gebhart/patrepeval huggingface dataset:
Huntingtin Is Ubiquitinated and Interacts with a Specific Ubiquitin-conjugating Enzyme (1996)

Using the yeast two-hybrid system, we have identified a human ubiquitin-conjugating enzyme (hE2-25K) as a protein that interacts with the gene product for Huntington disease (HD) (Huntingtin). This protein has complete amino acid identity with the bovine E2-25K protein and has striking similarity to the UBC-1, -4 and -5 enzymes of Saccharomyces cerevisiae. This protein is highly expressed in brain and a slightly larger protein recognized by an anti-E2-25K polyclonal antibody is selectively expressed in brain regions affected in HD. The huntingtin-E2-25K interaction is not obviously modulated by CAG length. We also demonstrate that huntingtin is ubiquitinated. These findings have implications for the regulated catabolism of the gene product for HD.
RNA Synthesis by Reverse Direction Process: Phosphoramidites and High Purity RNAs and Introduction of Ligands, Chromophores, and Modifications at 3′‐End (2011)

We have synthesized and studied the coupling properties of 3'-DMT-5'-CE phosphoramidites. The coupling efficiency per step surpasses 99% in the reverse-direction synthesis methodology, leading to high-purity RNA in a large number of 20- to 21-mers and long-chain oligonucleotides. Our data show that 5'→3' direction synthesis has a distinct advantage compared to the conventional method. As a result, this method of RNA synthesis is expected to be a very useful and practical method of choice for therapeutic-grade RNA. The phosphoramidites, Rev-A-n-bz, Rev-C-n-bz, Rev-C-n-ac, Rev-G-n-ac, and Rev-rU are routinely produced with an HPLC purity of greater than 98% and (31)P NMR purity greater than 99.5%.
Visual analysis tool for hierarchical additive time-series data (2015)

The authors developed a visual analysis tool for hierarchical additive time-series data. Additive time-series data are visualized via stacked graphs, and users can easily drill-down into the hierarchical structure by clicking a bar on the stacked graphs. The most important feature of the tool is showing multiple stacked graphs in parent-child relationship simultaneously.
Dispersive Ion Generation in Nematic Liquid Crystal Displays (2002)

Ion generation and recombination have been characterized in nematic liquid crystal displays. A model for dispersive generation may explain the time dependency of the leakage current through the cell This current leads to the build-up of a charge layer near the electrodes depending on the resistivity of the alignment layer (a.l.) used. The amount of transported charge can then be calculated and related to a compensating voltage, which gives rise to image retention problems. Agreement between the results of theoretical analysis and experiments was reached when the capacitances of the a.l. and the diffusion layer were taken into account. Furthermore, the gradual removal of the charge layer during a short circuit was analyzed. This effect, depending on the type of a.l. used, is related to the diffusion and recombination of the ions involved.
Exact Combinatorial Branch-and-Bound for Graph Bisection (2012)

We present a novel exact algorithm for the minimum graph bisection problem, whose goal is to partition a graph into two equally-sized cells while minimizing the number of edges between them. Our algorithm is based on the branch-and-bound framework and, unlike most previous approaches, it is fully combinatorial. We present stronger lower bounds, improved branching rules, and a new decomposition technique that contracts entire regions of the graph without losing optimality guarantees. In practice, our algorithm works particularly well on instances with relatively small minimum bisections, solving large real-world graphs (with tens of thousands to millions of vertices) to optimality.
Reaction of metallo <i>S</i>‐alkyl <i>N</i>‐cyanodithioiminocarbonates and alkyl <i>N</i>‐cyanocarbamates with hydrazine. A novel preparation of 5‐amino‐3‐mercapto‐1,2,4‐triazole (1998)

Abstract Metal salts of S ‐alkyl‐ N ‐cyanodithioiminocarbonates 7 react as electrophiles with hydrazine hydrate to form 5‐amino‐3‐mercapto‐1 H ‐1,2,4‐triazole 1 . The novel 4‐cyanothiosemicarbazide 9 is proposed as the intermediate which cyclizes to the aromatic triazole. The rate determining step is addition of hydrazine to the iminocarbonate and is second order. Other nucleophiles such as substituted hydrazines and amines failed to react. Exchange of either or both sulfurs with oxygen leads to decomposition or mixtures of products.
Structural requirements for interleukin 13 to bind IL13R-alpha2, a tumor associated receptor (2004)

4674 We have found that a vast majority of patients with high-grade astrocytoma (HGA) over-express IL13R-alpha2, a receptor (R) for an immune regulatory cytokine, interleukin 13 (IL13). The other receptor for IL13, IL13/4R, is shared with IL4, transduces intracellular signaling and is expressed comparably in both vital organs and human malignancies. In addition, IL13R-alpha2 can be induced in normal cells otherwise not-expressing this tumor-restricted receptor in response to IL13 alone. The cytokine also stimulates a signaling cascade in cancer cells that leads to further activation of oncogenic pathways. Thus, in the development of diagnostics/therapeutics the ligand should be deprived of any ability to bind and activate IL13/4R, unlike IL13, and bind tighter the IL13R-alpha2. Our laboratory documented that residues at positions 105, 106, and 109 in alpha-helix D of IL13 contribute to the binding of IL13 to IL13R-alpha2. We began to determine the structural requirements of IL13 to interact with IL13R-alpha2. In the Conolly’s algorithm surface analysis we found Lys-105 and Arg-109 lay one above the other with a depression in between the residues while Lys-106 lies farther away. It is plausible that the receptor-binding pocket for IL13R-alpha2 encompasses this specific region. Next, we analyzed the structural side-chain changes at position 105 upon substitution with various amino acids. We noted a proximity between the side chain −NH2 group of Lys-105 and −C (NH2)=NH- group of Lys-109, and we suggest that such orientation may in fact favor the residues to anchor the receptor site coordinately. All position 105 mutants of IL13 studied, namely IL13.K105E, IL13.K105D, IL13.K105A and IL13.K105L do not to have the extended side-chain and none of them competes for the IL13R-alpha2 binding. Accordingly, a mutant of IL13, IL13K105R, has the arginine side chain protruding in parallel to that of Lys-109 and competes for the IL13R-alpha2 sites even better than the wild type IL13. Another possible explanation for Arg-105 substitution enabling preserved or even better binding to IL13R-alpha2 is that the epsilon-N-group in Arg has a restricted rotation due to the partial double bond character due to resonance, and Arg is able to interact better with the backbone carbonyl oxygens providing structural rigidity to the protein. We suggest that in IL13.K105R, Arg increases the rigidity of the protein and influences the overall electrostatic potential of the protein surface. We thus propose that a positively-charged polar residue with an extended side-chain orientation at position 105 in the alpha-helix D region in IL13 may be crucial for its anchoring property towards the HGA-associated receptor. This knowledge should allow us to generate other IL13 mutants/peptidomimetics of desired characteristics for future development of specific tumor targeting molecules.
Solution of protein crystallographic structures by high-pressure cryocooling and noble-gas phasing (2006)

Room-pressure flash-cryocooling of protein crystals is the standard way to reduce radiation damage during data collection. Typically, it is necessary to find cryoprotection conditions by trial and error, a process that is not always successful. Recently, a new method, high-pressure cryocooling, was developed that does not require penetrative cryoprotectants and typically yields very high quality diffraction. Since this method involves helium gas as a pressurizing medium, it was of great interest to see whether the method could be extended to diffraction phasing by the incorporation of heavy noble gases such as krypton. A modified Kr-He high-pressure cyrocooling procedure is described wherein crystals are first pressurized with krypton gas to 10 MPa for 1 h. The krypton pressure is then released and the crystals are repressurized with helium over 150 MPa and cooled to liquid-nitrogen temperatures. Porcine pancreas elastase (PPE; 240 residues, 26 kDa) was selected as a test case for this study. Excellent diffraction was achieved by high-pressure cryocooling without penetrating cryoprotectants. A single 0.31 occupied krypton site in a PPE molecule [Bijvoet amplitude ratio (|DeltaF|/F) of 0.53%] was successfully used for SAD phasing at 1.3 A. This method has the potential to greatly simplify obtaining protein structures.
Simultaneous measurement by flow cytometry of sperm cell viability and mitochondrial membrane potential related to cell motility. (1982)

Free accessAbstractFirst published online January 5, 2017Simultaneous measurement by flow cytometry of sperm cell viability and mitochondrial membrane potential related to cell motility.D P Evenson, Z Darzynkiewicz, and M R MelamedView all authors and affiliationsVolume 30, Issue 3https://doi.org/10.1177/30.3.6174566
Common-Mode Voltage Mitigation of Dual T-Type Inverter Drives Using Fast MPC Approach (2021)

This article proposes an intensive study for common-mode voltage (CMV) elimination/reduction in a five-level dual T-type multilevel converter (MLC) drive. An advanced and fast model predictive control (MPC) approach is developed for CMV reduction (CMVR) and CMV elimination based on the preselection of the switching states (SS). In addition, the proposed approach considers the torque control and the capacitor balancing of the proposed drive as essential aspects of MLC drives. A detailed study of the impact of the converter SS on the CMV is presented. The main features of the proposed MPC approach are reducing the complexity of the cost-function, the tuning burden of the weighting factors, and the computation time by more than 80% compared to conventional MPC techniques. A hardware implementation based on Silicon Carbide T-type MLC is built. The experimental results demonstrate the effectiveness of the proposed MPC approach to mitigate/eliminate the CMV along with achieving the torque command and balancing the dc-link capacitors. Unlike conventional CMVR techniques, the proposed approach reduces the CMV by 75% of its normal values without jeopardizing the harmonic contents, drive efficiency, and flux as well as torque ripples.
Plant hydrocarbon recovery (1982)

A process for production and recovery of hydrocarbons from whole plants in a form suitable for use as chemical feedstocks or as hydrocarbon energy sources comprises: pulverizing by grinding or chopping the plants to a suitable particle size, drying and preheating the particles in a reducing atmosphere under positive pressure, passing the particles through a thermal conversion zone containing a reducing atmosphere and with a residence time of 1 s to approximately 30 min at approximately 200-1000 degrees, and separately recovering the condensable vapors as liquids and the noncondensable gases in a condition suitable for use as chemical feedstocks or as hydrocarbon fuels. Thus 1 g of dried Euphorbia marginata was thermally decomposed at 950/sup 0/. The respective yields of char, liquid products, CO, CO/sub 2/, CH/sub 4/, acetylene, ethylene, and total hydrocarbons were 31.1, 12.6, 13.3, 17.7, 3.9, 1.1, 4.0, and 21.6%.
Fast Growth of Thin Gate Dielectrics by Thermal Oxidation of Si in  N 2 O  Gas Ambient with Low Concentration of  NF 3 Addition (1993)

The effect of fluorine incorporation on the growth kinetics of silicon oxidation in ambient was studied. The oxidation was done by using a conventional thermal furnace with 100 ppm addition to the oxidant. The growth kinetics of oxide was found to follow a power law model. The added enhances the oxidation rate of the gas process several times higher than without this addition. A low thermal budget oxidation process and high quality thin dielectrics is achievable by using the combined effects of fluorine added to ambient.
A new mechanism for negative refraction and focusing using selective diffraction from surface corrugation (2007)

Refraction at a smooth interface is accompanied by momentum transfer normal to the interface. We show that corrugating an initially smooth, totally reflecting, non-metallic interface provides a momentum kick parallel to the surface, which can be used to refract light negatively or positively. This new mechanism of negative refraction is demonstrated by visible light and microwave experiments on grisms (grating-prisms). Single-beam all-angle-negative-refraction is achieved by incorporating a surface grating on a flat multilayered material. This negative refraction mechanism is used to create a new optical device, a grating lens. A planoconcave grating lens is demonstrated to focus plane microwaves to a point image. These results show that customized surface engineering can be used to achieve negative refraction even though the bulk material has positive refractive index. The surface periodicity provides a tunable parameter to control beam propagation leading to novel optical and microwave devices.
Selectivity of membrane electrodes based on derivatives of dibenzyltin dichloride (1991)

Selectivity properties are established for membrane electrodes prepared by incorporating bis(p-methylbenzyl)tin dichloride, dibenzyltin dichloride, and bis(p-chlorobenzyl)tin dichloride in plasticized polymer membranes. These electrodes display an unusually high level of selectivity for dibasic phosphate over many common anions. Electrodes prepared with the p-chloro derivative possess the best detection limit and the highest degree of selectivity for phosphate. Selectivity coefficients are calculated for phosphate relative to the following groups of anions: salicylate, benzoate, thiocyanate, iodide, nitrate, bromide, chloride, acetate, fluoride, pyrophosphate, arsenate, adenosine 5'-cyclic monophosphate, adenosine 5'-monophosphate, adenosine 5'-diphosphate, and adenosine 5'-triphosphate. Tin-carbon hyperconjugation within the organotin compound is hypothesized to be critically important in the selective response to phosphate. Enhancement of tin-carbon hyperconjugation by increasing the electron-withdrawing power of substituents on the benzyl ring is predicted to provide even higher levels of selectivity for phosphate.
Development of prolactin receptor antagonists with reduced pH‐dependence of receptor binding (2010)

The cytokine hormone prolactin has a vast number of diverse functions. Unfortunately, it also exhibits tumor growth promoting properties, which makes the development of prolactin receptor antagonists a priority. Prolactin binds to its cognate receptor with much lower affinity at low pH than at physiological pH and since the extracellular environment around solid tumors often is acidic, it is desirable to develop antagonists that have improved binding affinity at low pH. The pK(a) value of a histidine side chain is ∼6.8 making histidine residues obvious candidates for examination. From evaluation of known molecular structures of human prolactin, of the prolactin receptor and of different complexes of the two, three histidine residues in the hormone-receptor binding site 1 were selected for mutational studies. We analyzed 10 variants by circular dichroism spectroscopy, affinity and thermodynamic characterization of receptor binding by isothermal titration calorimetry combined with in vitro bioactivity in living cells. Histidine residue 27 was recognized as a central hot spot for pH sensitivity and conservative substitutions at this site resulted in strong receptor binding at low pH. Pure antagonists were developed earlier and the histidine mutations were introduced within such background. The antagonistic properties were maintained and the high affinity at low pH conserved. The implications of these findings may open new areas of research in the field of prolactin cancer biology.
Gate leakage in AlGaN/GaN HEMTs and its suppression by optimization of MOCVD growth (2005)

Gate-drain current-voltage characteristics in unpassivated AlGaN/GaN high electron mobility transistors (HEMTs) grown by metal-organic chemical vapor deposition (MOCVD) on sapphire substrates were investigated. Under a fixed V/III ratio for AlGaN layer growth, the growth window for getting low gate leakage and good two-dimensional electron gas mobility is narrow. We designed a multi-step growth of the AlGaN for HEMTs, i.e., high-V/III-ratio AlGaN layer starting from the AlGaN/GaN interface, then low-V/III-ratio AlGaN layer, which yielded the best 2DEG mobility and also reduced gate leakage. It was also found that the forward current and reverse current before pinch off can be explained by the thin surface barrier (TSB) model, and the AlGaN layer grown under lower effective V/III ratio shows a larger surface donor density but smaller leaky area. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Anti-HIV Activity of (−)-(2<i>R</i>,4<i>R</i>)-1- (2-Hydroxymethyl-1,3-dioxolan-4-yl)- thymine against Drug-Resistant HIV-1 Mutants and Studies of Its Molecular Mechanism (2005)

(-)-(2R,4R)-1-(2-Hydroxymethyl-1,3-dioxolan-4-yl)thymine (DOT) is the first thymidine kinase-activated nucleoside that is significantly active against all of the clinically significant NRTI-resistant HIV-1 mutants, including AZT (D67N/K70R/T215Y/K219Q), Tenofovir (K65R), and Lamivudine (M184V). To understand the molecular mechanism of drug resistance and the antiviral activity of DOT against drug-resistant RTs, molecular modeling studies of DOT-TP complexed with the wild-type (WT) and mutated RT were conducted. The key reason for this interesting antiviral activity profile is the presence of a dioxolane ring.
Intraocular Camera for Retinal Prostheses: Design Constraints Based on Visual Psychophysics (2007)

Optical system design constraints for an intraocular camera are determined by visual psychophysics techniques, including pixellation limits adequate for navigation and object identification, optimal pre- and post-pixellation blurring, and the elimination of gridding artifacts.
Incremental statistical static timing analysis with gate timing yield emphasis (2008)

Incremental analysis is indispensible for efficient circuit optimization, as it analyzes the effect by the modified circuit part only instead of analyzing a whole circuit again from beginning. This paper presents a new incremental statistical static timing analysis (SSTA) method, called timing yield-based incremental analysis (TYIA). TYIA uses the probability that the gate timing slack is non-negative to prune the timing change propagation after a gate replacement. In the experimental results using ISCAS-85 benchmarks, TYIA showed 2∼5 times better accuracy in timing yield analysis at comparable efficiency, when compared to the existing incremental SSTA methods.
Cloning, Sequencing, and Expression of the Cold-Inducible <i>hutU</i> Gene from the Antarctic Psychrotrophic Bacterium <i>Pseudomonas syringae</i> (2002)

A promoter-fusion study with a Tn 5-based promoter probe vector had earlier found that the hutU gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees C) in the Antarctic psychrotrophic bacterium Pseudomonas syringae. To examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutU and its upstream region from P. syringae were cloned, sequenced, and analyzed in the present study. Northern blot and primer extension analyses suggested that the hutU gene is inducible upon a downshift of temperature (22 to 4 degrees C) and that there is more than one transcription initiation site. One of the initiation sites was specific to the cells grown at 4 degrees C, which was different from the common initiation sites observed at both 4 and 22 degrees C. Although no typical promoter consensus sequences were observed in the flanking region of the transcription initiation sites, there was a characteristic CAAAA sequence at the -10 position of the promoters. Additionally, the location of the transcription and translation initiation sites suggested that the hutU mRNA contains a long 5'-untranslated region, a characteristic feature of many cold-inducible genes of mesophilic bacteria. A comparison of deduced amino acid sequences of urocanase from various bacteria, including the mesophilic and psychrotrophic Pseudomonas spp., suggests that there is a high degree of similarity between the enzymes. The enzyme sequence contains a signature motif (GXGX(2)GX(10)G) of the Rossmann fold for dinucleotide (NAD(+)) binding and two conserved cysteine residues in and around the active site. The psychrotrophic enzyme, however, has an extended N-terminal end.
Improved Multiscale Roughness Algorithm for Lunar Surface (2018)

The statistical analysis of surface roughness has been applied based on the roughness parameters calculated by the algorithms in spatial domain (SDAs). The morphological surface roughness (MSR), one of the SDAs based on the mathematical morphology, has been succeeded in mapping the lunar topographic roughness at multiscales. However, some typical roughness characteristics, such as the small sharp rock distribution and the inner irregular materials of craters, cannot be indicated on the multiscale MSR maps. In this paper, we improve the MSR method by utilizing the Fourier power spectra (FPS), which is applied to characterize these typical topographic variations by transforming them into their frequency forms. A synthesized parameter called improved morphological roughness (IMR) is designed for quantifying multiscale roughness based on the MSR and FPS values. Compared with the other methods (MSR, root mean square, multiscale morphological roughness, Fourier roughness, and kurtosis), IMR identifies more complicated roughness characteristics on the roughness map based on the Lunar Orbiter Laser Altimeter-derived digital elevation models (DEMs). For the multiscale analysis of different roughness maps, IMR can provide a stable scale-dependent distribution for the classifications of different terrains.
CLOSED-LOOP FEEDBACK CONTROL OF THE TURBULENT FLOW OVER A NACA-4412 AIRFOIL (2005)

We are developing methods to predict the dynamics of the flow field above a NACA-4412 airfoil using real-time measurements of the pressure from the surface of the airfoil only. Through Proper Orthogonal Decomposition (POD) and modified Linear Stochastic Measurement (mLSM) low-dimensional techniques (Lumley (1967), Adrian (1975), Taylor & Glauser (2004)) these pressure measurements are coupled to Particle Image Velocimetry (PIV) data of the flow to estimate the time dependent coefficients describing the flow. Based on a least-squares technique applied to the POD spatial modes, we obtain a system of ODEs that are solved to get the time-evolution of the POD coefficients, whereby an estimate of the evolution equation of the flow is obtained. This low-dimensional estimated plant will be used to explore different Proportional, Integral & Derivative (PID) control parameters and will enable us to implement a controller of the flow state above the airfoil using leading-edge zero net-mass flow actuators while pitching the airfoil.