gebhart/patrepeval huggingface dataset:
Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space (2008)

Chemogenomics is a new strategy in in silico drug discovery, where the ultimate goal is to understand molecular recognition for all molecules interacting with all proteins in the proteome. To study such cross interactions, methods that can generalize over proteins that vary greatly in sequence, structure, and function are needed. We present a general quantitative approach to protein-ligand binding affinity prediction that spans the entire structural enzyme-ligand space. The model was trained on a data set composed of all available enzymes cocrystallized with druglike ligands, taken from four publicly available interaction databases, for which a crystal structure is available. Each enzyme was characterized by a set of local descriptors of protein structure that describe the binding site of the cocrystallized ligand. The ligands in the training set were described by traditional QSAR descriptors. To evaluate the model, a comprehensive test set consisting of enzyme structures and ligands was manually curated. The test set contained enzyme-ligand complexes for which no crystal structures were available, and thus the binding modes were unknown. The test set enzymes were therefore characterized by matching their entire structures to the local descriptor library constructed from the training set. Both the training and the test set contained enzyme-ligand complexes from all major enzyme classes, and the enzymes spanned a large range of sequences and folds. The experimental binding affinities (p K i) ranged from 0.5 to 11.9 (0.7-11.0 in the test set). The induced model predicted the binding affinities of the external test set enzyme-ligand complexes with an r (2) of 0.53 and an RMSEP of 1.5. This demonstrates that the use of local descriptors makes it possible to create rough predictive models that can generalize over a wide range of protein targets.
Distributed collaborative decision support system for rocket launch operation (2006)

This paper presents an overview of a decision support system for rocket launch operation from the viewpoint of distributed collaboration mechanisms. The system comprises interface agents that mediate between operators on site or support engineers in distance and various Web services that function as large-grain-size task modules for operation support. In order to orchestrate the distributed Web services over the Internet, we have adopted semantic Web services technology that enable to compose the atomic Web services in order to achieve the given goal. The interface agent for operation support is also a Web service agent that behaves that composes Web services and executes them on behalf of each user
Integrated Sensing and Communications Enabled Low Earth Orbit Satellite Systems (2023)

Extreme crowding of electromagnetic spectrum in recent years has led to the challenges in designing sensing and communications systems. Both systems require a broad range of bandwidth, thus resulting in competing interests in exploiting the spectrum. Efficient spectrum and hardware utilization have led to the emergence of integrated sensing and communications (ISAC) systems, which have recently emerged as a candidate 6G technology. In particular, we provide potential techniques, namely the opportunistic ISAC and optimized ISAC. Rate-splitting multiple access (RSMA) is highlighted as an optimized ISAC technique for LEO-ISAC systems due to its effectiveness in simultaneously managing interference and enabling better communication-sensing trade-off performance.
Ultraproductive, Zinc‐Mediated, Immortal Ring‐Opening Polymerization of Trimethylene Carbonate (2008)

Cyclic carbonate surprise! Living controlled “immortal” bulk ring-opening polymerization of trimethylene carbonate proceeds in the presence of β-diketiminate zinc amido catalyst precursor [Zn(bdi){N(SiMe3)2}] (bdi=CH(CMeNC6H3-2,6-iPr2)2) and benzyl alcohol as chain-transfer agent (see scheme). Catalytic amounts of zinc as low as 20 ppm allowed the quantitative conversion of up to 50000 monomer units within 2 h at 110 °C. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2111/2008/z801416_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The First Extracellular Domain of Corticotropin Releasing Factor-R1 Contains Major Binding Determinants for Urocortin and Astressin (1998)

The CRF receptors are members of a 7-transmembrane receptor family that includes GH-releasing hormone (GRF), calcitonin, vasoactive intestinal peptide (VIP), secretin, and PTH receptors. To determine the structural features of the CRF receptor that may influence ligand recognition, a series of mutant receptors was analyzed for binding to astressin, a CRF antagonist, and to urocortin, a CRF agonist. Mutant receptors included chimeras between the CRF-R1 and GRF-R or Activin IIB-R, a single membrane spanning receptor serine/threonine kinase. Binding to the mutant receptors was assessed using 125I-[DTyr1] astressin (Ast*) and 125I-[Tyr0]-rat urocortin (Ucn*). There was no binding to a chimeric receptor in which the first extracellular domain (E1c) (i.e. the N-terminal region) of the CRF-R1 was replaced by that of the GRF-R. The complementary chimera in which E1 domain of the GRF-R was replaced by that of the CRF-R1 bound astressin and urocortin with Ki values approximately 10 nm, compared with inhibitory binding dissociation constant (Ki) values of approximately 2–4 nm for the wild-type CRF-R1. The chimera in which E1 of the activin IIB receptor was replaced by E1 of the CRF-R1 bound astressin with a Ki approximately 4 nm. A chimera in which both the first and fourth extracellular domains of the CRF-R1 replaced the corresponding domains of the GRF-R bound astressin with Ki approximately 4 nm and urocortin with a Ki approximately 2 nm. A chimera in which all four extracellular domains of the CRF receptor replaced those of the GRF-R bound astressin and urocortin with Ki values approximately 4 nm and approximately 1 nm, respectively. In conclusion, the major determinants for high affinity binding of CRF agonists and antagonists to CRF-R1 are found in the first extracellular domain of the receptor.
Gate oxide damage from polysilicon etching (1991)

Damage to thin gate oxides from etching of polysilicon gates was studied using gate oxide breakdown histograms and time-dependent dielectric breakdown measurements. The effect of various polysilicon etch parameters was investigated in a radio frequency (rf) triode etcher. Increasing rf power caused a substantial increase in damage. Reducing bias at constant power also resulted in an increase in damage, indicating that ion energy is not the only cause of damage. Area, isolation edge, and source/drain edge contributions to gate oxide defect densities were calculated as a function of rf power during polysilicon etch. As rf power was increased, the area contribution increased the most, indicating that gate oxide damage from polysilicon etching is not an edge phenomenon but a surface phenomenon. The effect of gate oxide thickness was investigated. Damage increased significantly as gate oxide thickness was reduced. Finally, the rf triode etcher was compared with a microwave electron cyclotron resonance (ECR) etcher. The ECR etcher caused fewer damaged capacitors, but some modifications to the triode etch process (such as lower rf power or pure chlorine chemistry) produced fewer damaged capacitors than the ECR.
U.S. Department of Energy Accident Resistant SiC Clad Nuclear Fuel Development (2011)

A significant effort is being placed on silicon carbide ceramic matrix composite (SiC CMC) nuclear fuel cladding by Light Water Reactor Sustainability (LWRS) Advanced Light Water Reactor Nuclear Fuels Pathway. The intent of this work is to invest in a high-risk, high-reward technology that can be introduced in a relatively short time. The LWRS goal is to demonstrate successful advanced fuels technology that suitable for commercial development to support nuclear relicensing. Ceramic matrix composites are an established non-nuclear technology that utilizes ceramic fibers embedded in a ceramic matrix. A thin interfacial layer between the fibers and the matrix allows for ductile behavior. The SiC CMC has relatively high strength at high reactor accident temperatures when compared to metallic cladding. SiC also has a very low chemical reactivity and doesn't react exothermically with the reactor cooling water. The radiation behavior of SiC has also been studied extensively as structural fusion system components. The SiC CMC technology is in the early stages of development and will need to mature before confidence in the developed designs can created. The advanced SiC CMC materials do offer the potential for greatly improved safety because of their high temperature strength, chemical stability and reduced hydrogen generation.
Approaches to designing micro‐solenoidal RF probes for 14 T MRI studies of millimeter‐range sized objects (2016)

Abstract Full‐wave electromagnetic simulations have been employed to analyze the design approaches that allow for solving the problems preventing inductive performance of micro‐solenoidal RF probes and formation of strong and homogeneous magnetic fields inside probes at the studies of millimeter‐range sized objects in 14 T MRI scanners. In particular, the effects of non‐uniform coil wrapping on field homogeneity inside extended coils and of partitioning the coils by dielectric separators on coil self‐resonances have been investigated. The possibility to utilize tunable C‐C matching circuits with the coils and to mitigate the effects of sample insertion on the probe resonance frequency has been demonstrated. Challenges of coil fabrication have been also addressed.
Dynamics of four-wave mixing on excitons in a quantum optical microcavity (1996)

A theory of degenerate four-wave mixing in a semiconductor optical cavity with quantum wells is constructed. The nonlinear response of a microcavity can be four to five orders of magnitude stronger than that of an isolated quantum well. For P 2 E-and P 3-type nonlinearities the damped diffracted signal oscillates with a period determined by the Rabi splitting. For a biexcitonic mechanism of nonlinearity, the signal contains damped overtones of the Rabi splitting and the biexciton binding energy.
Effects of plasma exposure on cultured hepatocytes: Implications for bioartificial liver support (2000)

In order to examine their potential for use in a bioartificial liver, hepatocytes maintained in a collagen sandwich configuration were cultured for 9 days in heparinized rat plasma. The cells exhibited a progressive accumulation of cytoplasmic lipid droplets which proved to be mainly triglyceride (TG). The rate of TG accumulation correlated with the free fatty acid (FFA) content of the plasma. Removal of FFA and TG from plasma by ether extraction significantly reduced the rate and extent of TG accumulation. A smaller reduction in the rate and extent of TG accumulation was observed when cells were maintained in an oxygen enriched environment. The lipid accumulation suppressed urea synthesis, but clearance of the drug diazepam, although constitutively depressed in plasma, appeared unaffected by the accumulation. The functional and morphological effects of plasma exposure could be fully reversed after at least 6 days of plasma exposure by returning the cells to culture medium.The results indicate that elevated FFA in plasma induces lipid accumulation, which inhibits urea synthesis in cultured hepatocytes. This suggests that estimates of the cell number needed for effective liver support should not be based upon function measurements conducted in culture media. Furthermore, optimization of bioartificial liver support device use may have to be governed by the need to limit the plasma exposure of cultured hepatocytes. However, the highly responsive nature of these cultures and the reversibility of the plasma effects suggest that the collagen sandwich culture system is a promising foundation for the development of an effective bioartificial liver support system. (c) 1996 John Wiley & Sons, Inc.
Sterically crowded monomeric neutral bis(benzamidinato) compounds of aluminium, [PhC(NSiMe3)2]2AlX (X = Cl, H); X-ray crystal structure of [PhC(NSiMe3)2]2AlH (1996)

AlCl3 reacts with [PhC(NSiMe3)2]Li(OEt2) to afford the bis(N,N′-bis(trimethylsilyl)benzamidinato)aluminium chloro compound which, on treatment with KBEt3H, yields the structurally characterized monomeric hydrido derivative, [PhC(NSiMe3)2]2AlH, whose reactivity towards unsaturated hydrocarbons illustrates the low electrophilicity of the aluminium and high basic character of the hydrido group.
High Performance Material for Rapid Durable Repair of Bridges and Structures (2006)

The research presented herein describes the development of High Early Strength Engineered Cementitious Composites (HES-ECC) under the guidance of micromechanical models for concrete bridges & structures repair applications. HES-ECC can achieve high early age compressive strength of around 3400 psi at 4h, 5000 psi at 6h, 6000 psi at 24h, and high late age compressive strength of around 7000 psi at 7d, 8000 psi at 28d, and 8200 psi at 60d. It also has high tensile strain capacity of more than 3% and toughness indicated by multiple micro-cracking behavior under uniaxial tensile loading. Besides material durability, HES-ECC can greatly improve durability and load carrying capacity of a simulated layered repair system. Experimental study showed that when subject to monotonic flexural loading, HES-ECC layered repair system exhibited 100% increased load carrying capacity, and 10 times the deformation capacity compared with HES-Concrete layered repair system. When under the same level of fatigue flexural loading, HES-ECC layered repair system showed significantly prolonged service life. In addition, the high ductility of HES-ECC relieved shrinkage induced stresses in the HES-ECC repair layer and at the HES-ECC/concrete interface, thereby suppressing large repair surface cracks and interface delamination. Based on the findings within, the larger scale batching of HES-ECC is applicable by using traditional concrete gravity mixers. The overall mixing of HES-ECC material can proceed smoothly and result in a fresh material which is homogeneous, flowable, and rheologically stable. Testing of hardened mechanical properties of HES-ECC showed that the early age and late age compressive strength and tensile strain capacity were similar to those mixes made in a laboratory size Hobart mixer, and continued to meet all of the targets set forth when developing this material. In this report, the results of larger scale batching (1, 3 and 6 cubic feet) and demonstration are summarized and recommendations are made along with material specifications, mix design and batching sequences for large scale mixing of HES-ECC. Overall, this project successfully developed a HES-ECC material which is high-early-strength, durable and can be easily applied. This HES-ECC material can be suitable for a wide range of concrete repair applications in transportation infrastructures with significantly shortened down time, greatly improved durability and reduced future maintenance.
Imbalanced mobilities causing S-shaped IV curves in planar heterojunction organic solar cells (2011)

We show that S-kinks in the current voltage characteristics, which decrease the fill factor significantly, can be caused by a strong imbalance of charge carrier mobilities (hole mobility in donor and electron mobility in acceptor) in planar/flat heterojunction organic solar cells. Electrical simulations according to a drift-diffusion model predict the occurrence of an S-kink for a mobility mismatch factor larger than 100. By combining a low-mobility donor material, (1,2,3,4,9,10,11,12-octaphenyl-diindeno[1,2,3-cd:1′,2′,3′-lm]perylene), with the acceptors C60 and N,N′-dimethylperylene-3,4:9,10-dicarboximide, which show different electron mobilities, we experimentally verify the predictions. Our results demonstrate that not only interface effects but also the photoactive material itself can cause S-kinks.
Improved uniformity of contact resistance in GaAs MESFET using Pd/Ge/Ti/Au ohmic contacts (1998)

Improved contact resistance uniformity, with a low resistance on high-low doped GaAs MESFET, was demonstrated using a Pd/Ge/Ti/Au ohmic contact. The lowest contact resistivity obtained was 2.8/spl times/10/sup -6/ /spl Omega/-cm/sup 2/. The average value and standard deviation (/spl Delta/Rc) of the contact resistance (Rc) were 0.73 and 0.07 /spl Omega/-mm, respectively, which were more uniform than those for AuGe/Ni contacts with an average Rc of 0.77 /spl Omega/-mm and /spl Delta/Rc of 0.16 /spl Omega/-mm. The improved uniformity was attributed to the uniform penetration of the ohmic junction into the buried high-doped channel layer by solid-state reactions, resulting in the improved uniformity of device performance.
Piggybacking an Additional Lonely Bit on Linearly Coded Payload Data (2012)

We provide a coding scheme, by which an additional lonely bit can be piggybacked on a payload data packet encoded with a linear channel code, at no essential extra cost in power or bandwidth. The underlying principle is to use the additional bit to select which of two linear codes that should be used for encoding the payload packet, this way effectively creating a nonlinear code. We give a fast algorithm for detecting the additional bit, without decoding the data packet. Applications include control signaling, for example, transmission of ACK/NACK bits.
Sorption in Zeolites Modified for Use in Organic−Inorganic Hybrid Membranes (2007)

Adding zeolites to polymer matrixes can provide improved materials for membrane-based separation of gases. To create such materials, the sorption in and diffusion through the zeolites must be relatively unhindered by the process of modification and bonding to the polymer. An attractive approach to achieve the stabilization and bonding of the zeolite phase involves silane treatment of external zeolite surfaces prior to dispersion. This study shows that standard treatments to achieve the silylation in an aqueous alcohol mixture with the assistance of ultrasonic energy can cause surprising and undesirable alterations in the sieve properties. Using zeolite 4A as a model and γ-aminopropyldimethylethoxysilane in both ethanol−water and isopropanol−water mixtures, the extent of sieve sorption property changes during reaction in the presence of ultrasound exposure is illustrated. Control studies with these alcohol−water systems further identify the impact of the alcohol type on the zeolite. Oxygen sorption kinetics and equilibria are reported for the modified and unmodified zeolite after activation and drying under typical conditions used for forming such hybrid materials. It is concluded that sonication appears to drive both isopropanol and ethanol into the sieves; however, drying at 250 °C appears to enable recovering most of the intrinsic sieve sorption and transport properties.
CpG oligodeoxynucleotide-enhanced humoral immune response and production of antibodies to prion protein PrPSc in mice immunized with 139A scrapie-associated fibrils (2007)

Prion diseases are characterized by conversion of the cellular prion protein (PrP(C)) to a protease-resistant conformer, the srapie form of PrP (PrP(Sc)). Humoral immune responses to nondenatured forms of PrP(Sc) have never been fully characterized. We investigated whether production of antibodies to PrP(Sc) could occur in PrP null (Prnp(-/-)) mice and further, whether innate immune stimulation with the TLR9 agonist CpG oligodeoxynucleotide (ODN) 1826 could enhance this process. Whether such stimulation could raise anti-PrP(Sc) antibody levels in wild-type (Prnp(+/+)) mice was also investigated. Prnp(-/-) and Prnp(+/+) mice were immunized with nondenatured 139A scrapie-associated fibrils (SAF), with or without ODN 1826, and were tested for titers of PrP-specific antibodies. In Prnp(-/-) mice, inclusion of ODN 1826 in the immunization regime increased anti-PrP titers more than 13-fold after two immunizations and induced, among others, antibodies to an N-terminal epitope, which were only present in the immune repertoire of mice receiving ODN 1826. mAb 6D11, derived from such a mouse, reacts with the N-terminal epitope QWNK in native and denatured forms of PrP(Sc) and recombinant PrP and exhibits a K(d) in the 10(-)(11) M range. In Prnp(+/+) mice, ODN 1826 increased anti-PrP levels as much as 84% after a single immunization. Thus, ODN 1826 potentiates adaptive immune responses to PrP(Sc) in 139A SAF-immunized mice. These results represent the first characterization of humoral immune responses to nondenatured, infectious PrP(Sc) and suggest methods for optimizing the generation of mAbs to PrP(Sc), many of which could be used for diagnosis and treatment of prion diseases.
Electrodeposition of Zinc from the Lewis Acidic Aluminum Chloride‐1‐Methyl‐3‐ethylimidazolium Chloride Room Temperature Molten Salt (1997)

The electrodeposition of zinc on polycrystalline gold, platinum, and tungsten and on glassy carbon was investigated in the 60.0–40.0 mole percent aluminum chloride‐1‐methyl‐3‐ethylimidazolium chloride molten salt containing electrogenerated zinc (II). The electrodeposition of zinc on all of the polycrystalline metal electrodes was preceded by underpotential deposition processes similar to those reported previously during studies carried out in aqueous solutions. The underpotential shift was found to vary linearly with the difference in the work functions of zinc and the metallic substrate. In contrast, the electrodeposition of zinc on glassy carbon required a substantial nucleation overpotential. Dimensionless chronoamperometric current‐time transients for the electrodeposition of zinc on this substrate were in good accord with the theoretical transients for the limiting case of progressive three‐dimensional nucleation with hemispherical diffusion‐controlled growth of the nuclei. Analysis of the nucleation kinetics by using the atomistic theory of nucleation suggested that active sites on the glassy carbon surface played the role of critical nuclei during the initial stages of the deposition process. The formal potential of the Zn(II)/Zn couple at 40°C was found to be vs. the Al(III)/Al couple in pure melt, and the diffusion coefficient of zinc(II) was determined to be .
Separation of Direct Sounds from Early Reflections Using the Entropy Rate Bound Minimization Algorithm (2016)

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The emerging interface of mass spectrometry with materials (2019)

Abstract Mass spectrometry (MS), a hundred-year-old subject, has been a technique of profound importance to molecular science. Its impact in solid-state materials science has not been evident, although many materials of modern science, such as fullerenes, have their origins in MS. Of late, mass spectrometric interface with materials is increasingly strengthened with advances in atomically precise clusters of noble metals. Advances in instrumentation along with recent developments in synthetic approaches have expanded the chemistry of clusters, and new insights into matter at the nanoscale are emerging. High-resolution MS coupled with soft ionization techniques enable efficient characterization of atomically precise clusters. Apart from that, techniques such as ion mobility, tandem MS, etc. reveal structural details of these systems. Growth, nucleation, and reactivity of clusters are also probed by MS. Some of the recent advancements in this field include the development of new hyphenated techniques. Finer structural details may be obtained by coupling MS with spectroscopic tools, such as photoelectron spectroscopy, vacuum ultraviolet spectroscopy, etc. With such advancements in instrumentation, MS can evolve into a universal tool for the characterization of materials. The present review captures highlights of this area.