioimmunoassay. Injection of zeranol resulted in a transient decrease in circulating LH and prolonged reduction in FSH concentrations during the 24-hour sampling period. Plasma concentrations of PRL, TSH, and GH in zeranol-injected and control animals were not different. Implantation of zeranol caused chronic reduction in plasma LH and FSH, an increase in PRL, and no change in plasma GH or TSH concentrations compared with values for control animals. In the challenge study, IV infusion of Gn-RH and TRH caused a significant increase in the concentration of each of the 5 hormones compared with preinfusion values, regardless of zeranol treatment. When the hormone-response profiles were compared between zeranol-treated and control sheep in this challenge study, only the LH response was different--being greater in zeranol-treated sheep. Generally, the administration of zeranol resulted in a more pronounced alteration in basal and stimulated secretion of reproductive hormones such as LH, FSH, and PRL than in GH or TSH, which are more commonly associated with growth and development.
Is circulating HER-2 more than just a tumor marker? (2001)

HER2/ neu (also known as neu and as c-erbB-2 ) is a proto-oncogene of the EGF[2][1] receptor family of receptor tyrosine kinases [(1)][2] . HER2/ neu encodes a M r185,000 transmembrane glycoprotein receptor (HER2, or c-erbB-2) that has partial homology with the other members of the EGF receptor
Geodesic domes and fullerenes (1993)

Abstract The structural form of geodesic domes, composed of pentagons and hexagons, played an important role in understanding the structure of carbon clusters. In this paper an analogy between geodesic domes and fullerenes is investigated. A brief survey is given of the geometry of geodesic domes applied in engineering practice, in particular of the geodesic domes bounded by pentagons and hexagons. A connection is also made between these sorts of geodesic domes and the mathematical problem of the determination of the smallest diameter of n equal circles by which the surface of a sphere can be covered without gaps. It is shown that the conjectured solutions to the sphere-covering problem provide topologically the same configurations as fullerene polyhedra for some values of n. Mechanical models of fullerenes, composed of equal rigid nodes and equal elastic bars are also investigated, and the equilibrium shapes of the space frames that model C28, C60 and C240 are presented.
Chemically Controlled Spatiotemporal Oscillations of Colloidal Assemblies (2017)

Abstract We report an autonomous oscillatory micromotor system in which active colloidal particles form clusters, the size of which changes periodically. The system consists of an aqueous suspension of silver orthophosphate microparticles under UV illumination, in the presence of varying concentrations of hydrogen peroxide. The colloid particles first attract each other to form clusters. After a short delay, these clusters abruptly disperse and oscillation begins, alternating between clustering and dispersion of particles. After a cluster oscillation initiates, the oscillatory wave propagates to nearby clusters and eventually all the clusters oscillate in phase‐shifted synchrony. The oscillatory behavior is governed by an electrolytic self‐diffusiophoretic mechanism which involves alternating electric fields generated by the competing reduction and oxidation of silver. The oscillation frequency is tuned by changing the concentration of hydrogen peroxide. The addition of inert silica particles to the system results in hierarchical sorting and packing of clusters. Densely packed Ag 3 PO 4 particles form a non‐oscillating core with an oscillating shell composed largely of silica microparticles.
Molecular Dynamics Simulations of Chiral Nematic Liquid Crystals (1994)

Preliminary results are presented on molecular dynamics simulations of the chiral nematic phase of (+)-4-(2''-metyl butyl)-4'-cyanobiphenyl. In this study, a molecular chirality is introduced by detailed atomic modeling. To treat helical structures of the chiral nematic phase, a new twisted simulation cell is introduced. The results show that the system with the twisted simulation cell gives a better fit and a lower potential energy than with an ordinary rectangular cell.
<title>Antialiasing and enhancement of passive mm-wave focal plane array imagery</title> (2000)

In this presentation we show how antialiasing can be achieved through image processing. Bandlimited images have their bandwidths extended using non-linear image restoration techniques. In these images the spatial frequencies within the passband are known but not the correct irradiance at nay point in the scene. In antialiasing however converse is true. When the bandwidth is to be increased by a factor of two the irradiance at alternate picture points is known but not the correct spectrum. Nevertheless bandwidth extension and removal of aliasing is possible using these non-linear techniques. They have been applied to real imagery using a recently developed 2D Lorentzian algorithm which has then bee used to further enhance the images.
Effect of neutral transport on the etch product lifecycle during plasma etching of silicon in chlorine gas (2002)

In this article, we report a computer simulation of silicon etching in chlorine gas. We focus on the lifecycle of silicon containing etch products and how this lifecycle is affected by neutral transport. The lifecycle of silicon in an etch reactor consists of etching, fragmentation by gas phase chemistry, deposition on the walls and wafer, and removal from the reactor. All of these processes are affected by neutral transport. Flow rate and reactor geometry are varied, and the characteristics of the resulting flow fields are analyzed. With the reactor inlet located at the center of the top dielectric, there is significant convective flow at the wafer surface at a chlorine feed rate of 500 sccm. The convective flow helps remove etch products from the reactor. This reduces etch product fragmentation to depositing species in the plasma; thereby reducing wall and wafer deposition. With a showerhead inlet, or with an inlet located at the outer rim of the top dielectric, there is little convective flow at the wafer for any of the simulated flow rates. This results in diffusion dominated transport of etch products. The diffusion is driven by species gradients induced by gas phase and surface reactions. As flow rate decreases, the primary redeposition precursor shifts from SiCl (at 500 sccm) to Si (at 45 sccm), changing the profile of redeposition on the wafer.
SLAM-based online calibration of asynchronous microphone array for robot audition (2011)

This paper addresses the online calibration of an asynchronous microphone array for robots. Conventional microphone array technologies require a lot of measurements of transfer functions to calibrate microphone locations, and a multi-channel A/D converter for inter-microphone synchronization. We solve these two problems using a framework combining Simultaneous Localization and Mapping (SLAM) and beamforming in an online manner. To do this, we assume that estimations of microphone locations, a sound source location, and microphone clock difference correspond to mapping, self-localization, observation errors in SLAM, respectively. In our framework, the SLAM process calibrates locations and clock differences of microphones every time a microphone array observes a sound like a human's clapping, and a beamforming process works as a cost function to decide the convergence of calibration by localizing the sound with the estimated locations and clock differences. After calibration, beamforming is used for sound source localization. We implemented a prototype system using Extended Kalman Filter (EKF) based SLAM and Delay-and-Sum Beamforming (DS-BF). The experimental results showed that microphone locations and clock differences were estimated properly with 10–15 sound events (handclaps), and the error of sound source localization with the estimated information was less than the grid size of beamforming, that is, the lowest error was theoretically attained.
Silicon Particle Formation by Pyrolysis of Silane in a Hot Wall Gasphase Reactor (2001)

The formation of silicon powder by pyrolysis of silane diluted in argon at different concentrations has been studied. A hot wall gasphase reactor was used for the thermal decomposition of SiH4 at 1000 °C and atmospheric pressure. The composition, morphology, size, and shape of the particles produced has been studied utilizing electron microscopy, X-ray diffraction, infrared spectroscopy, and BET gas adsorption. Depending on the experimental conditions, agglomerates of polycrystalline, sintered particles have been obtained, which are composed of nanocrystallites of about 25 nm in size.
SU‐F‐J‐212: Enabling Conventional Cone Beam CT with the Capability of Dual Energy Imaging Using a Simple Add‐On Beam Modifier (2016)

Purpose: In searching for a robust, efficient and cost‐effective dual energy cone beam CT (DECBCT) solution for various radiation oncology applications, in particularly for improved proton dose planning/replanning accuracy and DE‐CBCT guided radiation therapy, we investigate a novel energy modulation scheme using a beam modifier placed between the source and patient and optimize its geometric configuration for routine clinical use. Methods: The study was performed using a Hitachi CBCT scanner and the tube voltage was set at 125 kVp. The higher energy beam was obtained by filtering the incident utilizing a beam modulation layer (material: copper, thickness: 1.8 mm). To avoid the need for double scans (one with and one without the energy modulator), the modulation layer was configured to cover only the half of the X‐ray beam so that two sets of sinograms corresponding low and high energies were collected after a single gantry rotation of 360 deg. The average high energy and low energy HU numbers (HUhigh and HUlow) were derived for pixels in a defined region‐of‐interest, respectively. Results: The beam modifier increased the threshold of the energy spectrum from ∼20 keV up to ∼50 keV. Two complete sets of images were obtained with good alignment between the high energy and low‐energy cases without any artifact observed (Fig. 2). The HUlow/HUhigh is ∼0/0 (water), ∼394/238 (brain), ∼1283/1085 (cortical bone) and ∼3000/1800 (titanium). Conclusion: The feasibility of the proposed DECT implementation using a beam modifier has been demonstrated. Compared to the existing DECT solutions, the proposed scheme is much more cost‐effective and requires minimum hardware modification. The work lays foundation for us to study the quantification of HU values to derive material density images and atomic number (and electron density) of substances.
Fit-For-Purpose Model for Dielectric Data Interpretation for Enhanced Formation Evaluation (2023)

Abstract Great progress in technology development of dielectric logging has been made in the last decade, mainly by establishing the capability of multi-frequency measurements for more robust determination of near wellbore water-filled porosity and flush zone resistivity, in addition in providing the potential of characterizing reservoir petrophysical properties such as rock tortuosity. To interpret acquired dielectric data, several models have been developed and used in the industry. The objective of this laboratory study was to evaluate the commonly used models, identify conditions under which each model is applicable, and establish a workflow to select the most suitable model for targeted applications. This study was performed on limestone core samples. Routine and special core analysis including resistivity and dielectric measurements were conducted. Three commonly used dielectric models (CRIM, Bimodal, and SMD) were evaluated. Properties having major influence on these models are brine salinity, brine saturation, and Archie parameters m and n. Effects of these properties on the dielectric data interpretation models were studied systematically, by comparing the models’ outputs to direct laboratory measurements. For core samples fully saturated with fresh water of salinity ranging from 2 to 23 kppm NaCl, all three models provide consistent results of inverted water-filled porosity when compared with core weight porosity. The inversion results are robust and independent of whether the salinity is constrained or not. In a saline environment of 200 kppm NaCl, the inverted water-filled porosities are found to be slightly higher than core porosity. Comparing between inverted dielectric textural parameter MN and Archie resistivity parameter m shows that the Bimodal model performs better than the SMD model at this high-water salinity environment. Based on these results, a simple linear regression correction scheme is proposed for each salinity range investigated. The proposed algorithm is structured to correct the output of each model using statistical mean at specific salinity conditions. Finally, we introduce a fit-for-purpose model selection for dielectric data interpretation for enhanced formation evaluation.
A dynamic approach to selectivity in heterogeneous partial oxidation (1987)

Despite the rapid development of literature pertaining to fundamental (1-4) studies of oxidation catalysis, a general theory of heterogeneous selective oxidation catalysis explaining the selectivity behavior of different metal oxide systems has not yet been developed. Redox mechanisms have been widely invoked in the kinetic and mechanistic descriptions of selective oxidation reactions, suggesting a dynamic behavior of hydrocarbon and oxygen interactions with the catalyst surface. Nevertheless, most of the recent theoretical approaches of this subject matter (5-7) are essentially static in nature. Correlations are made with surface structure on the basis of crystallographic considerations with selectivity being related to the nature, number, bond-strength and nearness of oxygen atoms in the neighborhood of adsorption centers. The effect of the reaction medium on the configuration of the catalyst surface, and thus its influence on the reaction path, are generally not taken into account. The best dynamic approach is a kinetic one; however, since often the first reaction step is the rate determining step, it is not the most useful approach for mechanistic studies of selectivity. The aim of this paper is to present an approach of selectivity issues combining surface structure with kinetic concepts, in an attempt to develop a generalized dynamicmore » understanding of selectivity of oxide-based catalysts. In particular, the model considers the effect of reaction conditions (composition of reactants and reaction temperature) on catalyst selectivity and offers a key to the interpretation of the catalytic behavior of mixed metal oxides of modified redox properties.« less
Novel mode content analysis technique for multimode waveguides (2003)

This paper presents a novel technique for analyzing the mode content in multimode waveguides. The technique is based on measuring the frequency response between the two antennas coupled into a multimode waveguide and using that information to extract the frequency-averaged mode content at the location of the transmitting antenna. The technique is applicable to cases in which the complex mode amplitudes are approximately constant over the frequency range of interest. This method is valuable for determining the mode mix generated by arbitrary transmitting antennas in a multimode waveguide propagation environment, such as HVAC duct system used for indoor wireless communications.
Group secret key agreement over state-dependent wireless broadcast channels (2016)

We consider a group of $m$ trusted and authenticated nodes that aim to create a shared secret key $K$ over a wireless channel in the presence of an eavesdropper Eve. We assume that there exists a state dependent wireless broadcast channel from one of the honest nodes to the rest of them including Eve. All of the trusted nodes can also discuss over a cost-free, noiseless and unlimited rate public channel which is also overheard by Eve. For this setup, we develop an information-theoretically secure secret key agreement protocol. We show the optimality of this protocol for "linear deterministic" wireless broadcast channels. This model generalizes the packet erasure model studied in literature for wireless broadcast channels. For "state-dependent Gaussian" wireless broadcast channels, we propose an achievability scheme based on a multi-layer wiretap code. Finding the best achievable secret key generation rate leads to solving a non-convex power allocation problem. We show that using a dynamic programming algorithm, one can obtain the best power allocation for this problem. Moreover, we prove the optimality of the proposed achievability scheme for the regime of high-SNR and large-dynamic range over the channel states in the (generalized) degrees of freedom sense.