gebhart/patrepeval huggingface dataset:
Proteomic Identification of Lynchpin Urokinase Plasminogen Activator Receptor Protein Interactions Associated with Epithelial Cancer Malignancy (2007)

Urokinase plasminogen activator (uPA) and its high affinity receptor (uPAR) play crucial proteolytic and non-proteolytic roles in cancer metastasis. In addition to promoting plasmin-mediated degradation of extracellular matrix barriers, cell surface engagement of uPA through uPAR binding results in the activation of a suite of diverse cellular signal transduction pathways. Because uPAR is bound to the plasma membrane through a glycosyl-phosphatidylinositol anchor, these signalling sequelae are thought to occur through the formation of multi-protein cell surface complexes involving uPAR. To further characterize uPAR-driven protein complexes, we co-immunoprecipitated uPAR from the human ovarian cancer cell line, OVCA 429, and employed sensitive proteomic methods to identify the uPAR-associated proteins. Using this strategy, we identified several known, as well as numerous novel, uPAR associating proteins, including the epithelial restricted integrin, alphavbeta6. Reverse immunoprecipitation using anti-beta6 integrin subunit monoclonal antibodies confirmed the co-purification of this protein with uPAR. Inhibition of uPAR and/or beta6 integrin subunit using neutralizing antibodies resulted in the inhibition of uPA-mediated ERK 1/2 phosphorylation and subsequent cell proliferation. These data suggest that the association of beta6 integrin (and possibly other lynchpin cancer regulatory proteins) with uPAR may be crucial in co-transmitting uPA signals that induce cell proliferation. Our findings support the notion that uPAR behaves as a lynchpin in promoting tumorigenesis by forming functionally active multiprotein complexes.
Semiconductor Cocrystals Based on Boron: Generated Electrical Response with π-Rich Aromatic Molecules (2019)

Cocrystallization of a nonconductive, boron-based host with aromatic guests generates conductive cocrystals. Carrier mobilities of the cocrystals with either pyrene or tetrathiafulvalene were measured using conducting probe atomic force microscopy. The incorporation of the π-electron-rich aromatic guests results in electrically conductive cocrystals. The cocrystal with tetrathiafulvalene as a guest shows an approximately seven times higher charge carrier mobility than the cocrystal with pyrene.
Identification of epitopes on a mutant form of Pseudomonas exotoxin using serum from humans treated with Pseudomonas exotoxin containing immunotoxins (1997)

PE38 is a 38-kDa derivative of the 66-kDa Pseudomonas exotoxin (PE) in which the cell binding domain of PE (domain Ia, amino acids 1-252) and a portion of domain Ib (amino acids 365-380) are deleted. The immunotoxins LMB-1 and LMB-7 contain PE38 and kill cancer cells by exploiting the cytotoxic action of PE38. The major human B cell epitopes of PE38 were mapped by measuring the reactivity of 45 serum samples from patients treated with the PE38-containing immunotoxins LMB-1 or LMB-7 to two panels of overlapping synthetic peptides representing the sequence of PE38. One panel of peptides is ten amino acids long and overlap by seven amino acids, and the second panel of peptides is twenty amino acids long and overlap by ten. Five major epitopes were identified: amino acids 274-283, 470-492, 531-540, 555-564, and the C-terminal amino acids 596-609. Two minor epitopes were identified as well: amino acids 501-510 and 582-589. These epitopes are predominantly located on the surface of the protein. The amino acids believed to be critical for binding are highly solvent-accessible residues. The results of the human antibody response to peptides are compared to the pattern of reactivity previously identified with serum samples obtained from monkeys administered LMB-1 and LMB-7. The epitopes between monkey and human are almost identical, demonstrating similarity in the response of antibody repertoires between the two species and providing further support that these are the immunodominant epitopes. This information is critical for genetically engineering less immunogenic immunotoxins and provides a foundation for the development of a vaccine against pseudomonal infections which plague immunocompromised individuals and individuals with cystic fibrosis.
Improved Resolution of Hydrocarbon Structures and Constitutional Isomers in Complex Mixtures Using Gas Chromatography-Vacuum Ultraviolet-Mass Spectrometry (2012)

Understanding the composition of complex hydrocarbon mixtures is important for environmental studies in a variety of fields, but many prevalent compounds cannot be confidently identified using traditional gas chromatography/mass spectrometry (GC/MS) techniques. This work uses vacuum-ultraviolet (VUV) ionization to elucidate the structures of a traditionally "unresolved complex mixture" by separating components by GC retention time, t(R), and mass-to-charge ratio, m/z, which are used to determine carbon number, N(C), and the number of rings and double bonds, N(DBE). Constitutional isomers are resolved on the basis of t(R), enabling the most complete quantitative analysis to date of structural isomers in an environmentally relevant hydrocarbon mixture. Unknown compounds are classified in this work by carbon number, degree of saturation, presence of rings, and degree of branching, providing structural constraints. The capabilities of this analysis are explored using diesel fuel, in which constitutional isomer distribution patterns are shown to be reproducible between carbon numbers and follow predictable rules. Nearly half of the aliphatic hydrocarbon mass is shown to be branched, suggesting branching is more important in diesel fuel than previously shown. The classification of unknown hydrocarbons and the resolution of constitutional isomers significantly improves resolution capabilities for any complex hydrocarbon mixture.
An Inhibitory Effect of Interleukin-la on Basal Gonadotropin Release in the Ovariectomized Rhesus Monkey: Reversal by a Corticotropin-Releasing Factor Antagonist* (1991)

Interleukin-1 (IL-1), an important component of the immune system, has recently been shown to influence the release of several hormones in the rodent. In this paper, the effectiveness of IL-1a in modulating basal gonadotropin secretion as well as cortisol release in the primate has been investigated. Eight adult ovariectomized rhesus monkeys were given a 30-min intracerebroventricular infusion of physiological saline (n = 5), various doses of IL-1a (17 micrograms n = 5; 8.5 micrograms; n = 3; 4.2 micrograms n = 5; and 2.1 micrograms n = 4) or IL-1a plus a CRF antagonist (n = 5). LH and FSH concentrations were measured at 15-min intervals during the 3-h preinfusion baseline control and the 5-h postinfusion period, while cortisol concentrations were determined at 45-min intervals. While LH concentrations remained unchanged in the monkeys receiving saline only, they decreased significantly after the 30-min IL-1a infusion. By hour 5 after IL-1a administration, mean (+/- SE) hourly areas under the LH curves (expressed as a percentage of preinfusion baseline) were 27.7% +/- 7.3 (17 micrograms IL-1a), 31.9% +/- 8.4 (8.5 micrograms), 33.3% +/- 5.5 (4.2 micrograms), and 39% +/- 4.0 (2.1 micrograms) (P less than 0.05 vs. morning control). FSH concentrations were also significantly decreased after IL-1a, 17 micrograms: by hour 5, they were 67.4% +/- 5.0 of baseline control. While cortisol concentrations decreased thoughout the experiment in the animals receiving saline, they increased with all IL-1a doses: overall mean (+/- SE) postinfusion concentrations were 21.8 +/- 1.1 (saline), 49.5 +/- 2.2 (IL-1a, 17 micrograms), 35.1 +/- 1.9 (8.5 micrograms), 45.7 +/- 1.5 (4.2 micrograms), and 39.5 +/- 1.5 (2.1 micrograms) micrograms/dl (P less than 0.05 IL-1a vs. saline). Concomitant infusion of the CRF antagonist, [D-Phe12, NLE 21,38caMe LEU37] CRF (12-41), (120-360 micrograms), prevented the IL-1a induced LH inhibition. By hour 5, areas under LH curves were 33.5% +/- 1.7 for IL-1a alone and 99.2% +/- 4.2 (NS vs. saline) for IL-1a + CRF antagonist. The CRF antagonist also blocked the ability of IL-1a to increase cortisol secretion: mean cortisol concentrations were 28.6 +/- 1.4 micrograms/dl (NS vs. saline). The results clearly indicate that the cytokine IL-1a inhibits pulsatile LH and FSH secretion in the ovariectomized rhesus monkey and demonstrate that this inhibition is causally related to the activation of CRF by this cytokine.(ABSTRACT TRUNCATED AT 400 WORDS)
Complementary strand relocation may play vital roles in RecA-based homology recognition (2012)

RecA-family proteins mediate homologous recombination and recombinational DNA repair through homology search and strand exchange. Initially, the protein forms a filament with the incoming single-stranded DNA (ssDNA) bound in site I. The RecA-ssDNA filament then binds double-stranded DNA (dsDNA) in site II. Non-homologous dsDNA rapidly unbinds, whereas homologous dsDNA undergoes strand exchange yielding heteroduplex dsDNA in site I and the leftover outgoing strand in site II. We show that applying force to the ends of the complementary strand significantly retards strand exchange, whereas applying the same force to the outgoing strand does not. We also show that crystallographically determined binding site locations require an intermediate structure in addition to the initial and final structures. Furthermore, we demonstrate that the characteristic dsDNA extension rates due to strand exchange and free RecA binding are the same, suggesting that relocation of the complementary strand from its position in the intermediate structure to its position in the final structure limits both rates. Finally, we propose that homology recognition is governed by transitions to and from the intermediate structure, where the transitions depend on differential extension in the dsDNA. This differential extension drives strand exchange forward for homologs and increases the free energy penalty for strand exchange of non-homologs.
Developing a Neurosurgical Simulation-Based Educational Curriculum (2013)

The Congress of Neurological Surgeons has successfully incorporated simulation into an educational curriculum with both didactic and technical components. This appears to be a powerful educational tool, and its uses are being further expanded.
Long-lived layered silicates-immobilized 2,6-bis(imino)pyridyl iron (II) catalysts for hybrid polyethylene nanocomposites by in situ polymerization: Effect of aryl ligand and silicate modification Part A Polymer chemistry (2009)

Heterogeneous-layered silicate-immobilized 2,6-bis(imino)pyridyl iron (II) dichloride/MMAO catalysts, in which the active polymerization species are intercalated within sodium- and organomodified-layered silicate galleries, were prepared for producing hybrid exfoliated polyethylene (PE) nanocomposites by means of in situ polymerization. The inorganic filler was first treated with modified-methylaluminoxane (MMAO) to produce a supported cocatalyst: MMAO reacts with silicates replacing most of the organic surfactant, thus modifying the original crystallographic clay order. MMAO anchored to the nanoclay was able to activate polymerization iron complexes initiating the polymer growth directly from the filler lamellae interlayer. The polymerization mechanism taking place in between the montmorillonite lamellae separates the layers, thus promoting deagglomeration and effective clay dispersion. Transmission electron microscopy revealed that in situ polymerization by catalytically active iron complexes intercalated within the lower organomodified clay led to fine dispersion and high exfoliation extent. The intercalated clay catalysts displayed a longer polymerization life-time and brought about ethylene polymerization more efficiently than analogous homogeneous systems. PEs having higher molecular masses were obtained. These benefits resulted to be dependent more on the filler nature than on the ligand environment around the iron metal center and the experimental synthetic route.
Nobody likes Mondays (2013)

Streams of images from large numbers of surveillance webcams are available via the web. The continuous monitoring of activities at different locations provides a great opportunity for research on the use of vision systems for detecting actors, objects, and events, and for understanding patterns of activity and anomaly in real-world settings. In this work we show how images available on the web from surveillance webcams can be used as sensors in urban scenarios for monitoring and interpreting states of interest such as traffic intensity. We highlight the power of the cyclical aspect of the lives of people and of cities. We extract from long-term streams of images typical patterns of behavior and anomalous events and situations, based on considerations of day of the week and time of day. The analysis of typia and atypia required a robust method for background subtraction. For this purpose, we present a method based on sparse coding which outperforms state-of-the-art works on complex and crowded scenes.
The magnitude of lift forces acting on drops and bubbles in liquids flowing inside microchannels (2012)

Hydrodynamic lift forces offer a convenient way to manipulate particles in microfluidic applications, but there is little quantitative information on how non-inertial lift mechanisms act and compete with each other in the confined space of microfluidic channels. This paper reports measurements of lift forces on nearly spherical drops and bubbles, with diameters from one quarter to one half of the width of the channel, flowing in microfluidic channels, under flow conditions characterized by particle capillary numbers Ca(P) = 0.0003-0.3 and particle Reynolds numbers Re(P) = 0.0001-0.1. For Ca(P) < 0.01 and Re(P) < 0.01 the measured lift forces were much larger than predictions of deformation-induced and inertial lift forces found in the literature, probably due to physicochemical hydrodynamic effects at the interface of drops and bubbles, such as the presence of surfactants. The measured forces could be fit with good accuracy using an empirical formula given herein. The empirical formula describes the power-law dependence of the lift force on hydrodynamic parameters (velocity and viscosity of the carrier phase; sizes of channel and drop or bubble), and includes a numerical lift coefficient that depends on the fluids used. The empirical formula using an average lift coefficient of ~500 predicted, within one order of magnitude, all lift force measurements in channels with cross-sectional dimensions below 1 mm.
Mechanisms for solids ejection from gas‐fluidized beds (1983)

Abstract The bubble eruption process was studied in two‐ and three‐dimensional (2D and 3D) beds using a high‐speed video system for flow visualization. The results show the existence of four different ejection mechanisms; one occurring with singlebubble eruptions in both 2D and 3D beds, two others occurring in 2D and 3D beds with two bubbles coalescing at the bed‐free surface, and the fourth occurring only in 3D beds with bubbles coalescing at the bed surface.
Lung recruitment prevents collapse during laparoscopy in children (2017)

NCT02824146.
Next generation multimode terminals (2004)

The following paper describes the one possible direction for the future evolution of mobile handsets towards multimode operation, where the terminal supports multiple air interface technologies. One of the challenges faced by the manufacturers of such devices is how to take best advantage of the available interfaces in such a way as to conform to user preferences and application requirements. This paper introduces an architecture outlining the additional functionality required to support intelligent multimode operation, where the terminal is able to decide autonomously which of the active interfaces is best for an application session, and to move these applications between available interfaces when appropriate. The paper also highlights some of the open issues that should be addressed in order to enable fully autonomous operation of these devices.
Near-Infrared Analysis of Whole Kernel Barley: Comparison of Three Spectrometers (2008)

This study was conducted to develop calibration models for determining quality parameters of whole kernel barley using a rapid and nondestructive near-infrared (NIR) spectroscopic method. Two hundred and five samples of whole barley grains of three winter-habit types (hulled, malt, and hull-less) produced over three growing seasons and from various locations in the United States were used in this study. Among these samples, 137 were used for calibration and 68 for validation. Three NIR instruments with different resolutions, one Fourier transform instrument (4 cm(-1) resolution), and two dispersive instruments (8 nm and 10 nm bandpass) were utilized to develop calibration models for six components (moisture, starch, beta-glucan, protein, oil, and ash) and the results were compared. Partial least squares regression was used to build models, and various methods for preprocessing of spectral data were used to find the best model. Our results reveal that the coefficient of determination for calibration models (NIR predicted versus reference values) ranged from 0.96 for moisture to 0.79 for beta-glucan. The level of precision of the model developed for each component was sufficient for screening or classification of whole kernel barley, except for beta-glucan. The higher resolution Fourier transform instrument gave better results than the lower resolution instrument for starch and beta-glucan analysis. The starch model was most improved by the increased resolution. There was no advantage of using a higher resolution instrument over a lower resolution instrument for other components. Most of the components were best predicted using first-derivative processing, except for beta-glucan, where second-derivative processing was more informative and precise.
Engineering the Mechanical Properties of Polymer Networks with Precise Doping of Primary Defects (2017)

Polymer networks are extensively utilized across numerous applications ranging from commodity superabsorbent polymers and coatings to high-performance microelectronics and biomaterials. For many applications, desirable properties are known; however, achieving them has been challenging. Additionally, the accurate prediction of elastic modulus has been a long-standing difficulty owing to the presence of loops. By tuning the prepolymer formulation through precise doping of monomers, specific primary network defects can be programmed into an elastomeric scaffold, without alteration of their resulting chemistry. The addition of these monomers that respond mechanically as primary defects is used both to understand their impact on the resulting mechanical properties of the materials and as a method to engineer the mechanical properties. Indeed, these materials exhibit identical bulk and surface chemistry, yet vastly different mechanical properties. Further, we have adapted the real elastic network theory (RENT) to the case of primary defects in the absence of loops, thus providing new insights into the mechanism for material strength and failure in polymer networks arising from primary network defects, and to accurately predict the elastic modulus of the polymer system. The versatility of the approach we describe and the fundamental knowledge gained from this study can lead to new advancements in the development of novel materials with precisely defined and predictable chemical, physical, and mechanical properties.
Synchronizing real and predicted synthetic video imagery for localization of a robot to a 3D environment (2009)

A mobile robot moving in an environment in which there are other moving objects and active agents, some of which may represent threats and some of which may represent collaborators, needs to be able to reason about the potential future behaviors of those objects and agents. In previous work, we presented an approach to tracking targets with complex behavior, leveraging a 3D simulation engine to generate predicted imagery and comparing that against real imagery. We introduced an approach to compare real and simulated imagery using an affine image transformation that maps the real scene to the synthetic scene in a robust fashion. In this paper, we present an approach to continually synchronize the real and synthetic video by mapping the affine transformation yielded by the real/synthetic image comparison to a new pose for the synthetic camera. We show a series of results for pairs of real and synthetic scenes containing objects including similar and different scenes.
Chemie und Biologie der Stimulatoren und Aktivatoren der löslichen Guanylatcyclase (2013)

Abstract Die gefäßerweiternden Eigenschaften von Stickstoffmonoxid (NO) werden in der Pharmakotherapie bereits seit mehr als 130 Jahren genutzt, und auch heute noch spielen NO‐Donatoren eine bedeutende Rolle bei der Behandlung von Herzkreislauferkrankungen. Inhaliertes NO oder organische Nitrate und NO‐freisetzende Medikamente sind jedoch mit erheblichen therapeutischen Nachteilen behaftet, beispielsweise einer Toleranzentwicklung bei Langzeitbehandlung und unspezifischen Effekten wie der posttranslationalen Modifikation von Proteinen. Die positiven Wirkungen von NO werden durch die Stimulation der löslichen Guanylatcyclase (sGC) vermittelt, einem Häm‐haltigen Enzym, welches das intrazelluläre Signalmolekül cyclisches Guanosinmonophosphat (cGMP) bildet. Vor kurzem wurden zwei Substanzklassen entdeckt, die die Wirkung der sGC NO‐unabhängig verstärken, die sogenannten sGC‐Stimulatoren und sGC‐Aktivatoren. Der erste Vertreter dieser neuen Medikamentenklassen, der sGC‐Stimulator Riociguat, zeigte überzeugende Wirksamkeit in klinischen Phase‐III‐Studien bei unterschiedlichen Formen des Lungenhochdrucks.
AUTOMATION OF THE SCHONFELD METHOD OF HIGHWAY SURFACE TEXTURE CODE ASSIGNMENT. VOLUME II. THREE DIMENSIONAL CLASSIFICATION TECHNIQUE TECHNICAL APPROACH (1975)

The volume contains details of the technical approach followed to classify the pavement texture samples in accordance with the Schonfeld methodology.
On Improved Commutation for Moving-Magnet Planar Actuators (2023)

The demand for high-precision and high-throughput motion control systems has increased significantly in recent years. The use of moving-magnet planar actuators (MMPAs) is gaining popularity due to their advantageous characteristics, such as complete environmental decoupling and reduction of stage mass. Nonetheless, model-based commutation techniques for MMPAs are compromised by misalignment between the mover and coil array and mismatch between the ideal electromagnetic model and the physical system, often leading to decreased system performance. To address this issue, a novel improved commutation approach is proposed in this paper, which is applicable for general planar motor applications, by means of dynamic regulation of the position dependence of the ideal model-based commutation algorithm, which allows for attenuation of magnetic misalignment, manufacturing inaccuracies and other unmodelled phenomena. The effectiveness of the proposed approach is validated through experiments using a state-of-the-art moving-magnet planar actuator prototype.