gebhart/patrepeval huggingface dataset:
A Naturally Occurring Substitution in Human Immunodeficiency Virus Tat Increases Expression of the Viral Genome (2003)

A natural amino acid substitution in the human immunodeficiency virus type 1 (HIV-1) transcriptional activator Tat increases its activity and compensates for deleterious mutations elsewhere in the Tat protein. Substitution of asparagine for threonine 23 increases Tat transactivation of the HIV-1 promoter and the binding of Tat to the cellular kinase positive transcription elongation factor b (P-TEFb). Of nine other position 23 mutations tested, only the serine substitution retained wild-type activity. Correspondingly, asparagine is the most frequent amino acid at this position in HIV-1 isolates, followed by threonine and serine. Asparagine is prevalent in Tat proteins of viruses in clades A, C, and D, which are major etiologic agents of AIDS. We suggest that selection for asparagine in position 23 confers an advantage to the virus, since it can compensate for deleterious mutations in Tat. It may also support the replication of otherwise less fit drug-resistant viruses and permit the emergence of virulent strains.
ENHANCEMENTS AND APPLICATIONS OF THE CEMENT QUALITY PREDICTIVE SYSTEM (2013)

前報1）にて、セメント品質を予測するシステムの構築を行い、セメントキャラクターからそのプロパティーを予測することに成功した。本報告では、システムの実運用の結果、キャラクターとプロパティーをより良く関係付けるためには、工場単位でシステムを運用するべきとの結論を得た。また、さらなる予測精度向上のためにシステムを拡張し、プロセスデータ、キャラクターおよびプロパティーを相互に関連付けることを可能とした。これにより、キャラクターのみならず、プロセス条件から、プロパティーを制御することが可能になり、これまで以上に品質の安定化が達成される見込みを得た。
Engineer <i>P. multocida</i> Heparosan Synthase 2 (PmHS2) for Size-Controlled Synthesis of Longer Heparosan Oligosaccharides (2020)

<i>Pasteurella multocida</i> heparosan synthase 2 (PmHS2) is a dual-function polysaccharide synthase having both α1-4-N-acetylglucosaminyltransferase (α1-4-GlcNAcT) and β1-4-glucuronyltransferase (β1-4-GlcAT) activities located in two separate catalytic domains. We found that removing PmHS2 N-terminal 80-amino acid residues improved enzyme stability and expression level while retaining its substrate promiscuity. We also identified the reverse glycosylation activities of PmHS2 which complicated its application in size-controlled synthesis of oligosaccharides longer than hexasaccharide. Engineered Δ80PmHS2 single-function-glycosyltransferase mutants Δ80PmHS2_D291N (α1-4-GlcNAcT lacking both forward and reverse β1-4-GlcAT activities) and Δ80PmHS2_D569N (β1-4-GlcAT lacking both forward and reverse α1-4-GlcNAcT activities) were designed and showed to minimize side product formation. They were successfully used in a sequential one-pot multienzyme (OPME) platform for size-controlled high-yield production of oligosaccharides up to decasaccharide. The study draws attention to the consideration of reverse glycosylation activities of glycosyltransferases, including polysaccharide synthases, when applying them in the synthesis of oligosaccharides and polysaccharides. The mutagenesis strategy has the potential to be extended to other multifunctional polysaccharide synthases with reverse glycosylation activities to generate catalysts with improved synthetic efficiency.
Abstract 4928: Natural Endothelium Mimicking Self-Assembled Nanomatrix for Drug Eluting Stent Applications (2008)

Deployment of stents has been a major therapeutic method for treatment of cardiovascular diseases. However, poor endothelialization and intimal hyperplasia in bare metal stents lead to restenosis. Drug eluting stents (DES) are designed to deliver therapeutic drugs to prevent intimal hyperplasia and have been implanted in about 6 million patients for last three years. However, recent reports suggest that DES have been associated with a higher risk of late thrombosis which may be related to inadequate endothelialization. Therefore, the main goal of this project is to develop the next generation of DES using a natural endothelium mimicking self-assembled nanomatrix which will inhibit both restenosis and thrombosis while enhancing endothelialization from surrounding endothelium and endothelial progenitor cells circulating in the blood stream. The nanomatrix is formed by self-assembly of peptide amphiphiles (PAs) which contain nitric oxide (NO) producing donors and endothelial cell adhesive ligand YIGSR along with enzyme-mediated degradable sites. Successful synthesis of PAs and the self-assembly of the PAs into nanofibers with the diameter of 8 nm forming the nanomatrix were characterized by MALDI-TOF mass spectrometry and transmission electron microscope, respectively. The nanomatrix showed significantly greater attachment and spreading of human umbilical vein endothothelial cells (HUVECs) compared to human aortic smooth muscle cells (AoSMCs). The nanomatrix was reacted with NO solution and NO was released from the nanomatrix rapidly within 24 hours followed by sustained release over period of 5 days. The NO releasing nanomatrix demonstrated a significantly enhanced proliferation of HUVECs (51 ± 3 % to 67 ± 2 %) but reduced proliferation of AoSMCs (35 ± 2 % to 16 ± 3 %) after 48 hrs of incubation. Platelet attachment on the nanomatrix is under investigation. A natural endothelium mimicking nanomatrix was successfully synthesized and supported growth of endothelial cells while inhibiting growth of smooth muscle cells. Therefore this nanomatrix could have a great potential to improve clinical patency of DES as a coating material by enhancing endothelialization but reducing restenosis.
Characterization of a low-noise superconductor–insulator–superconductor-based microwave amplifier with local oscillator phase-adjusting architecture (2023)

This paper describes a low-noise microwave amplifier based on up- and down-frequency-conversion processes in quasiparticle superconductor–insulator–superconductor (SIS) tunnel junctions. The SIS amplifier was configured with two SIS frequency-converter modules and a cryogenic millimeter-wave isolator inserted between them. Moreover, a local oscillator (LO) using millimeter-wave attenuators and a phase shifter was considered. This setup allowed the control of individual LO power and differential phase in these SIS frequency converters to optimize the amplifier performance. The SIS amplifier showed noise temperatures as low as 11 K and a 6–8 dB gain from nearly DC to 5 GHz. The attained microwave performance is promising for obtaining large-format arrays, such as multibeam heterodyne receivers. Moreover, this two-frequency-converter concept based on SIS junctions might enable microwave applications, such as wideband non-reciprocal circuits in isolators, gyrators, and circulators, which are essential devices in the quantum computing and radio astronomy fields.
Image Reconstruction Using TOF Back Projection and a Deblurring Neural Network (2019)

The increasing timing resolution of PET/CT scanners has facilitated more precise localization of annihilation events, but has yet to achieve enough certainty to produce a crisp image in one step directly from raw data. Hence simple back-projection of time-of-flight (TOF) data, while very fast, produces a blurry output called a histo-image. This article proposes a novel reconstruction pipeline consisting of a back-projection of TOF sinograms to create an intermediate histo-image and a neural network to deblur the histo-image producing a crisp high quality reconstructed image. The proposed pipeline is tested on a simulated data set of 1,083 PET images and obtains a worst case normalized mean squared error of less than 0.1% and a SSIM measure of 0.9998. These results show the promise of combining TOF back-projection and a neural network to rapidly produce high quality images.
Automated measurement of alpha-amylase isoenzymes with 6(3)-deoxymaltotriose as selective amylase inhibitor (1995)

We developed an automated method for measurement of alpha-amylase isoenzymes in serum by a single kinetic assay (SKA) and a double kinetic assay (DKA) with 2-chloro-4-nitrophenyl-6(5)-azido-6(5)-deoxy-beta-maltopentaoside as a substrate and 6(3)-deoxymaltotriose (DOG3) as a novel selective amylase inhibitor. DOG3 showed a large difference in inhibitory activity between human pancreatic alpha-amylase (HPA; 86.9% inhibition) and salivary alpha-amylase (32.1% inhibition) at 0.33 mmol/L. Constant inhibition was obtained immediately after addition of DOG3. The inhibitory effect did not change with variation in concentrations of amylase up to approximately 3000 U/L. The results obtained by SKA correlated well with those obtained by three methods: monoclonal antibody (r = 0.988), wheat germ inhibitor (r = 0.989), and DKA (r = 0.995). The within-run and between-run CVs for HPA were 0.63-2.32% on SKA, 0.69-1.81% on DKA. No significant interferences by endogenous serum compounds were observed with the proposed methods.
Particle velocity estimation based on a two-microphone array and Kalman filter (2013)

A traditional method to measure particle velocity is based on the finite difference (FD) approximation of pressure gradient by using a pair of well matched pressure microphones. This approach is known to be sensitive to sensor noise and mismatch. Recently, a double hot-wire sensor termed Microflown became available in light of micro-electro-mechanical system technology. This sensor eliminates the robustness issue of the conventional FD-based methods. In this paper, an alternative two-microphone approach termed the u-sensor is developed from the perspective of robust adaptive filtering. With two ordinary microphones, the proposed u-sensor does not require novel fabrication technology. In the method, plane wave and spherical wave models are employed in the formulation of a Kalman filter with process and measurement noise taken into account. Both numerical and experimental investigations were undertaken to validate the proposed u-sensor technique. The results have shown that the proposed approach attained better performance than the FD method, and comparable performance to a Microflown sensor.
Molecular distinctions among clinical isolates of Mycoplasma pneumoniae (1990)

Restriction enzyme fingerprinting of genomic DNA and Southern blots probed with subclones of the Mycoplasma pneumoniae cytadhesin P1 gene were used to characterize clinical isolates of M. pneumoniae. On the basis of the examination of 29 individual M. pneumoniae isolates, two distinct groups were established. Group 1, which displayed a 12-kilobase band following DNA digestion with HindIII, consisted of strain M129-B16 and three others obtained in the state of Washington during the 1960s. The remaining M. pneumoniae strains belonged to group 2, which lacked the 12-kilobase band and included samples from the 1940s, 1970s, and 1980s. This category also included the only M. pneumoniae strain isolated from the synovial fluid of an arthritic patient.
Design of a folding inhibitor of the HIV-1 protease (2005)

A novel way to inhibit HIV-1 protease by destabilizing its native state is discussed. A simplified protein model is used together with Monte Carlo simulations, to assess the destabilizing effect of peptides displaying the same sequence as specific fragments of the protein which are essential for its stability. Model calculations also show that it is unlikely that the protein can escape the inhibitory peptide by point mutations.
3D Graphene Foam Reinforced Low‐Temperature Ceramic with Multifunctional Mechanical, Electrical, and Thermal Properties (2019)

Graphene foam reinforced multifunctional ceramic composite is fabricated in this study. Graphene foam has a 3D macroporous architecture, which is filled with a low temperature co‐fired (LTCC) ceramic phase. The composite microstructure is engineered by three‐step fabrication scheme: infiltration of porous graphene foam with ceramic slurry, solidification to form a green body, and finally, pressure and temperature‐assisted sintering to produce a dense composite with intimate ceramic/graphene interface. Graphene foam is found to retain its 3D structure. The interconnected network of nodes and branches induces superior fracture toughness, load‐bearing capacity, and thermal − electrical transport characteristics. Addition of mere 0.18 wt% graphene foam results in a 480% improvement in the fracture energy. Sub‐surface examination reveals extensive crack deflection due to graphene foam's cellular units, highlighting the advantage of a 3D filler. Graphene foam also induces an impressive electrical conductivity of 165 S m −1 in an otherwise insulator ceramic. In situ infrared thermal imaging demonstrates enhanced thermal transportability in ceramic due to graphene foam. These findings attest the significance of 3D graphene foam to develop multifunctional ceramic composites in load‐bearing structures, thermal management, and electro‐mechanical devices. The synthesis scheme presented here is promising for facile and scalable manufacturing of this new class of materials.
Development of a laboratory extreme-ultraviolet lithography tool (1994)

The development of a laboratory EUV lithography tool based on a laser plasma source, a 10x Schwarzchild camera, and a magnetically levitated wafer stage is presented. Interferometric measurements of the camera aberrations are incorporated into physical-optics simulations to estimate the EUV imaging performance of the camera. Experimental results demonstrate the successful matching of five multilayer reflecting surfaces, coated to specification for a wide range of figure and incidence angle requirements. High-resolution, 10x-reduction images of a reflection mask are shown.
Millimeter-Wave Oscillators Using Image-Line or Microstrip Waveguides (Short Paper) (1986)

A low-cost Gunn oscillator using a coaxial cavity coupled into either dielectric image guide or microstrip line has been developed. A unique feature is the broad frequency range off mechanical tunability of 10 to 11 GHz centered around 56 GHz. This range of tunability is beyond the range of standard metal waveguide cavities. Power levels up to 43 mW have been observed in image-line structures and 20 mW for microstrip lines. The construction allows an easy and quick replacement of diodes, when necessary hence, the structure is easily modified to operate in different ranges.
Structural and Functional Consequences of Haloenol Lactone Inactivation of Murine and Human Glutathione <i>S</i>-Transferase (1998)

Mass spectrometric analysis of proteolysis products of haloenol lactone-modified glutathione S-transferase isozyme mGSTP1 indicates that the haloenol lactone 3-cinnamyl-5(E)-bromomethylidenetetrahydro-2-furanone is covalently attached to the protein at Cys-47. Comparisons of the extent of adduct formation with losses in enzymatic activity indicate that mGSTP1 exhibits greatest reactivity toward the haloenol lactone, followed by mGSTM1 and mGSTA3. Activities of mGSTP1 and mGSTM1 decrease in inverse proportion to haloenol lactone concentration, whereas modification had no apparent effect on catalytic activity of mGSTA3. Decreases in activity agree with the extent of protein modification observed in ESI mass spectra for mGSTP1 and mGSTM1 but not for mGSTA3. Kinetic studies employing recombinant human proteins with replacement of cysteine by serine at Cys-47 and Cys-101 indicate that rapid inactivation (t1/2 = 2 min) occurs only when residue 47 is cysteine. Mass spectra of C47S-hGSTP1 incubated with haloenol lactone demonstrate covalent attachment of a haloenol lactone-glutathione conjugate and suggest that an ester forms between the lactone and Ser-47. Therefore, we propose that initial opening of the lactone ring is promoted by Cys-47 through thioester formation between the lactone carbonyl and the Cys-47 sulfhydryl. Enol-keto tautomerization and enzyme-mediated hydrolytic cleavage of the thioester produces a reactive alpha-bromoketone which reacts a second time with Cys-47 and inactivates the enzyme. These results suggest that Pi class GSTs have thioesterase activity and that haloenol lactone inactivation occurs through an enzyme-mediated process.
A novel conducting polyacetylene derivative (1978)

Doping of predominantly cis polyacetylene with FSO2OOSO2F in SO2F2 solutions at low temperatures yields materials that possess apparently metallic electrical conductivities with, for example, σRT= 700 Ω–1 cm–1, increasing to a maximum of 800 Ω–1 cm–1 at 150 K before declining to 640 Ω–1 cm–1 at 4·2 K.
Model-based correction of Coriolis mass flowmeters (2002)

Coriolis mass flowmeters (CMF) are direct mass flowmeters and form a real mean along the flow profile. They do not exploit secondary physical properties of the specific liquid, such as fluid velocity and fluid density in the measuring process, but directly exploit the primary property inertia to measure mass flow. However, there is some evidence from field applications that the devices, in particular those using a single straight pipe, suffer from parameter variation. Therefore, the flowmeter has to be carefully adjusted with respect to physical properties of the liquid, operating conditions, and site installation. When modeling the CMF using two oscillatory systems referring to the first and second mode, the mass flow enforces the coupling of these oscillatory systems. In the ideal case, the coupling is only affected by the mass flow. Detailed analysis, however, reveals that asymmetries in installation, sensors, actuators, as well as pipe-inhomogeneities heavily contribute to this coupling and thus lead to a parameter variation. In this paper, a model-based approach is presented to identify the parameters of the model using an auxiliary excitation of the system.
Cyclometalated <i>Z</i>-Selective Ruthenium Metathesis Catalysts with Modified N-Chelating Groups (2015)

In order to design improved ruthenium catalysts for Z-selective olefin metathesis reactions, four cyclometalated catalysts with new chelated architectures were synthesized, structurally characterized, and tested in metathesis assays. The mechanism of formation of each was explored using DFT calculations. Of note, two complexes are derived from activation of a tertiary C–H bond, and one features a four-membered chelating architecture. In addition, two dipivalate complexes that did not undergo further C–H activation were isolated and studied to elucidate information about the factors affecting cyclometalation.
A Numerical Solution to Groundwater Flow in Full Tensorial Permeability Fields (2006)

The description of flow through heterogeneous porous media is of primary interest to many fields such as reservoir engineering or hydrology. Because of porosity and permeability heterogeneity, flow equations are usually solved on the basis of numerical techniques. The discretization technique most commonly used is the finite-difference method. Thus, a conventional discretization scheme involves a 5 point stencil for two-dimensional media and a 7 point stencil for three-dimensional media. Continuity of flux and pressure is readily incorporated into the discretization by deriving the coefficients at the interface between adjacent gridblocks from the harmonic average of the permeabilities of the two contiguous gridblocks. This approximation holds as far as permeability tensor is diagonal. <br><br>Today, very detailed geological models are built on grids containing millions of gridblocks. Although computers are growing ever more powerful, fluid flow simulations on such grids are tremendously CPU-time consuming. To make them tractable, the number of gridblocks must be reduced to about 105. This motivated the development of techniques for upscaling the geological model to a manageable level of detail. Upscaling consists in determining the equivalent permeabilities of the coarse gridblocks. These equivalent permeabilities are usually full tensors. Discretization techniques in which interface fluxes are determined from more than two points have been developed to solve full tensorial flow equations. In this case, the discretization stencil requires 9 points for two dimensional media and even more for three-dimensional media. These techniques, known as multipoint flux approximations (MPFA) have recently enjoyed increased popularity. To date, to our knowledge, there is no straightforward generalization of the harmonic average to estimate fluxes at interfaces with MPFAs. <br><br>We develop an alternative to MPFAs based upon numerical spectral methods so that the full tensorial pressure equation is solved on regular grids. We also consider source or sink terms as well as gravity. Contrary to MPFAs, the proposed spectral technique does not call for any kind of approximation to estimate fluxes at the interface between adjacent gridblocks. Specific applications are presented and discussed.<br>
A low-cost architecture for the implementation of worst-case-fair schedulers in ATM switches (2002)

The discrete-rate approach has been proposed in Bennett et al. (1997) as a low-complexity solution for the implementation of worst-case-fair schedulers which approximate the generalized processor sharing (GPS) policy in ATM systems. The total implementation cost with this approach is even competitive with the cost of non-worst-case-fair schedulers implemented with conventional priority queues. Two discrete-rate techniques have been proposed. The one presented in Bennett et al. achieves near-optimal delay and fairness properties, but the discrete-rate scheduler needs to maintain a timestamp for each connection, which significantly contributes to the total cost. The second technique, presented in Chiussi and Francini (1998), does not require per-connection timestamps, and thus further reduces complexity; however, although the scheduler achieves near-optimal delay bounds and is worst-case fair, its fairness in distributing excess bandwidth is compromised. In this paper, we introduce a new discrete-rate technique for reducing the implementation cost of worst-case-fair GPS-related schedulers in ATM systems while maintaining near-optimal performance; the technique uses only a single bit per connection, and achieves delay bounds and fairness indices that are identical to the ones of the discrete-rate scheduler using per-connection timestamps. The new technique works well with the generalized discrete-rate approach presented in Chiussi and Francini to increase the number of discrete rates that the scheduler can support.
High‐frequency vaccine‐induced CD8<sup>+</sup> T cells specific for an epitope naturally processed during infection with <i>Mycobacterium tuberculosis</i> do not confer protection (2014)

Relatively few MHC class I epitopes have been identified from Mycobacterium tuberculosis, but during the late stage of infection, CD8(+) T-cell responses to these epitopes are often primed at an extraordinary high frequency. Although clearly available for recognition during infection, their role in resistance to mycobacterial infections still remain unclear. As an alternative to DNA and viral vaccination platforms, we have exploited a novel CD8(+) T-cell-inducing adjuvant, cationic adjuvant formulation 05 (dimethyldioctadecylammonium/trehalose dibehenate/poly (inositic:cytidylic) acid), to prime high-frequency CD8 responses to the immunodominant H2-K(b) -restricted IMYNYPAM epitope contained in the vaccine Ag tuberculosis (TB)10.4/Rv0288/ESX-H (where ESX is mycobacterial type VII secretion system). We report that the amino acid C-terminal to this minimal epitope plays a decisive role in proteasomal cleavage and epitope priming. The primary structure of TB10.4 is suboptimal for proteasomal processing of the epitope and amino acid substitutions in the flanking region markedly increased epitope-specific CD8(+) T-cell responses. One of the optimized sequences was contained in the closely related TB10.3/Rv3019c/ESX-R Ag and when recombinantly expressed and administered in the cationic adjuvant formulation 05 adjuvant, this Ag promoted very high CD8(+) T-cell responses. This abundant T-cell response was functionally active but provided no protection against challenge, suggesting that CD8(+) T cells play a limited role in protection against M. tuberculosis in the mouse model.