gebhart/patrepeval huggingface dataset:
Antiviral agent blocks breathing of the common cold virus (1998)

A dynamic capsid is critical to the events that shape the viral life cycle; events such as cell attachment, cell entry, and nucleic acid release demand a highly mobile viral surface. Protein mass mapping of the common cold virus, human rhinovirus 14 (HRV14), revealed both viral structural dynamics and the inhibition of such dynamics with an antiviral agent, WIN 52084. Viral capsid digestion fragments resulting from proteolytic time-course experiments provided structural information in good agreement with the HRV14 three-dimensional crystal structure. As expected, initial digestion fragments included peptides from the capsid protein VP1. This observation was expected because VP1 is the most external viral protein. Initial digestion fragments also included peptides belonging to VP4, the most internal capsid protein. The mass spectral results together with x-ray crystallography data provide information consistent with a "breathing" model of the viral capsid. Whereas the crystal structure of HRV14 shows VP4 to be the most internal capsid protein, mass spectral results show VP4 fragments to be among the first digestion fragments observed. Taken together this information demonstrates that VP4 is transiently exposed to the viral surface via viral breathing. Comparative digests of HRV14 in the presence and absence of WIN 52084 revealed a dramatic inhibition of digestion. These results indicate that the binding of the antiviral agent not only causes local conformational changes in the drug binding pocket but actually stabilizes the entire viral capsid against enzymatic degradation. Viral capsid mass mapping provides a fast and sensitive method for probing viral structural dynamics as well as providing a means for investigating antiviral drug efficacy.
A centrifugal fluidic immunoassay for ocular diagnostics with an enzymatically hydrolyzed fluorogenic substrate (2014)

We present a novel "Lab-on-a-Disk" platform and demonstrate its capability for rapid and sensitive measurement of vascular endothelial growth factor (VEGF) intended for patients suffering from diabetic retinopathy (DR) and age-related macular degeneration (AMD). This approach combines sedimentation principles applied to microspheres under centrifugal force with signal amplification using an enzyme and a fluorogenic substrate for readout. The simple single channel per assay platform separates, washes and concentrates antibody-coated microspheres from excess label to produce a sensitive fluorogenic response proportional to the amount of VEGF in the sample. This platform has comparable sensitivity to conventional ELISA and can generate a readout within 16-18 min with no sample preparation beyond mixing assay reagents and loading on the disk. In the context of ocular diagnostics, this device has the potential to facilitate accurate dosing of anti-VEGF medications utilized to treat DR and AMD, as well as identify patients whose ocular VEGF levels are not elevated and who would therefore not benefit from standard anti-VEGF medications.
Multiple imaging phase-encoded optical elements written as programmable spatial light modulators (1990)

We report a multiple imaging capability of replicated binary Fresnel phase-encoded lenses written on programmable spatial light modulators (SLMs). These lenses produce a large number (up to 9 x 9) of equally intense replica images from either an external object or from a pattern which is encoded onto the SLM along with the phase-encoded lens. Theoretical details and experimental results using the magnetooptic spatial light modulator are presented.
The Carbon Impacts of Wood Products (2014)

Abstract Wood products have many environmental advantages over nonwood alternatives. Documenting and publicizing these merits helps the future competitiveness of wood when climate change impacts are being considered. The manufacture of wood products requires less fossil fuel than nonwood alternative building materials such as concrete, metals, or plastics. By nature, wood is composed of carbon that is captured from the atmosphere during tree growth. These two effects—substitution and sequestration—are why the carbon impact of wood products is favorable. This article shows greenhouse gas emission savings for a range of wood products by comparing (1) net wood product carbon emissions from forest cradle–to–mill output gate minus carbon storage over product use life with (2) cradle-to-gate carbon emissions for substitute nonwood products. The study assumes sustainable forest management practices will be used for the duration of the time for the forest to regrow completely from when the wood was removed for product production during harvesting. The article describes how the carbon impact factors were developed for wood products such as framing lumber, flooring, moulding, and utility poles. Estimates of carbon emissions saved per unit of wood product used are based on the following: (1) gross carbon dioxide (CO 2 ) emissions from wood product production, (2) CO 2 from biofuels combusted and used for energy during manufacturing, (3) carbon stored in the final product, and (4) fossil CO 2 emissions from the production of nonwood alternatives. The results show notable carbon emissions savings when wood products are used in constructing buildings in place of nonwood alternatives.
Mussel-Inspired Polydopamine: A Biocompatible and Ultrastable Coating for Nanoparticles <i>in Vivo</i> (2013)

Bioinspired polydopamine (PDA) has served as a universal coating to nanoparticles (NPs) for various biomedical applications. However, one remaining critical question is whether the PDA shell on NPs is stable in vivo. In this study, we modified gold nanoparticles (GNPs) with finely controlled PDA nanolayers to form uniform core/shell nanostructures (GNP@PDA). In vitro study showed that the PDA-coated GNPs had low cytotoxicity and could smoothly translocate to cancer cells. Transmission electron microscopy (TEM) analysis demonstrated that the PDA nanoshells were intact within cells after 24 h incubation. Notably, we found the GNP@PDA could partially escape from the endosomes/lysosomes to cytosol and locate close to the nucleus. Furthermore, we observed that the PDA-coated NPs have very different uptake behavior in two important organs of the liver and spleen: GNP@PDA in the liver were mainly uptaken by the Kupffer cells, while the GNP@PDA in the spleen were uptaken by a variety of cells. Importantly, we proved the PDA nanoshells were stable within cells of the liver and spleen for at least six weeks, and GNP@PDA did not show notable histological toxicity to main organs of mice in a long time. These results provided the direct evidence to support that the PDA surface modification can serve as an effective strategy to form ultrastable coatings on NPs in vivo, which can improve the intracellular delivery capacity and biocompatibility of NPs for biomedical application.
Purification and properties of cystathionine .gamma.-synthase from overproducing strains of Escherichia coli (1990)

To characterize the methionine biosynthetic enzyme cystathionine gamma-synthase from Escherichia coli, we have constructed high copy number plasmids containing the metB structural gene but lacking the closely linked metJ regulatory gene. When cloned into an appropriate strain, these plasmids can direct the overproduction of cystathionine gamma-synthase such that about 10% of the soluble protein is this enzyme. An efficient purification scheme has been developed that has allowed us to obtain gram quantities of enzyme. The active form is a tetramer with subunits of about 40,000 daltons and one pyridoxal phosphate cofactor per monomer. The kinetic constants for several enzyme-catalyzed reactions were determined at 25 degrees C. The Km value for the elimination reaction with O-succinyl-L-homoserine was calculated to be 0.33 mM with maximal velocity of 460 min-1. The Km for the elimination (deamination) reaction with vinylglycine was 5.6 mM with maximal velocity of 900 min-1. The Km values for the replacement reaction were calculated to be 1.0 mM for O-succinyl-L-homoserine and 0.05 mM for L-cysteine with maximal velocity of 700 min-1. The enzyme shows an absorption band at 422 nm (epsilon = 8463 M-1 cm-1) attributable to the Schiff base form of the pyridoxal phosphate cofactor. Steady-state spectra of reaction complexes show appearance of new longer wavelength absorbing materials during reaction with O-succinyl-L-homoserine, vinylglycine, or vinylglycine and L-cysteine. Reaction with O-succinyl-L-homoserine and L-cysteine produces only a red shift and slight reduction of the band at 422 nm.
Requirement of protein phosphatase 5 in DNA-damage-induced ATM activation (2004)

The checkpoint kinase ATM is centrally involved in the cellular response to DNA double-strand breaks. However, the mechanism of ATM activation during genotoxic stress is only partially understood. Here we report a direct regulatory linkage between the protein serine-threonine phosphatase 5 (PP5) and ATM. PP5 interacts with ATM in a DNA-damage-inducible manner. Reduced expression of PP5 attenuated DNA-damage-induced activation of ATM. Expression of a catalytically inactive PP5 mutant inhibited the phosphorylation of ATM substrates and the autophosphorylation of ATM on Ser 1981, and caused an S-phase checkpoint defect in DNA-damaged cells. Together our findings indicate that PP5 plays an essential role in the activation and checkpoint signaling functions of ATM in cells that have suffered DNA double-strand breaks.
A Rod Pumping System for California Lift Requirements (1983)

Abstract Artificial lift requirements in California oilfields cover a full range of demanding operating and environmental conditions. These extend from typical demands of lifting depth and volume, to atypical requirements of heavy crude, thermal enhancement and the unique environmental restrictions of our urban sites and offshore fields. A new rod pumping system has been developed which deals with these requirements. Performance results to date confirm reduced power consumption and improved pumping performance. Combined with the compact equipment size, these characteristics appear to offer benefits to California operators.
Additional Use of a Phosphodiesterase 5 Inhibitor in Patients with Pulmonary Hypertension Secondary to Chronic Systolic Heart Failure: A Meta-Analysis (2013)

Additional sildenafil treatment is a potential therapeutic method to improve pulmonary exercise capacity and quality of life by ameliorating PH in patients with chronic systolic heart failure.
ChemInform Abstract: BROMAMINE ACID ‐ ANTHRAQUINONIC INTERMEDIATE USED IN DYE SYNTHESES (1976)

Abstract Anthraquinonic Intermediate Used in Dyes Syntheses.
Theoretical study of the effects of intermolecular interactions in self‐assembled long‐chain alkanes adsorbed on graphite surface (2001)

Abstract In this paper, we studied the physisorption of long‐chain alkanes C n H 2 n +2 ( n = 8, 16, 24, 34) on a graphite surface using molecular mechanics simulations. The computed results illustrated that the interactions between adsorbed molecules and substrate are dominated by van der Waals forces whereas the electrostatic interactions are very small. It was found that the ratio of the alkane molecule–molecule interactions (two‐dimensional crystallization energy) to the interactions between alkane and graphite (adsorption energy) ranges from ∼2 : 5 to 3 : 5. The adsorption stability and immobility of the alkanes increases proportionally with an increase in the chain length. It was concluded that the lateral interactions between adsorbed molecules are important to the formation of ordered two‐dimensional lamellae. The theoretical results support the scanning tunneling microscopy (STM) observation of alkylated aromatic compounds on a graphite surface. Copyright © 2001 John Wiley & Sons, Ltd.
Knitted 3D Scaffolds of Polybutylene Succinate Support Human Mesenchymal Stem Cell Growth and Osteogenesis (2018)

Polybutylene succinate (PBS) is a biodegradable polyester with better processability and different mechanical properties compared to polylactides (PLAs), the most commonly used synthetic polymers in tissue engineering (TE). Since only few studies have evaluated PBS-containing materials for bone TE, we prepared PLA-PBS blends and analyzed material properties as well as cell attachment, proliferation, and osteogenic differentiation of human mesenchymal stem cells (hMSCs) on scaffolds. In addition to PLA, PBS, and PLA-PBS blends, PLA-polycaprolactone and PLA-poly(trimethylene carbonate) blends were evaluated. Polymer fibers were prepared using melt spinning. Pure PBS was observed to have the highest crystallinity and strain at break compared to the tougher PLA and PLA blends. No degradation occurred during the 4-week hydrolysis in either of the materials. Knitted and rolled scaffolds were manufactured, seeded with hMSCs, and cultured for 27 days. Human MSC viability was good on all the materials, but cell spreading along the fibers was only detected in PBS-containing scaffolds. They also induced the strongest proliferative response and osteogenic differentiation, which diminished with decreasing PBS content. Based on these results, PBS is superior to PLA with respect to hMSC attachment, proliferation, and osteogenesis. This encourages utilizing PBS-based biomaterials more widely in bone TE applications.
Identification of a nonlinear driver model via NARMAX modeling (2000)

Most existing driver steering models consist of a linear function and a time delay element. Driving simulator data, however, indicates the possible existence of "complacency" nonlinearity. Three possible nonlinear structures are investigated to model this effect. The effectiveness of each structure in reducing the model uncertainty is evaluated.
Recognition and understanding of meetings (2010)

This paper is about interpreting human communication in meetings using audio, video and other signals. Automatic meeting recognition and understanding is extremely challenging, since communication in a meeting is spontaneous and conversational, and involves multiple speakers and multiple modalities. This leads to a number of significant research problems in signal processing, in speech recognition, and in discourse interpretation, taking account of both individual and group behaviours. Addressing these problems requires an interdisciplinary effort. In this paper, I discuss the capture and annotation of multimodal meeting recordings—resulting in the AMI meeting corpus—and how we have built on this to develop techniques and applications for the recognition and interpretation of meetings. 1
Signal transduction by G proteins in cardiac tissues. (1992)

The role of G proteins in mediating the responses of the heart to circulating catecholamines and to the influences of the autonomic nervous system is of special interest to cardiologists. It is evident that G proteins are essential links in the cascade of biochemical events that ensure when neurotransmitters and hormones interact with receptors on myocardial cells. It is likely [corrected] that dysfunction of G proteins plays a role in cardiovascular pathophysiology. With current methodologies, especially molecular biological and recombinant DNA techniques, and with transgenic animal models that can relate physiological function and specific gene dosage, some cardiovascular diseases may be traced to G protein-related defects.
Suspension Plasma Spraying of Intermediate Temperature SOFC Components Using an Axial Injection DC Torch (2007)

Intermediate temperature SOFC components, such as dense, nanostructured SDC electrolytes (samarium doped ceria) and porous anode sublayers were fabricated by suspension plasma spraying using an axial feed dc plasma torch. The liquid carrier employed in this approach allowed for controlled injection of much finer particles than in conventional thermal spraying, leading to thin coatings with a refined microstructure. Dense, thin (<10(m) and non-fractured electrolytes were created. Various processing routes for SOFC half-cells, using tape-cased, plasmasprayed and suspension-sprayed anodes, were explored. Loss of integrity and non-continuous coverage of the anode constituted the principal difficulties in the subsequent electrolyte deposition. The role of suspension feedstock particle size is discussed. Amongst various schemes investigated, a processing route that employs sequential suspension plasma spraying steps for both the electrolyte and the anode, using relatively large primary particles in the feedstock, constituted the most promising approach.
AudioViewer : learning to visualize sound (2021)

Sensory substitution can help persons with perceptual deficits. In this work, we attempt to visualize audio with video. Our long-term goal is to create sound perception for hearing impaired people, for instance, to facilitate feedback for training deaf speech. Different from existing models that translate between speech and text or text and images, we target an immediate and low-level translation that applies to generic environment sounds and human speech without delay. No canonical mapping is known for this artificial translation task. Our design is to translate from audio to video by compressing both into a common latent space with a shared structure. Our core contribution is the development and evaluation of learned mappings that respect human perception limits and maximize user comfort by enforcing priors and combining strategies from unpaired image translation and disentanglement. We demonstrate qualitatively and quantitatively that our AudioViewer model maintains important audio features in the generated video and that generated videos of faces and numbers are well suited for visualizing high-dimensional audio features since they can easily be parsed by humans to match and distinguish between sounds, words, and speakers.
Iteration-based Scan-Trajectory Design and Control with Output-Oscillation Minimization: Atomic Force Microscope Example (2007)

In this article, two practical issues occurring in the design and control of scan trajectories are studied: one, the reduction of the output oscillations during the scanning, and two, the effect of the modeling errors on the output precision during the scanning. Output oscillations need to be minimized in scanning operations of systems such as the piezo actuator and the flexible structure, while modeling errors widely exists in practical applications. The proposed approach extends the developed optimal scan trajectory design and control method, by introducing the design of a prefilter into the framework to reduce the output oscillations. Furthermore, a novel inversion-based iterative control algorithm is proposed and integrated with the optimal scan method to compensate for the modeling error effect on the scanning. The convergence of the iterative control law is discussed, and the convergence range is quantified. The proposed approach is illustrated by implementing it on the high-speed adhesion force measurement using AFM. Simulation and experimental results are presented and discussed to demonstrate the efficacy of the proposed approach.
Whey-protein / polysaccharide coacervates : structure and dynamics (2004)

This thesis studied the interactions between food ingredients under acidic conditions (like in yoghurt or in soft drinks for instance). In the chapters 2, 3, and 4, the author investigated the conditions under which a complex was formed between positively charged whey proteins (proteins derived from milk) and a negatively charged polysaccharide. Three different polysaccharides, which are commonly added into food products as thickeners, were used: gum arabic, the exopolysaccharide EPS B40 and carrageenan. The properties of whey protein / polysaccharide electrostatic complexes could be tuned by varying key parameters such as pH, ionic strength and concentrations. The last chapters focused on the system whey protein / gum arabic. A concentrated phase was made of whey proteins and gum arabic, also called coacervate phase. This phase had very interesting features; it was very viscous but always remained liquid. The properties of the coacervate phase were studied in chapters 5, 6, and 7 and they could be explained by the strength of electrostatic interactions. At the pH where the interactions were the strongest, the coacervate phase was the most concentrated in polymer, the most viscous, the densest and the most structured. At this pH the diffusion of the polymer was also slower. The coacervate phase was made of protein and polysaccharide that moved independently within the coacervate phase. In time the coacervate phase rearranged, became transparent, and the diffusion of the polymer was slower. Finally, in chapter 8, a direct application of the whey protein / gum arabic coacervate was used as a coating around sensitive materials (like flavors or drugs) and, as an example, flavors were added to cheese.
Experience with a Simplified Method of Radio‐isotopic Assay of Serum Vitamin B<sub>12</sub> (1969)

Summary: A simplified method for the assay of serum vitamin B 12 by isotopedilution is described. Results obtained by this method correlated well with those obtained by microbiological assay using Lactobacillus leichmannii ; reproducibility was of the same order and the range of values obtained in normal subjects fell within the accepted range. There was no difficulty in detecting clinical vitamin B 12 deficiency.
Correction: The Transcriptional Regulator Np20 Is the Zinc Uptake Regulator in Pseudomonas aeruginosa (2013)

Zinc is essential for all bacteria, but excess amounts of the metal can have toxic effects. To address this, bacteria have developed tightly regulated zinc uptake systems, such as the ZnuABC zinc transporter which is regulated by the Fur-like zinc uptake regulator (Zur). In Pseudomonas aeruginosa, a Zur protein has yet to be identified experimentally, however, sequence alignment revealed that the zinc-responsive transcriptional regulator Np20, encoded by np20 (PA5499), shares high sequence identity with Zur found in other bacteria. In this study, we set out to determine whether Np20 was functioning as Zur in P. aeruginosa. Using RT-PCR, we determined that np20 (hereafter known as zur) formed a polycistronic operon with znuC and znuB. Mutant strains, lacking the putative znuA, znuB, or znuC genes were found to grow poorly in zinc deplete conditions as compared to wild-type strain PAO1. Intracellular zinc concentrations in strain PAO-Zur (zur) were found to be higher than those for strain PAO1, further implicating the zur as the zinc uptake regulator. Reporter gene fusions and real time RT-PCR revealed that transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur, suggesting that the P. aeruginosa Zur homolog (ZurPA) directly regulates expression of znuA. Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator N,N,Ntetrakis(2-pyridylmethyl) ethylenediamine (TPEN). Taken together, these data support the notion that Np20 is the P. aeruginosa Zur, which regulates the transcription of the genes encoding the high affinity ZnuABC zinc transport system.