gebhart/patrepeval huggingface dataset:
Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase (2005)

C3 exoenzymes (members of the ADP-ribosyltranferase family) are produced by Clostridium botulinum (C3bot1 and -2), Clostridium limosum (C3lim), Bacillus cereus (C3cer), and Staphylococcus aureus (C3stau1-3). These exoenzymes lack a translocation domain but are known to specifically inactivate Rho GTPases in host target cells. Here, we report the crystal structure of C3bot1 in complex with RalA (a GTPase of the Ras subfamily) and GDP at a resolution of 2.66 A. RalA is not ADP-ribosylated by C3 exoenzymes but inhibits ADP-ribosylation of RhoA by C3bot1, C3lim, and C3cer to different extents. The structure provides an insight into the molecular interactions between C3bot1 and RalA involving the catalytic ADP-ribosylating turn-turn (ARTT) loop from C3bot1 and helix alpha4 and strand beta6 (which are not part of the GDP-binding pocket) from RalA. The structure also suggests a molecular explanation for the different levels of C3-exoenzyme inhibition by RalA and why RhoA does not bind C3bot1 in this manner.
Liquid-Phase Exfoliation of Magnetically and Optoelectronically Active Ruthenium Trichloride Nanosheets (2022)

α-RuCl<sub>3</sub> is a layered transition metal halide that possesses a range of exotic magnetic, optical, and electronic properties including fractional excitations indicative of a proximate Kitaev quantum spin liquid (QSL). While previous reports have explored these properties on idealized single crystals or mechanically exfoliated samples, the scalable production of α-RuCl<sub>3</sub> nanosheets has not yet been demonstrated. Here, we perform liquid-phase exfoliation (LPE) of α-RuCl<sub>3</sub> through an electrochemically assisted approach, which yields ultrathin, electron-doped α-RuCl<sub>3</sub> nanosheets that are then assembled into electrically conductive large-area thin films. The crystalline integrity of the α-RuCl<sub>3</sub> nanosheets following LPE is confirmed through a wide range of structural and chemical analyses. Moreover, the physical properties of the LPE α-RuCl<sub>3</sub> nanosheets are investigated through electrical, optical, and magnetic characterization methods, which reveal a structural phase transition at 230 K that is consistent with the onset of Kitaev paramagnetism in addition to an antiferromagnetic transition at 2.6 K. Intercalated ions from the electrochemical LPE protocol favorably alter the optical response of the α-RuCl<sub>3</sub> nanosheets, enabling large-area Mott insulator photodetectors that operate at telecommunications-relevant infrared wavelengths near 1.55 μm. These photodetectors show a linear photocurrent response as a function of incident power, which suggests negligible trap-mediated recombination or photothermal effects, ultimately resulting in a photoresponsivity of ≈2 mA/W.
Novel diffraction-based spectroscopic method for overlay metrology (2003)

A spectroscopic, diffraction based technique is proposed in this paper as an alternative solution for overlay metrology in technology nodes below 90 nanometers. This novel technique extracts alignment error from broadband diffraction efficiency of specially designed diffraction targets in real-time. Feasibility of the technique is studied for a front-end process flow by measuring grating targets printed on a series of wafers which were intentionally mis-processed to introduce inter-die (grid) level programmed overlay errors. Correlation to conventional imaging overlay measurements is demonstrated. Short term and long term data sets demonstrate sub-half-nanometer in 3-sigma statistical parameters that characterize the diffraction overlay system, repeatability, reproducibility, Tool-Induced-Shift and tool-to-tool matching. The resulting total measurement uncertainty for this technique is thus demonstrated to be in the sub-nanometer range.
Verification of Hybrid Physical System Models (1996)

Abstract Physical systems are by nature continuous, but often nonlinear. This increases model complexity and causes numerical stiffness in simulation. By modeling these nonlinearities as discontinuities, the models can be linearized and operate in multiple modes. This paper discusses a hybrid modeling methodology that combines continuous energy flow modeling using bond graphs and discrete signal flow modeling using controlled junctions with associated finite state automata to generate complex, multi-mode behavior. When threshold values are crossed, multiple discontinuous changes may occur before a new continuous mode of operation is reached. An analysis method is presented to establish physically inconsistent areas based on the energy distribution in the system at the time of switching. Time complexity of the method is constrained by a model partitioning approach based on identifying areas of instantaneous change.
Complexity scalable motion compensated wavelet video encoding (2005)

We present a framework for the systematic analysis of video encoding complexity, measured in terms of the number of motion estimation (ME) computations, that we illustrate on motion compensated wavelet video coding schemes. We demonstrate the graceful complexity scalability of these schemes through the modification of the spatiotemporal decomposition structure and the ME parameters, and the use of spatiotemporal prediction. We generate a wide range of rate-distortion-complexity (R-D-C) operating points for different sequences, by modifying these options. Using our analytical framework we derive closed form expressions for the number of ME computations for these different coding modes and show that they accurately capture the computational complexity independent of the underlying content characteristics. Our framework for complexity analysis can be combined with rate-distortion modeling to determine the encoding structure and parameters for optimal R-D-C tradeoffs.
Generalized Space-Filling Gosper Curves and Their Application to the Design of Wideband Modular Planar Antenna Arrays (2010)

The Peano-Gosper space-filling curve provides an excellent framework for designing planar antenna array distributions with modular architectures and suppressed sidelobes over a relatively wide bandwidth. The curve consists of a self-avoiding path that intersects a triangular lattice and its construction is based on the iterative application of a generating curve. There exist a number of other recently discovered curves, coined generalized Gosper curves, that possess properties similar to those of the Peano-Gosper curve but are based on larger and more complex generating curves. In this paper these generalized curves will be examined as the framework for antenna array layouts. It will be shown that arrays based on these curves have a number of excellent characteristics while offering modular array configurations and sizes that are not inherent to Peano-Gosper arrays. Moreover, when combined with a simple recursive-perturbation technique, the element distributions of these arrays can be efficiently adjusted to generate designs with bandwidths that far exceed that of standard periodic- and triangular-lattice arrays. The efficacy of this technique will be demonstrated through design examples, including one that has more than a 10:1 bandwidth. Full-wave simulations of a wideband patch array will also be used to investigate the effects of mutual coupling on these array distributions.
Role of Phosphoglucomutase of Stenotrophomonas maltophilia in Lipopolysaccharide Biosynthesis, Virulence, and Antibiotic Resistance (2003)

A homologue of the algC gene, responsible for the production of a phosphoglucomutase (PGM) associated with LPS and alginate biosynthesis in Pseudomonas aeruginosa, spgM, was cloned from Stenotrophomonas maltophilia. The spgM gene was shown to encode a bifunctional enzyme with both PGM and phosphomannomutase activities. Mutants lacking spgM produced less LPS than the SpgM(+) parent strain and had a tendency for shorter O polysaccharide chains. No changes in LPS chemistry were obvious as a result of the loss of spgM. Significantly, however, spgM mutants displayed a modest increase in susceptibility to several antimicrobial agents and were completely avirulent in an animal model of infection. The latter finding may relate to the resultant serum sensitivity of spgM mutants which, unlike the wild-type parent strain, were rapidly killed by human serum. These data highlight the contribution made by LPS to the antimicrobial resistance and virulence of S. maltophilia.
Filling-Enforced Obstructed Atomic Insulators (2021)

Topological band theory has achieved great success in the high-throughput search for topological band structures both in paramagnetic and magnetic crystal materials. However, a significant proportion of materials are topologically trivial insulators at the Fermi level. In this paper, we show that, remarkably, for a subset of the topologically trivial insulators, knowing only their electron number and the Wyckoff positions of the atoms we can separate them into two groups: the obstructed atomic insulator (OAI) and the atomic insulator (AI). The interesting group, the OAI, have a center of charge not localized on the atoms. Using the theory of topological quantum chemistry, in this work we first derive the necessary and sufficient conditions for a topologically trivial insulator to be a filling enforced obstructed atomic insulator (feOAI) in the 1651 Shubnikov space groups. Remarkably, the filling enforced criteria enable the identification of obstructed atomic bands without knowing the representations of the band structures. Hence, no ab-initio calculations are needed for the filling enforced criteria, although they are needed to obtain the band gaps. With the help of the Topological Quantum Chemistry website, we have performed a high-throughput search for feOAIs and have found that 957 ICSD entries (638 unique materials) are paramagnetic feOAIs, among which 738 (475) materials have an indirect gap. The metallic obstructed surface states of feOAIs are also showcased by several material examples.
Differentiation of finite element solutions to non‐linear problems (2000)

Two extended numerical differentiation methods based on Green's second identity are presented. These may be used for postprocessing approximate solutions in general material distributions, including inhomogeneous and discontinuous material characteristics. The first method uses a general formulation with Green's functions and extended Poisson kernels for standard domains, while the second applies Green's functions to certain restricted, analytically known configurations. The singularities encountered in the necessary integral kernels for second derivatives are evaluated using finite part integration techniques. Both methods are illustrated by numerical experiments, and results are shown for differentiation of quasi-harmonic functions in inhomogeneous domains. Copyright © 2000 John Wiley & Sons, Ltd.
Robust Control for Linear Stages in Electronic Manufacturing (2007)

This paper considers the control of an x-y linear stage commonly used in electronic manufacturing. The challenge of the control problem includes coupled and nonlinear dynamics, flexibility due to the air bearing dynamics, geometric nonlinearity due to the interferometer position measurement, and tight cross-axis positioning requirements. We evaluate two control design approaches: robust control and gain scheduling. For the robust controller, a nominal linear time invariant design model is chosen with nonlinear dynamics considered as uncertainties. The choice of uncertainty characterization and weighting functions significantly affect the performance of the controller. For the gain scheduling controller design, robust controllers based on linearized models at several operating points within the workspace are combined. From the nonlinear simulation, it is shown that with suitable tuning, good performance is obtained throughout the work volume.
Optimization of 1700V SiC MOSFET for Short Circuit Ruggedness (2019)

This work focuses on the ruggedness aspect of SiC MOSFET technology discussing design advances to maximize SiC device benefits for industrial and transportation power conversion applications. These improvements were studied as a tradeoff between short circuit withstand time (τ sc ) and device on-state resistance (R DS(on) ) at operating temperature (150°C) utilizing 1.7kV MOSFETs fabricated on 2.25x4.5mm 2 die. Up to two times improvement in τ sc with only 20% of R DS(on) increase was achieved for design with reduced source region doping.
Bioaktív okta- és hexadeka-merek szintézise és vizsgálata = Synthesis and investigations of bioactive octa- and hexadeca-meric compounds (2007)

Új, biológiailag aktív oligomer hordozó molekulákat terveztünk, szintetizáltunk és teszteltünk. A kismolekulasúlyú oligomer molekulák alkalmasaknak bizonyultak arra, hogy hozzájuk 3-8 darab egy szabad karbonsavval rendelkező aminosav-, peptid- vagy peptidmimetikus származékot lehessen kapcsolni. Az oligofunkciós hordozó molekula 1-4 tercier amino csoportja elősegíti poláros oldószerekben való oldékonyságot. A gonadotrop hormon releasing hormon, a szomatosztatin és a multi drog rezisztenciát gátló peptideket illetve származékaikat szintetizáltuk és in vitro sejkultúrákon teszteltük. Különösen aktívak voltak anyagaink az angiogenezis stimulálásában valamint a neurogén-gyulladás gátlásában. Egy szabadalmi bejelentést tettünk, egy pedig készülőben van. | New biologically active oligomeric carrier molecules having exact chemical structures and homogen molecular weight were designed, synthesized, tested and patented. The compounds are suitable to conjugate 3-8 biologically active peptide derivatives or peptidmimetics having a free carboxyl group. The carrier molecules are more soluble in polar solvents because of the 1-4 tertier nitrogen groups. The gonadotrop hormone releasing hormone agonists and inhibitors, somatostatin inhibitors and multi drug resistance inhibitors were especially active on stimulation of angiogenesis and against neurogenic inflammation. The new compounds were tested on cell cultures in vitro. It has been shown that the oligomeric conjugates i.e. the biologically active analogs coupled to the oligo-cation carrier resulted in non-toxic conjugates. We have prepared two patent applications.
Search for neutrino events in the KAMIOKANDE II detector in correlation with the solar flare activity in 1989 March (1990)

The Kamiokande II water Cerenkov detector has been used to search for neutrino events correlated with the great solar flare activity observed in March 1989. No evidence for such a correlation is found. A search has also been made for low-energy events correlated with flares of importance two or greater and with solar proton flux of 10 Mev or greater. Again, no significant signal is found.
EFFECTS OF BWH-4 ANTI-CD4 MONOCLONAL ANTIBODY ON RAT VASCULARIZED CARDIAC ALLOGRAFTS BEFORE AND AFTER ENGRAFTMENT (1991)

We studied the effects and mechanism of action of BWH-4, an IgG2a mouse antirat CD4 monoclonal antibody that recognizes a distinct epitope on the CD4 molecule, in LEW recipients of (LEW x BN)F1 vascularized heterotopic cardiac allografts. Ten animals received daily injections of 700 micrograms BWH-4 for ten days after engraftment. Median actuarial allograft survival was 37 days for the treated animals compared with 7.5 days for controls (n = 6). There was depletion of peripheral blood CD4+ lymphocytes to 4 +/- 1% one week posttransplant (normal = 48 +/- 4%, n = 6). Six additional animals were treated with a lower dose (100 micrograms) of BWH-4 daily for ten days. Median actuarial allograft survival was 10 days and the circulating CD4+ cells decreased to 30 +/- 6% at one week posttransplant. All six low-dose-treated animals mounted an anti-BN alloantibody response by 3 weeks, while only one of the ten high-dose-treated animals had positive alloantibodies two weeks posttransplant. Lymphocyte-mediated cytotoxicity against donor lymphoblasts was completely abolished in the high-dose-treated animals when compared with acutely rejecting controls. We also used low-dose (100 micrograms) BWH-4 to pretreat eleven experimental animals for 7 days prior to engraftment. The circulating CD4+ cells decreased to only 12 +/- 2% on the day of transplantation and 26 +/- 9% one week posttransplant. However, six (55%) pretreated animals survived more than 55 days. There was a 66% decrease in lymphocyte-mediated cytotoxicity against donor lymphoblasts when compared with acutely rejecting controls. We conclude that the anti-CD4 mAb, BWH-4, prevents acute rejection of vascularized heterotopic rat cardiac allografts; this effect is mediated by depletion of the CD4+ T cell subset, suppression of alloantibody production, and inhibition of lymphocyte-mediated cytotoxicity.
Crystal Structures of Dipeptides Containing the Dmt-Tic Pharmacophore (2002)

The crystal structures of three analogues of the potent delta-opioid receptor antagonist H-Dmt-Tic-OH (2',6'-dimethyl-L-tyrosine-L-1,2,3,4-tetrahydroisoquinoline-3-carboxylate), N,N (CH(3))(2)-Dmt-Tic-OH (1), H-Dmt-Tic-NH-1-adamantane (2), and N,N(CH(3))(2)-Dmt-Tic-NH-1-adamantane (3) were determined by X-ray single-crystal analysis. Crystals of 1 were grown by slow evaporation, while those of 2 and 3 were grown by vapor diffusion. Compounds 1 and 3 crystallized in the monoclinic space group P2(1), and 2 crystallized in the tetragonal space group P4(3). Common backbone atom superimpositions of structures derived from X-ray diffraction studies resulted in root-mean-square (rms) deviations of 0.2-0.5 A, while all-atom superimpositions gave higher rms deviations from 0.8 to 1.2 A. Intramolecular distances between the aromatic ring centers of Dmt and Tic were 5.1 A in 1, 6.3 A in 2, and 6.5 A in 3. The orientation of the C-terminal substituent 1-adamantane in 2 and 3 was affected by differences in the psi torsion angles and strong hydrogen bonds with adjacent molecules. Despite the high delta-opioid receptor affinity exhibited by each analogue (K(i) < 0.3 nM), high mu receptor affinity (K(i) < 1 nM) was manifested only with the bulky C-terminal 1-adamantane analogues 2 and 3. Furthermore, the bioactivity of both 2 and 3 exhibited mu-agonism, while 3 also had potent delta-antagonist activity. Those data demonstrated that a C-terminal hydrophobic group was an important determinant for eliciting mu-agonism, whereas N-methylation maintained delta-antagonism. Furthermore, the structural results support the hypothesis that expanded dimensions between aromatic nuclei is important for acquiring mu-agonism.
Angiopoietin‐1 negatively regulates expression and activity of tissue factor in endothelial cells (2001)

Normally, tissue factor (TF) is not expressed on the surface of endothelial cells, but its expression can be induced by vascular endothelial growth factor (VEGF) and tumor necrosis factor (TNF)-a. However, the signaling pathway(s) affecting this induction is unknown. Using human umbilical vein endothelial cells, we found that inhibitors of guanine-cytosine-rich DNA binding protein and nuclear factor (NF)-kB suppressed VEGF- and TNF-a-induced expression and activity of TF. However, unexpectedly, phosphatidylinositol (PI) 3'-kinase inhibitor enhanced the VEGF- and TNF-a-induced expression and activity of TF. Angiopoietin-1 (Ang1), a strong activator of intracellular PI 3'-kinase/Akt, inhibited the induction of TF by VEGF and TNF-a, whereas Ang1 itself did not produce any significant effect on TF. Selective activation (or inactivation) of PI 3'-kinase/Akt by using adenoviral transfer reduced (or enhanced) TNF-a-induced expression of TF mRNA and protein, regardless of Ang1 treatment. From these results, we conclude that Ang1 inhibits the up-regulation of TF expression, possibly through activation of PI 3'-kinase/Akt in endothelial cells. Ang1 may be useful as an inhibitor of VEGF- and TNF-a-induced coagulation, inflammation, and cancer progression.
Extended Thevenin models for transient analysis of non-uniform dispersive lossy multiconductor transmission lines (2003)

The authors present a new time-varying equivalent circuit model for transient analysis of uniform and nonuniform multiconductor transmission lines with arbitrary linear and nonlinear loads. Calculated or measured scattering parameter data are used to characterize the interconnection structures. Both sides of the transmission line structure are modeled as extended Thevenin equivalents, which consist of constant resistances and time-dependent voltage sources. This new circuit model is compatible with existing simulation programs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Silicate cathodes for lithium batteries: alternatives to phosphates? (2011)

Polyoxyanion compounds, particularly the olivine-phosphate LiFePO4, are receiving considerable attention as alternative cathodes for rechargeable lithium batteries. More recently, an entirely new class of polyoxyanion cathodes based on the orthosilicates, Li2MSiO4 (where M = Mn, Fe, and Co), has been attracting growing interest. In the case of Li2FeSiO4, iron and silicon are among the most abundant and lowest cost elements, and hence offer the tantalising prospect of preparing cheap and safe cathodes from rust and sand! This Highlight presents an overview of recent developments and future challenges of silicate cathode materials focusing on their structural polymorphs, electrochemical behaviour and nanomaterials chemistry.
65. CLOT EMBOLIC STROKE IN THE VERTEBROBASILAR SYSTEM OF RABBITS (1987)

The University of Texas System Cancer Center, M.D. Anderson Hospital and Tumor Institute, Houston, Texas 77030
Wavelength division multiplexers with large number of channels (1989)

Wavelength division multiplexers (WDMs) with a large number of channels and extremely low cross-coupling losses (less than −35 dB), based on holographic optical elements in 3-D and planar geometries are proposed. The basic architecture of holographic WDMs consists of volume holograms in 3-D or waveguide geometry. Based on the optical performance of high efficiency holographic technology 1 developed at POC, the losses per channel can be &lt;1 dB. The number of channels in both multiplexing and demultiplexing modes can exceed ten with channel separation between 10 and 30 nm. The multichannel WDMs with low loss and low crosstalk are particularly desirable in the next-generation fiber optics local area network applications.
Homogeneous coexistence and phase segregation in 1111 iron-based pnictides studied via NMR (2013)

We performed 75As and 51Co nuclear magnetic resonance (NMR) measurements on LaFeAsO1−x F x (La1111), a prototype of iron-based superconductors, and on Ca(Fe1−x Co x )AsF (Ca1111), which has a small overlap between the antiferromagnetic (AF) and superconducting (SC) domes in the electronic phase diagram. We found in the Ca1111 series that AF and SC states coexist homogeneously in the overlapped region, while in the La1111 series, we found that paramagnetic (PM) and SC domains coexist around the AF-SC phase boundary. The coexistence of these domains indicates that the AF and SC domes segregate from each other in the electronic phase diagram.