gebhart/patrepeval huggingface dataset:
Remediating agitation-induced antibody aggregation by eradicating exposed hydrophobic motifs (2014)

Therapeutic antibodies must encompass drug product suitable attributes to be commercially marketed. An undesirable antibody characteristic is the propensity to aggregate. Although there are computational algorithms that predict the propensity of a protein to aggregate from sequence information alone, few consider the relevance of the native structure. The Spatial Aggregation Propensity (SAP) algorithm developed by Chennamsetty et. al. incorporates structural and sequence information to identify motifs that contribute to protein aggregation. We have utilized the algorithm to design variants of a highly aggregation prone IgG2. All variants were tested in a variety of high-throughput, small-scale assays to assess the utility of the method described herein. Many variants exhibited improved aggregation stability whether induced by agitation or thermal stress while still retaining bioactivity.
Highly ordered horizontal indium gallium arsenide/indium phosphide multi-quantum-well in wire structure on (001) silicon substrates (2016)

We report the characteristics of indium gallium arsenide stacked quantum structures inside planar indium phosphide nanowires grown on exact (001) silicon substrates. The morphological evolution of the indium phosphide ridge buffers inside sub-micron trenches has been studied, and the role of inter-facet diffusion in this process is discussed. Inside a single indium phosphide nanowire, we are able to stack quantum structures including indium gallium arsenide flat quantum wells, quasi-quantum wires, quantum wires, and ridge quantum wells. Room temperature photoluminescence measurements reveal a broadband emission spectrum centered at 1550 nm. Power dependent photoluminescence analysis indicates the presence of quasi-continuum states. This work thus provides insights into the design and growth process control of multiple quantum wells in wire structures for high performance nanowire lasers on a silicon substrate with 1550 nm band emission.
Omega-3s and cardiovascular health. (2014)

Despite the recent negative data about n-3 fatty acids, the overall evidence still supports the American Heart Association recommendation of 1 gram of eicosapentaenoic acid/docosahexaenoic acid per day for patients with coronary heart disease.
Impact of Annual Operator and Institutional Volume on Percutaneous Coronary Intervention Outcomes (2014)

Overall in-hospital mortality after PCI was low. An increase in operator and institutional volume of PCI was found to be associated with a decrease in adverse outcomes, length of hospital stay, and cost of hospitalization.
Acceleration of Control Intensive Applications on Coarse-Grained Reconfigurable Arrays for Embedded Systems (2023)

Embedded systems confront two opposite goals: low-power operation and high performance. The current trend to reach these goals is toward heterogeneous platforms, including multi-core architectures with heterogeneous cores and hardware accelerators. The latter can be divided into custom accelerators (e.g., ASICs) and programmable domain-specific cores (e.g., DSIPs). VWR2A Denkinger et al. 2022 is a programmable architecture that integrates high computational density and low power memory structures. The flexibility of VWR2A allows a large portion of applications to be covered, resulting in better performance and energy efficiency than ASICs and general-purpose processors. However, while this has been well studied for data-intensive kernels, this is not the case for control-intensive kernels —code with complex if-else and nested loop structures. Traditionally, control-intensive code is left to be executed by the host processor. This situation unnecessarily restricts the potential impact of energy-efficient acceleration, especially at the application level. In this paper, we evaluate the performance and energy consumption of VWR2A for control-intensive code and compare it with an ARM Cortex-M4 processor and a RISC-V Ibex processor. The performance and energy consumption are evaluated at the kernel and application levels. Our results confirm that VWR2A is faster and more energy-efficient than the two considered general-purpose processors also for control-intensive code.
Updating the low-frequency model in time-lapse seismic inversion: A case study from a heavy-oil steam-injection project (2015)

Abstract A workflow to update the time-lapse low-frequency model in a data-driven manner in time-lapse inversion studies is applied to a heavy-oil reservoir produced using the steam-assisted gravity drainage (SAGD) method. The base seismic survey and the difference between the base and monitor surveys are inverted in two separate inversion runs, and no assumptions are made regarding the reservoir changes or the relationships between elastic or reservoir parameters. The effects of production are estimated from the inversion of the difference between the base and monitor surveys. This information is used to update the low-frequency model in the time-lapse sense. A good match can be observed between the inversion results and other available information from the field, confirming the validity of the method.
In Vivo Degradation Behavior of Photo-Cross-Linked <i>star</i>-Poly(ε-caprolactone-<i>c</i><i>o</i>-<scp>d</scp>,<scp>l</scp>-lactide) Elastomers (2005)

We have recently reported on the preparation of biodegradable elastomers through photo-cross-linking acrylated star-poly(epsilon-caprolactone-co-D,L-lactide). In this paper we assess the change in their physical properties during in vivo degradation in rats after subcutaneous implantation over a 12 week period. These parameter changes were compared to those observed in vitro. Two different cross-link densities were examined, representing the range from a high Young's modulus to a low Young modulus. Elastomers having a high cross-link density exhibited degradation behavior consistent with a surface erosion mechanism, and degraded at the same rate in vivo as observed in vitro. Young's modulus and the stress at break of these elastomers decreased linearly with the degradation time, while the strain at break decreased slowly. Elastomers having a low cross-link density exhibited a degradation mechanism consistent with bulk erosion. Young's modulus and the stress at break of these elastomers decreased slowly initially, followed by a marked increase in mechanical strength loss after 4 weeks. The elastomers were well tolerated by the rats over the 12 week period in vivo.
Direct Observation of N<sub>2</sub>Self-Diffusion in Zeolitic Adsorbents Using<sup>15</sup>N PFG NMR (1996)

Standard methodologies used for studying hydrocarbon diffusion (using 1H PFG NMR) were applied for the first time to the diffusion of 15N2 in beds of finely powdered commercial zeolites 5A and 13X. Unlike 1H PFG NMR on hydrocarbon adsorbents, crystallite size, gradient strength, observation time, and gyromagnetic ratio are more critical in the measurement of N2 self-diffusion in commercial-grade crystals. In fact, with the available hardware configuration and crystallite diameter constraints, we were restricted to the measurement of long-range diffusivities. These diffusivities were found to be similar for both adsorbents, varying from 3.2 × 10-6 to 1.3 × 10-8 m2/s over the temperature range studied (289−167 K). We also found the intercrystalline diffusion (Dinter) from the measured long-range diffusivities (Dlong-range) and adsorption isotherms. We found them to be similar to bulk diffusion of N2 at the conditions studied. Finally, the experimentally determined Dlong-range results were shown to compare favorably to those calculated from simple gas kinetic theory.
Visco-acoustic Reverse-time Migration Using the Pseudo-analytical Method (2015)

Summary We derive a new reverse-time migration solution that uses a pseudo-analytical, two-way extrapolator in order to compensate for attenuation losses in visco-acoustic media. The algorithm permits large time stepping and shares the advantages of spectral methods in allowing coarse computational grids. The extrapolation accounts for spatial variations in attenuation by using a series expansion approximation of the equations for constant attenuation. We apply the new scheme to a dual-sensor field survey from the North Sea, in which the resolution of the images is clearly improved after compensating for attenuation.
Numerical three dimensional simulation of cold compaction and springback for prealloyed powder composites (2004)

Unlike conventional iron based alloys, prealloyed powder composites experience significant dimensional changes during springback and sintering. As a result, the final compact size is significantly different from the die geometry. This dimensional change presents one of the challenges to the wide usage of prealloyed powder composites in traditional press and sinter applications. Finite element modelling of the compaction and sintering of these composites can help predict the dimensional changes and enable tooling design for net shape moulding without the need for multiple iterations on the die design. Constitutive models for powder compaction are used to simulate the compaction of a gear made of prealloyed powder composite. Numerical simulation is used to predict the relative density and stress distribution within the compact as well as the stress distribution within the tooling. The simulation tracks the relative density and stress distributions during compaction and ejection; the springback after ejection of the part from the die is also calculated. Measurements of the density distribution within a compact and springback show good agreement with the FEA simulation results.
Follow-up of restoration of works of art of the patrimony by infrared thermography (2019)

Infrared thermography is a non-destructive testing technique that affects many areas. This technique of analysis is, for example, very interesting in the field of restoration and conservation of heritage works. The possibilities of active thermography can help in the early detection of defects in works of art and their characterization. In this work we will demonstrate that it is possible to detect old restorations in frescoes and murals by flash method. This new possibility offered by thermography will make it possible, for example, to verify the compatibility of a restoration with the original work, which can prevent the appearance of a defect and may allow the conservator to follow up on restoration. First we will show the feasibility of this approach on a laboratory specimen containing different types of clogging materials and then present results of analysis carried out in situ at one restoration sites that reveal the possibility of locating these restorations but also to characterize the pictorial technique used in this one.
The cytotoxic effector cells in preparations of adherent mononuclear cells from human peripheral blood. (1984)

We have characterized the effector cells present in fresh adherent cell preparations from human peripheral blood that are responsible for the lysis of K562 and IgG antibody-sensitized P815Y target tumor cells. Purified lymphocytes and monocytes, separated from adherent cell preparations by using techniques that utilized light scatter properties and reactivity of the cells with monoclonal antibodies, were used as effectors for the spontaneous and antibody-dependent cytotoxicity. The role of monocytes was also studied at the single cell level. Our results indicate that when a subpopulation of adherent cells that is B73.1+ (NK cells), B44.1- (non-monocyte), with light scatter characteristics of lymphocytes, is removed from the total adherent cell population, the resultant purified monocytes are unable to spontaneously kill K562 target cells. This data suggests that fresh unstimulated adherent cell cytotoxicity against K562 cells is mediated by lymphocyte contamination in these preparations and that the cell responsible for this killing is probably the NK cell. In contrast antibody-dependent cellular cytotoxicity against P815Y target cells is mediated by monocytes and lymphocytes.
Challenging the efficacy of checkpoint inhibitors: a new 3D model for a precision medicine approach. (2018)

Challenging the efficacy of checkpoint inhibitors: a new 3D model for a precision medicine approach.
Deposition of Parylene C and characterization of its hermeticity for the encapsulation of MEMS and medical devices (2016)

Following the recent trend of miniaturization of MEMS and the approach to improve the comfort of medical implants for patients by reducing their size the polymer Parylene is a promising candidate for encapsulation issues. Parylene combines a number of excellent properties like biocompatibility/biostability, chemical inertness, transparency and low water permeability. Within the presented work the deposition characteristics and properties like conformity, permeability of water vapor, etc. are examined.
Synthesis and verification of digital circuits using functional simulation and boolean satisfiability (2008)

A solid-state system designed for compensation of asymmetry potentials between microelectrodes, for bioelectric measurements, is described. Advantages over the manual compensator are the following: synchronic compensation of electrodes, application to automatized systems against aging effects in electordes, high speed, and elimination of general muisances of manual circuits. Besides, the system allows to measure digitally the polarization difference and resting membrane potential with precision of +/- 1 mV.
Capillary suction predictions in granular materials subjected to 1D compression and triaxial loading with emphasis on projectile penetration (2022)

The role of partial saturation in penetration resistance of projectiles in granular materials is not clear due to experimental constraints imposed by high cost and special considerations in equipment design. In this work, granular material near the tip and far-field of the projectile is numerically simulated based on 1D compression and triaxial stress paths, respectively, using the finite discrete element method. The crushing of grains in 1D compression simulations is implemented by pre-inserting cohesive interface elements in regular finite element mesh. The capillary suction is numerically predicted by extracting the deformed granular assembly microstructure at different loading steps as an input to the pore morphology method. The results demonstrate the development of high capillary suction in 1D compression loading due to the significant crushing of grains. The evolution of capillary suction is negligible during triaxial loading compared to the 1D compression loading. This suggests that future simulations related to projectile penetration in partially saturated granular materials should account for coupled hydromechanical effects near the tip whereas the far-field can be approximated as a dry material. Finally, the capillary suction corresponding to extreme comminution near the projectile tip is estimated from a 3D assembly of spherical grains with a mean grain size of 1 µm.
Evidence from rat hepatocytes of an unrecognized pathway of 5-fluorouracil metabolism with the formation of a glucuronide derivative. (1985)

Isolated rat hepatocytes in suspension were exposed to [3H]-5-fluorouracil for intervals over 2 h, following which the cells were removed from the media and sonicated, and the cytoplasm was sampled. High-performance liquid chromatography was used to separate 5-fluorouracil (FUra) from its known anabolites and catabolites, with subsequent quantitation of these metabolites by measurement of radioactivity. As the extracellular concentration of FUra was increased above 30 microM, the intracellular levels of FUra increased, with detection of a new peak of radioactivity distinct from any of the known anabolites or catabolites. This new metabolite, "G," increased in concentration as the extracellular concentration of FUra was raised above 1 mM. Inhibition of FUra catabolism by 2 mM thymine resulted in a further increase in intracellular FUra (approaching the extracellular FUra concentration) and was accompanied by a further increase in the intracellular concentration of "G," demonstrating that "G" was not formed via the catabolic pathway. The increase in intracellular FUra and "G" was not accompanied by an increase in intracellular anabolites, suggesting that "G" was formed via a novel metabolic pathway. "G" was retained within the hepatocytes, although it was not bound to intracellular macromolecules. "G" was converted to FUra in the presence of beta-D-glucuronidase; this reaction was inhibited with the addition of saccharo-1,4-beta-lactone, a specific inhibitor of the beta-D-glucuronidase. This data, together with evidence from hepatocyte homogenates in which formation of "G" was shown to be dependent on the concentration of uridine-5'-diphosphoglucuronic acid, demonstrates that "G" is a glucuronide of FUra. The formation of "G" suggests that FUra is metabolized via a previously unrecognized metabolic pathway.
(Endo)cannabinoids mediate different Ca2+ entry mechanisms in human bronchial epithelial cells (2009)

In human bronchial epithelial (16HBE14o(-)) cells, CB(1) and CB(2) cannabinoid receptors are present, and their activation by the endocannabinoid virodhamine and the synthetic non-selective receptor agonist CP55,940 inhibits adenylyl cyclase and cellular interleukin-8 release. Here, we analyzed changes in intracellular calcium ([Ca2+](i)) evoked by Delta(9)-tetrahydrocannabinol (Delta(9)-THC), CP55,940, and virodhamine in 16HBE14o(-) cells. Delta(9)-THC induced [Ca2+](i) increase and a large transient [Ca2+](i) mobilization, the latter probably reflecting store-depletion-driven capacitative Ca2+ entry (CCE). In contrast, CP55,940 induced a rather moderate Ca2+ influx and a sustained [Ca2+](i) mobilization. CP55,940-induced Ca2+ influx was inhibited by Ni2+, indicating CCE, possibly mediated by transient receptor potential channel TRPC1, the mRNA of which is expressed in 16HBE14o(-) cells. CP55,940-induced calcium alterations were mimicked by virodhamine concentrations below 30 microM. Interestingly, higher virodhamine induced an additional Ca2+ entry, insensitive to Ni2+, but sensitive to the TRPV1 antagonist capsazepine, the TRPV1-TRPV4 inhibitor ruthenium red, and the non-CCE (NCCE) inhibitors La3+ and Gd3+. Such pharmacological profile is supported by the presence of TRPV1, TRPV4, and TRPC6 mRNAs as well as TRPV1 and TRPC6 proteins in 16HBE14o(-) cells. Cannabinoid receptor antagonists increased virodhamine-induced Ca2+ entry. Virodhamine also enhanced arachidonic acid release, which was insensitive to cannabinoid receptor antagonism, but sensitive to the phospholipase A(2) inhibitor quinacrine, and to capsazepine. Arachidonic acid induced [Ca2+](i) increase similar to virodhamine. Collectively, these observations suggest that [Ca2+](i) alterations induced by Delta(9)-THC, CP55,940 and by low concentrations of virodhamine involve mobilization and subsequent CCE mechanisms, whereas such responses by high virodhamine concentrations involve NCCE pathways.
Synthesis of a Novel Bisphosphonium Salt Based on 2,2′-Bis(diphenylphosphino)-1,1′-binaphthyl (Binap) (2008)

The reaction between 2,2′-bis(diphenylphosphino)-1,1′-binaphthyl (Binap) and an equimolar amount of [Cu(OTf)2] (where OTf = trifluoromethylsulfonate) in acetonitrile afforded the new bisphosphonium salt 1 by a mechanism that must involve two C−H bond activations and the consequent intramolecular formation of two new C−P bonds. Compound 1 was characterized by spectroscopic and X-ray diffraction methods.
Purification and characterization of two xylanases from <i>Trichoderma longibrachiatum</i> (1991)

Two endoxylanases were purified from the culture medium of Trichoderma longibrachiatum . Both enzymes were highly basic, and lacked activity on carboxymethyl‐cellulose. An enzyme of 21.5 kDa (xylanase A) had a specific activity of 510 U/mg protein, a K m of 0.15 mg soluble xylan/ml, possessed transglycosidase activity and generated xylobiose and xylotriose as the major endproducts from xylan or xylose oligomers. A larger enzyme of 33 kDa (xylanase B) had a specific activity of 131 U/mg protein, a K m of 0.19 mg soluble xylan/ml, lacked detectable transglycosidase activity and generated xylobiose and xylose as major endproducts from xylan and xylose oligomers. Xylotriose was the smallest oligomer attacked by both enzymes. In addition, xylotriose inhibited hydrolysis of xylopentanose by both enzymes, while xylobiose appeared to inhibit xylanase B, but not xylanase A.
Synthesis of near-infrared absorbing and fluorescent bis(pyrrol-2-yl)squaraines and their halochromic properties (2021)

1,2-Squaraines (partially conjugated neutral structure) showed blue-shifted λ max compared to the corresponding 1,3-squaraines (fully conjugated zwitterionic structure) and the mono-protonated thiophene-fused 1,3-squaraine showed λ max at 1007 nm.
Acute effects of olanzapine on behavioural expression including the behavioural satiety sequence in female rats (2009)

Olanzapine is a novel antipsychotic drug known to induce clinically significant weight gain. Although the cause of such weight gain is not fully known, drug-induced changes in appetite and food intake are likely to play a significant role together with other possible mechanisms enhancing weight and/or adiposity. We assessed acute drug effects on 1 hour intake and behavioural expression in female rats. Low doses of olanzapine (0.5 and 1 mg/kg) enhanced acute mash intake. Marked drug effects were seen on a number of behaviours following olanzapine over a range of doses. These effects included dose-related reductions in activity and exploratory behaviours and associated substantial dose-related increases in resting behaviour. Behavioural data were also used to plot drug effects over time, including behavioural satiety sequence (BSS) profiles, to evaluate whether olanzapine's hyperphagic effects might be a consequence of altered satiety development. BSS profiles reflected enhanced eating behaviour at low doses (0.5 and 1 mg/kg) but showed dose-related increases in resting, indicative of drug-induced sedation, which meant that it was impossible to fully discern olanzapine's effects on satiety. Acute olanzapine induces both hyperphagia and sedation, both of which may promote weight gain and adiposity, but which interact competitively.
Modeling of the intensity channel impulse response for the East China Sea (2006)

Results of modeling the intensity channel impulse response in shallow and comparison with measurements are presented. The measurements were made in the East China Sea (depth 100 m, range ∼ 500 m) as part of the Asian Seas International Acoustics Experiment (ASIAEX). The intensity channel impulse response is obtained by incoherent summation of separate impulse response functions for each path (eigenray); the latter are modeled using ray and bistatic scattering methods. Measured sea surface spectral information and inverted seabed properties (from previously published works) are incorporated in the modeling. The modeled channel impulse response is convolved with representations of the CW (center frequency 8 and 16 kHz) or FM (frequency range 8–16 kHz) waveforms that were transmitted for comparison with observations. This talk will discuss (1) the influence of two-dimensional (out-of-plane) scattering including near-surface bubbles and the volume inhomogeneities in the sediment, on the intrapath time spread, and (2) the contribution of each arrival (up to the sixth path) to the channel impulse response. [Work supported by Office of Naval Research.]