gebhart/patrepeval huggingface dataset:
Improving the electrical integrity of Cu-CoSi/sub 2/ contacted n/sup +/p junction diodes using nitrogen-incorporated Ta films as a diffusion barrier (2002)

The study on improving the electrical integrity of Cu-CoSi/sub 2/ contacted-junction diodes by using the reactively sputtered TaN/sub x/ as a diffusion barrier is presented in this paper. In this study, the Cu (300 nm)-CoSi/sub 2/ (50 nm)/n/sup +/p junction diodes were intact with respect to metallurgical reaction up to a 350/spl deg/C thermal annealing while the electrical characteristics started to degrade after annealing at 300/spl deg/C in N/sub 2/ ambient for 30 min. With the addition of a 50-nm-thick TaN/sub x/ diffusion barrier between Cu and CoSi/sub 2/, the junction diodes were able to sustain annealing up to 600/spl deg/C without losing the basic integrity of the device characteristics, and no metallurgical reaction could be observed even after a 750/spl deg/C annealing in a furnace. In addition, the structure of TaN/sub x/ layers deposited on CoSi/sub 2/ at various nitrogen flow rates has been investigated. The TaN/sub x/ film with small grain sizes deposited at nitrogen flow ratios exceeding 10% shows better barrier capability against Cu diffusion than the others.
<b><i>Porphyromonas gingivalis</i></b> Gingipains-Mediated Degradation of Plasminogen Activator Inhibitor-1 Leads to Delayed Wound Healing Responses in Human Endothelial Cells (2021)

Plasminogen activator inhibitor-1 (PAI-1), a serine protease inhibitor, is constitutively produced by endothelial cells and plays a vital role in maintaining vascular homeostasis. Chronic periodontitis is an inflammatory disease characterized by bleeding of periodontal tissues that support the tooth. In this study, we aimed to determine the role of PAI-1 produced by endothelial cells in response to infections caused by the primary periodontal pathogen Porphyromonas gingivalis. We demonstrated that P. gingivalis infection resulted in significantly reduced PAI-1 levels in human endothelial cells. This reduction in PAI-1 levels could be attributed to the proteolysis of PAI-1 by P. gingivalis proteinases, especially lysine-specific gingipain-K (Kgp). We demonstrated the roles of these degradative enzymes in the endothelial cells using a Kgp-specific inhibitor and P. gingivalis gingipain-null mutants, in which the lack of the proteinases resulted in the absence of PAI-1 degradation. The degradation of PAI-1 by P. gingivalis induced a delayed wound healing response in endothelial cell layers via the low-density lipoprotein receptor-related protein. Our results collectively suggested that the proteolysis of PAI-1 in endothelial cells by gingipains of P. gingivalis might lead to the deregulation of endothelial homeostasis, thereby contributing to the permeabilization and dysfunction of the vascular endothelial barrier.
Photovoltaics: Nonhazardous Solvent Systems for Processing Perovskite Photovoltaics (Adv. Energy Mater. 14/2016) (2016)

In article number 1600386, Jeffrey G. Tait and co-workers develop non-hazardous ink systems, based on solvent-alcohol-acid, for coating perovskite photovoltaic films in a single step. Coating was further developed from spin to blade, while the high yield process produced efficient 4 cm2 modules.
Acquired Iron-Deficiency Anemia Caused by an Antibody against the Transferrin Receptor (1984)

We report a case of anemia due to autoantibodies to the transferrin receptor interfering with iron incorporation by erythroid progenitors. A previously healthy woman with severe acquired microcytic anemia had increased serum iron levels, electrophoretically normal transferrin concentrations, and very high levels of free protoporphyrin in red cells. The bone marrow had no stainable iron but had an excess of normal-appearing plasma cells. Erythroid precursors stained with fluorescent mouse antihuman IgM. The serum contained an antibody that reduced 59Fe incorporation by erythroleukemia K562 cells in vitro but did not inhibit iron transferrin binding. An IgM fraction of the patient's serum immunoprecipitated the human transferrin receptor obtained from solubilized [35S]methionine-labeled K562 membranes. Binding of [59Fe]transferrin or fluorescent iron transferrin was not diminished by the patient's serum at 4 degrees C, but at 37 degrees C uptake was markedly reduced, as was the binding of fluorescent monoclonal antibodies to either surface transferrin or the human transferrin receptor. A complete clinical and hematologic remission occurred with azathioprine and prednisone therapy. We conclude that the patient's autoreactive IgM down-regulated the number of transferrin receptors and diminished iron incorporation by erythroblasts, leading to an iron-deficiency anemia.
Methods for Reducing Audible Artifacts in a Wavelet-Based Broad-Band Denoising System (1998)

A wavelet-based method for denoising broad-band noisy audio signals is proposed and implemented. The method is a modified algorithm based on the method of Coifman and Wickerhauser (1992). The modified algorithm shows noticeable improvement in quality and computational overhead compared to the original method when denoising digitized music signals with different levels of additive broad-band noise. Several implementation issues are described.
Structural vibration control of micro/macro-manipulator using feedforward and feedback approaches (1995)

Pacific Northwest Laboratory (PDL) researchers investigated the combined use of two control approaches to minimize micro/macro-manipulator structural vibration: (1) modified input shaping and (2) inertial force active damping control. Modified input shaping (MIS) is used as a feedforward controller to modify reference input by canceling the vibratory motion. Inertial force active damping (IFAD) is applied as a feedback controller to increase the system damping and robustness to unexpected disturbances. Researchers implemented both control schemes in the PNL micro/macro flexible-link manipulator testbed collaborating with Georgia Institute of Technology. The experiments successfully demonstrated the effectiveness of two control approaches in reducing structural vibration. Based on the results of the experiments, the combined use of two controllers is recommended for a micro/macro manipulator to achieve the fastest response to commands while canceling disturbances from unexpected forces.
Fast PCB Stack-Up Optimization Using Integer Programming (2023)

This article presents a flexible and efficient methodology to optimize stack-up for multilayer printed circuit boards (PCBs) with enormous search space and various design constraints. PCB stack-up optimization is crucial in high-speed system design to achieve the desired electrical performance while reducing system costs. The stack-up optimization process is labor-intensive and time-consuming for a large number of layers. Moreover, after the optimization process, the electrical performance of a real design, such as the impedance and loss, may deviate from the target design due to manufacturing variations. Estimating the worst cases due to the manufacturing variations, referred to as “corner cases” in this article, is essential for a confident PCB design but challenging since the number of related parameters is large. In this article, PCB stack-up optimization and corner-case searching are addressed and greatly accelerated using the integer programming technique. All constraints are converted to mathematical equalities and inequalities that can be solved rapidly by an integer programming solver to obtain feasible stack-up solutions. After the cross sections of the transmission lines are optimized based on the stack-up design to achieve a target electrical performance, the upper and lower bound of impedance and loss are acquired using integer programming when the design parameters vary in a particular range. The proposed method is verified using multilayer PCB designs with practical constraints and demonstrates its effectiveness and high efficiency.
Regulated Cleavage of Glycan Strands by the Murein Hydrolase SagB in Staphylococcus aureus Involves a Direct Interaction with LyrA (SpdC) (2021)

LyrA (SpdC), a homologue of eukaryotic CAAX proteases that act on prenylated substrates, has been implicated in the assembly of several pathways of the envelope of <i>Staphylococcus aureus.</i> We described earlier the <u>Ly</u>sostaphin <u>r</u>esistance (Lyr) and <u>S</u>taphylococcal <u>p</u>rotein A <u>d</u>isplay (Spd) phenotypes associated with loss of the <i>lyrA</i> (<i>spdC</i>) gene. However, a direct contribution to the assembly of pentaglycine crossbridges, the target of lysostaphin cleavage in <i>S. aureus</i> peptidoglycan, or of Staphylococcal protein A attachment to peptidoglycan could not be attributed directly to LyrA (SpdC). These two processes are catalyzed by the Fem factors and Sortase A, respectively. To gain insight into the function of LyrA (SpdC), here we use affinity chromatography and LC-MS/MS analysis and report that LyrA interacts with SagB. SagB cleaves glycan strands of peptidoglycan to achieve physiological length. Similar to <i>sagB</i> peptidoglycan, <i>lyrA</i> peptidoglycan contains extended glycan strands. Purified <i>lyrA</i> peptidoglycan can still be cleaved to physiological length by SagB <i>in vitro</i> LyrA does not modify or cleave peptidoglycan, it also does not modify or stabilize SagB. The membrane bound domain of LyrA is sufficient to support SagB activity but predicted 'CAAX enzyme' catalytic residues in this domain are dispensable. We speculate that LyrA exerts its effect on bacterial prenyl substrates, specifically undecaprenol-bound peptidoglycan substrates of SagB, to help control glycan length. Such an activity also explains the Lyr and Spd phenotypes observed earlier.<b>IMPORTANCE</b> Peptidoglycan is assembled on the <i>trans</i> side of the plasma membrane from lipid II precursors into glycan chains that are crosslinked at stem peptides. In <i>S. aureus</i>, SagB, a membrane-associated N-acetylglucosaminidase, cleaves polymerized glycan chains to their physiological length. Deletion of <i>sagB</i> is associated with longer glycan strands in peptidoglycan, altered protein trafficking and secretion in the envelope, and aberrant excretion of cytosolic proteins. It is not clear whether SagB, with its single transmembrane segment, serves as the molecular ruler of glycan chains or whether other factors modulate its activity. Here, we show that LyrA (SpdC), a protein of the CAAX type II prenyl endopeptidase family, modulates SagB activity via interaction though its transmembrane domain.
Internal high-reflectivity omni-directional reflectors (2005)

An internal high-reflectivity omni-directional reflector (ODR) for the visible spectrum is realized by the combination of total internal reflection using a low-refractive-index (low-n) material and reflection from a one-dimensional photonic crystal (1D PC). The low-n layer limits the range of angles in the 1D PC to values below the Brewster angle, thereby enabling high reflectivity and omni-directionality. This ODR is demonstrated using GaP as ambient, nanoporous SiO2 with a very low refractive index (n=1.10), and a four-pair TiO2/SiO2 multilayer stack. The results indicate a two orders of magnitude lower angle-integrated transverse-electric-transverse-magnetic polarization averaged mirror loss of the ODR compared with conventional distributed Bragg reflectors and metal reflectors. This indicates the high potential of the internal ODRs for optoelectronic semiconductor devices, e.g., light-emitting diodes.
HighLight: Efficient and Flexible DNN Acceleration with Hierarchical Structured Sparsity (2023)

Due to complex interactions among various deep neural network (DNN) optimization techniques, modern DNNs can have weights and activations that are dense or sparse with diverse sparsity degrees. To offer a good trade-off between accuracy and hardware performance, an ideal DNN accelerator should have high flexibility to efficiently translate DNN sparsity into reductions in energy and/or latency without incurring significant complexity overhead.
4,5‐Bis(chloromethyl)uracil (1976)

Abstract A one‐step synthesis of 4,5‐bis(chloromethyl)uracil from readily available starting materials has been accomplished. This substance is a stable, crystalline solid which undergoes facile nucleophilic attack to produce various di‐substituted uracil derivatives.
Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements (2020)

Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of Δ<i>C</i><sub>p</sub> as well as Δ<i>G</i>, Δ<i>H</i>, and Δ<i>S</i> for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)2at 1.6 and 1.8 Å resolution (2005)

The structures of the complexes formed between two anticancer minor-groove-binding quinolinium quaternary salts and the dodecamer d(CGCGAATTCGCG)(2) have been refined to resolutions of 1.6 and 1.8 Angstrom. The complexes crystallized in space group P2(1)2(1)2(1) and the structures are isomorphous with previously solved dodecamer structures. The ligands both bind in the central AT region of the minor groove and although the crystallization conditions and structures of the ligands are very similar, they bind in opposing orientations. The structures are compared with two previously published structures of quinolinium quaternary salts, refined at 2.5 Angstrom resolution, complexed with d(CGCGAATTCGCG)(2) and an e(6)G-modified DNA.
Cerebrospinal fluid-iophendylate contrast on gradient-echo MR images. (1988)

The effect on the signal intensities of cerebrospinal fluid (CSF) and iophendylate (Pantopaque) and on CSF-iophendylate contrast was studied in vitro with a small-nutation-angle (alpha) gradient refocused magnetic resonance (MR) imaging technique (GRASS) as alpha, repetition time (TR), and echo time (TE) were varied. CSF signal intensity was consistently greater than that of iophendylate. Therefore, retained intraspinal iophendylate may be considered in the differential diagnosis of focal areas of low signal intensity at the periphery of the spinal canal on GRASS images. At constant TE and TR, an increase in alpha from 6 degrees to 45 degrees increased the signal intensities of CSF and iophendylate but decreased CSF-iophendylate contrast. At constant alpha and TR, an increase in TE from 13 to 28 msec decreased the signal intensities of CSF and iophendylate but increased contrast. At constant alpha and TE, an increase in TR from 50 to 400 msec increased the signal intensities of CSF and iophendylate, as well as contrast. Clinical examples of the contrast behavior of retained intraspinal iophendylate on both spin-echo and GRASS images corroborate the experimental findings. Retained intraspinal iophendylate may mimic the appearance of intra-or extra-dural lesions, magnetic susceptibility artifact, and flow on gradient-echo MR images of the spine.
Linear trimeric, dimeric, and monomeric titanium(III) aryloxides (1992)

Reactions of trans-Ti(TMEDA)2Cl2 (TMEDA = N,A,N,N'-tetramethylethylenediamine) with 2 equiv of RONa IR = Ph, 3,5-(t-Bu)2C6H3] formed the paramagnetic light-green linear trimeric Ti(III) derivative Ti3(PhO)9-(TMEDA)2 (1) and the pink dimeric complex [Ti(RO)Cl(TMEDA)]2(mu-OR)2[R = 3,5-(t-Bu)2C6H3](2),respectively. Complex 1 could also be conveniently synthesized from TiCl3(THF)3 and PhONa in the presence of TMEDA. Conversely, complex 2 could be obtained from TiCl3(THF)3 only when the reaction was carried out in toluene, since bright-yellow crystals of the mononuclear anionic complexes [Ti(RO)2(TMEDA)Cl2] [M'] [M' = Na(TMEDA)2+ (3a), 1/2(TMEDA)H+ (3b)] were isolated when the reaction was performed in THF. Reaction of Ti[N(SiMe3)2]3 with 3 equiv of 2,6-Me2C6H3OH in toluene led to the formation of the first dinuclear homoleptic complex [Ti(RO)3)2 [R = 2,6-Me2C6H3 (4)], which was isolated as green-blue crystals. A similar reaction with the more bulky 2,6-(i-Pr)2C6H3OH led to the formation of the neutral homoleptic Ti(IV) species Ti[OC6H3-2,6-(i-Pr)2]4 (6). Conversely, the anionic homoleptic complex {Ti[OC6H3-2,6-(i-Pr)2]4}{Li(TMEDA)2}.toluene (7) was obtained by reacting the corresponding lithium phenoxide with TiCl3(THF)3. The structures of 1, 3b, and 4 were determined by X-ray analysis. Crystal data are as follows. 1: monoclinic, C2/c, a = 14.758 (5) angstrom, b = 21.920 (2) angstrom, c = 11.855 (1) angstrom, beta = 102.339 (4)-degrees, V = 6274 (7) angstrom3, Z = 4, R = 0 058 (R(w) = 0.024) for 417 parameters and 2425 significant reflections out of 4648. 3b: triclinic, P1Bar, a = 12.877 (2) angstrom, b = 16.850 (3) angstrom, c = 12.605 (2) angstrom, alpha = 106.65 (1)-degrees, beta = 100.65 (1)-degrees, gamma = 68.63 (1)-degrees, V = 2430.4 (7) angstrom3, Z = 2, R = 0.080 (R(w) = 0.081) for 435 parameters and 4685 significant reflections out of 7234. 4: triclinic, P1Bar, a = 11.372 (3) angstrom, b = 11.458 (3) angstrom, c = 10.859 (4) angstrom, alpha = 117.04 (2)-degrees, beta = 115.29 (3)-degrees, gamma = 93.56 (4)-degrees, V = 1080.1 (9) angstrom3, Z = 2, R = 0.036 (R(w) = 0.051) for 362 parameters and 3297 significant reflections out of 4020.
Detailed Kinetic Investigations on the Selective Oxidation of Biomass to Formic Acid (OxFA Process) Using Model Substrates and Real Biomass (2017)

A detailed kinetic analysis of the selective catalytic oxidation of different biogenic model substrates to formic acid (OxFA process) is presented using two different polyoxometalate catalysts, HPA-2 (H5PV2Mo10O40) and HPA-5 (H8PV5Mo7O40). By using high oxygen pressures (30–60 bar) and temperatures of 80–90 °C in aqueous solution, we were able to investigate the rate-determining substrate oxidation step catalyzed by the oxidized form of the polyoxometalates (POMs) by keeping the concentration of the catalytic active species constant. Under these conditions, kinetic parameters like effective reaction order and reaction rate constants could be determined by the differential method for model substrates like glucose, fructose, sorbitol, and gluconic acid. Furthermore, kinetic experiments using the two different catalysts showed a different behavior for various functionalities within the carbon framework of the substrate with the tendency of higher reaction rates with the HPA-5 catalyst. This effect was more pronounced for disaccharides like cellobiose and sucrose than for monosaccharides. Finally, a detailed kinetic study for water-insoluble biomasses like beech and spruce wood showed differences in formic acid (FA) formation and product selectivities depending on the composition of the wood in terms of their ratios of lignin, cellulose, and hemicellulose.
Enhancing Hit Quality and Diversity within Assay Throughput Constraints (2005)

This chapter contains sections titled: Introduction What Makes a Good Lead Molecule? Compound Collections – Suitability as Leads Compound Collections – Diversity Data Reliability Selection Methods Enhancing Quality and Diversity of Actives Methods Screening Library Determination of Activity Threshold Filtering High-Throughput Screen Clustering Algorithm (HTSCA) Diversity Analysis Data Visualization Results Peptide Hydrolase Protein Kinase Protein–Protein Interaction Discussion and Conclusion
595. Nasal Delivery of Adenovirus Expressing the Ebola Glycoprotein Protects Mice Against Ebola Virus in the Presence of Preexisting Immunity to the Vaccine Carrier (2006)

The Ebola hemorrhagic fever virus has drawn increasing interest in the past years due to an augmentation in the number of natural outbreaks and its potential use as a bioterror agent. To date, only vaccine based on Vesicular Stomatitis virus and Adenovirus as the vaccine carrier have successfully protected nonhuman primates against a lethal dose of Ebola virus. Adenovirus vector derived from human adenovirus serotype 5 (AdHu5) has the advantage of having a well document track record following in vivo administration to thousand of individuals in different clinical trials. However, natural exposure to Adenovirus may result in the generation of a potent immunity capable of compromising adenovirus-based vaccine efficacy. 30 to 50% of the human population in North America has levels of serum antibodies that can neutralize relatively high doses of AdHu5. The present study evaluated mucosal vaccination of mice with AdHu5 expressing the Ebola glycoprotein (Ad-EboGP) and the impact of pre-existing immunity to the Adenovirus vector on vaccine efficacy. Intramuscular (I.M.), oral or nasal administration of Ad-EboGP fully protected mice against a lethal challenge with mouse-adapted Ebola virus. However, oral or I.M. vaccination of mice pretreated with pooled human antibodies, mimicking the presence of pre-existing immunity as evidenced by neutralizing antibody (NAB) to AdHu5 in mice sera, resulted in 0 to 10% survival after challenge with mouse-adapted Ebola virus. Interestingly, nasalvaccination with Ad-EboGP was protective even in the presence of preexisting immunity and resulted in 100% survival with no weight loss after challenge with Ebola virus. In untreated mice, T (INF-γ positive CD8 T cells following peptide re-stimulation) and B cell (NAB) responses were detected in all EboGP vaccinated groups although both responses were lower in mice receiving oral or nasal immunization when compared to mice administered I.M.. The presence of pre-existing immunity severely compromised the T and B cell responses in mice vaccinated orally or I.M. but not in mice receiving nasal immunization. Interestingly, PEGylation of the adenovirus vector partially rescued the B cell response but diminished the T cell response after oral vaccination of mice with pre-existing immunity and failed to improve survival. This study highlights the importance of vaccine delivery routes with regards to efficacy in the presence or absence of pre-existing immunity and provides new evidence for successful vaccination with AdHu5 and possibly readministration. James Wilson had equity in Targeted Genetics at the time of the study.