gebhart/patrepeval huggingface dataset:
Stimulation of the HIV‐1 integrase enzymatic activity and cDNA integration by a peptide derived from the integrase protein (2010)

Abstract Here we describe the features of a peptide that was selected from the human immunodeficiency virus Type 1 (HIV‐1) Integrase (IN) peptide library which interacts with both, the viral Rev and IN proteins. Because of its ability to stimulate the IN enzymatic activity this peptide was designated INS (IN stimulatory). Modification of its amino acid sequence revealed that replacement of its C‐terminal lysine by glutamic acid (INS K188E) converts it from a stimulatory peptide to an inhibitory one. Both peptides promoted the dissociation of a previously described complex formed between Rev and IN whose formation results in IN inactivation. INS and INS K188E penetrated HIV‐1‐infected cells and caused stimulation and inhibition of viral genome integration, respectively. Using cultured cells infected with a ΔRev HIV revealed that INS can directly activate the viral IN. These results suggest that the stimulatory effect of INS in wild‐type virus‐infected cells is due to a dual effect: it dissociates the inactive Rev‐IN complex and directly activates the free IN. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 740–751, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Error correction and partial information rewriting for flash memories (2014)

This paper considers the partial information rewriting problem for flash memories. In this problem, the state of information can only be updated to a limited number of new states, and errors may occur in memory cells between two adjacent updates. We propose two coding schemes based on the models of trajectory codes. The bounds on achievable code rates are shown using polar WOM coding. Our schemes generalize the existing rewriting codes in multiple ways, and can be applied to various practical scenarios such as file editing, log-based file systems and file synchronization systems.
Asymmetric Synthesis of an Endothelin Receptor Antagonist. (1999)

Two distinct synthetic approaches to the biologically active and structurally unique endothelin antagonist J-104132 (1) have been developed Each synthesis involves a highly selective intramolecular cyclization of a late stage intermediate (bottom to top vs top to bottom) produced from a common early intermediate. Both routes initially yielded multi-gram quantities of the desired product, with the former ultimately developed to pilot scale readiness. Several novel reactions have been developed throughout the course of our studies. These involve a mild bromination of a pyridone to form a bromopyridine, a mild and efficient TEMPO catalyzed oxidation of an alcohol to give a carboxylic acid, as well as a novel stereoselective samarium iodide mediated deoxygenation reaction. These reactions have proved to be quite general and have been applied to a wide variety of substrates.
Data from ONCR-177, an Oncolytic HSV-1 Designed to Potently Activate Systemic Antitumor Immunity (2023)

<div>Abstract<p>ONCR-177 is an engineered recombinant oncolytic herpes simplex virus (HSV) with complementary safety mechanisms, including tissue-specific miRNA attenuation and mutant UL37 to inhibit replication, neuropathic activity, and latency in normal cells. ONCR-177 is armed with five transgenes for IL12, FLT3LG (extracellular domain), CCL4, and antagonists to immune checkpoints PD-1 and CTLA-4. <i>In vitro</i> assays demonstrated that targeted miRNAs could efficiently suppress ONCR-177 replication and transgene expression, as could the HSV-1 standard-of-care therapy acyclovir. Although ONCR-177 was oncolytic across a panel of human cancer cell lines, including in the presence of type I IFN, replication was suppressed in human pluripotent stem cell–derived neurons, cardiomyocytes, and hepatocytes. Dendritic cells activated with ONCR-177 tumor lysates efficiently stimulated tumor antigen–specific CD8<sup>+</sup> T-cell responses. <i>In vivo</i>, biodistribution analyses suggested that viral copy number and transgene expression peaked approximately 24 to 72 hours after injection and remained primarily within the injected tumor. Intratumoral administration of ONCR-177 mouse surrogate virus, mONCR-171, was efficacious across a panel of syngeneic bilateral mouse tumor models, resulting in partial or complete tumor regressions that translated into significant survival benefits and to the elicitation of a protective memory response. Antitumor effects correlated with local and distant intratumoral infiltration of several immune effector cell types, consistent with the proposed functions of the transgenes. The addition of systemic anti–PD-1 augmented the efficacy of mONCR-171, particularly for abscopal tumors. Based in part upon these preclinical results, ONCR-177 is being evaluated in patients with metastatic cancer (ONCR-177-101, NCT04348916).</p></div>
Initial performance of large area neutron imager based on boron coated straws (2010)

US government plans to equip major seaports with large area neutron detectors, in an effort to intercept the smuggling of nuclear materials, have precipitated a critical shortage of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He gas. This is strongly limiting the prospects of neutron science, whose annual demand of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He is on the order of 20 kiloliters. Clearly, alternate neutron detection technologies that can support large sensitive areas, and have low gamma sensitivity and low cost must be developed. We propose a technology based on close-packed arrays of long aluminum tubes (straws), 4 mm in diameter, coated on the inside with a thin layer of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B-enriched boron carbide ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> C). In addition to the high abundance of boron on Earth and low cost of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B enrichment, the boron-coated straw (BCS) detector offers significant advantages over conventional <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He tubes in neutron imaging applications, including higher counting rate capability, parallax-free position decoding, lower cost, safer operation and a wide array of geometry configurations. A prototype imager with a 1 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> sensitive area has been developed and tested at ORNL's High Flux Isotope Reactor (HFIR). The imager incorporates 22 detector modules (only 1 with enriched B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> C), each consisting of a 5×10 close-packed array of aluminum straws. Straws were 4 mm in diameter, and 100 cm long, and lined with a nominal 1 μm thick coating of B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> C. The applied potential was 1150 V and the gas mixture was Ar/CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (90%/10%, continuous flow). Initial testing focused on detection efficiency over the range of neutron wavelengths present in the beam. Neutron time-of-flight data were collected and used to identify the energy of incident neutrons. A 30% efficiency was measured in the enriched module for 1.8 Å neutrons.
Selective Direct Synthesis of Trialkoxysilanes in a Packed Bed Flow Tubular Reactor (2016)

Trialkoxysilanes were synthesized in a packed bed flow tubular reactor by the reaction of silicon and alcohol in the presence of a variety of copper catalysts. The effect of key parameters, which affect the silicon conversion rates and selectivity for the desired trialkoxysilanes, were investigated and optimized using ethanol as the model reagent. The study was extended to the other alcohols namely methanol, n-propanol, and n-butanol. Copper catalysts which were tested in the alkoxylation reaction included CuCl, Cu(OH)2, CuO, and CuSO4; with CuCl showing the most activity while the uncatalysed reaction resulted in negligible reaction rates. High temperature catalyst preheating (>500 °C) resulted in a lower rate of reaction than when lower temperatures were used (<350 °C). The optimum reaction temperature range and alcohol flow rate were 230–240 °C and 0.1 mL/min, respectively. The reaction was deduced to be best described by the first-order kinetic model. The effect of alcohol (C1–C4) on the reaction revealed that conversion and selectivity generally decrease with an increase in carbon chain length. Ethanol showed the highest selectivity (97%) and conversion (64%) as compared to other alcohols studied, showing that it was the most efficient and stable alkoxylation alcohol for this reaction.
Accurate noninvasive measurement of cell size and compartment shape anisotropy in yeast cells using double‐pulsed field gradient MR (2011)

The accurate characterization of pore morphology is of great interest in a wide range of scientific disciplines. Conventional single-pulsed field gradient (s-PFG) diffusion MR can yield compartmental size and shape only when compartments are coherently ordered using q-space approaches that necessitate strong gradients. However, double-PFG (d-PFG) methodology can provide novel microstructural information even when specimens are characterized by polydispersity in size and shape, and even when anisotropic compartments are randomly oriented. In this study, for the first time, we show that angular d-PFG experiments can be used to accurately measure cellular size and shape anisotropy of fixed yeast cells employing relatively weak gradients. The cell size, as measured by light microscopy, was found to be 5.32 ± 0.83 µm, whereas the results from noninvasive angular d-PFG experiments yielded a cell size of 5.46 ± 0.45 µm. Moreover, the low compartment shape anisotropy of the cells could be inferred from experiments conducted at long mixing times. Finally, similar experiments were conducted in a phantom comprising anisotropic compartments that were randomly oriented, showing that angular d-PFG MR provides novel information on compartment eccentricity that could not be accessed using conventional methods. Angular d-PFG methodology seems to be promising for the accurate estimation of compartment size and compartment shape anisotropy in heterogeneous systems in general, and biological cells and tissues in particular.
Indole Derivatives as a New Class of Steroid 5α-Reductase Inhibitors (1996)

A series of indole derivatives with varied substituents on the alpha, beta-unsaturated double bond were synthesized and evaluated for their ability to inhibit rat prostatic 5 alpha-reductase. Compounds possessing an ethyl substituent at the beta-position of the double bond showed potent inhibitory activity. Among them, (Z)-4-{2-[[3-[1-(4,4'-difluorobenzhydryl)indol-5-yl]-2-pentenoy l]- amino]phenoxy}butyric acid (16, KF20405) showed the maximum potency with an IC50 value of 0.48 +/- 0.086 nM, which was 20-fold higher potency than 1 (MK-906). Compound 16 effectively inhibited DHT production 4 h after a 3 mg/kg oral administration. Several potent indole derivatives, 1 and 2 ((+/-)-ONO-3805), were tested versus rat and human isozymes. Nonsteroidal inhibitors such as indole derivatives and 2 were 2-3 orders of magnitude less potent for human type 2 isozyme than steroidal inhibitor 1 and expressed a significant species deference for these isozymes.
Development of the X'tal Cube: A 3D Position-Sensitive Radiation Detector With All-Surface MPPC Readout (2012)

We have developed a new three-dimensional (3D) position sensitive radiation detector, called the X'tal cube. The X'tal cube is composed of a scintillation crystal block and a number of multi-pixel photon counters (MPPCs) which are coupled on all six sides of the block. The block is segmented into cubes and no reflector is used between the segments. Scintillation light originating in a crystal segment accordingly propagates three-dimensionally along the alignment of the crystal segments and is efficiently detected by the MPPCs. The X'tal cube could be used as the detector element of a PET system, for instance. We constructed two prototypes of the X'tal cube and evaluated their performance using gamma-ray sources. The crystal block of each prototype is composed of a 3D array of Lu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2x</sub> Gd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2(1-x)</sub> SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> : Ce (LGSO, x = 0.9) crystal segments. Each crystal volume is 3.0 mm × 3.0 mm × 3.0 mm. MPPCs of a 3.0 mm × 3.0 mm active area are coupled to each surface of the crystal block. In this work, we show that all crystal segments are identified by a simple Anger-type calculation performed on the MPPC signals for both prototypes. The X'tal cube provides high spatial resolution in three dimensions regardless of the incident angle of the radiation.
Calibrating Canopy Reflectance Sensors to Predict Optimal Mid‐Season Nitrogen Rate for Cotton (2012)

Inadequate N supply can limit yield of cotton ( Gossypium hirsutum L.), while too much N can cause excessive vegetative growth and delayed maturity. Reflectance sensors offer the potential to diagnose N need and to translate this diagnosis into a variable‐rate application of N in real time. Our objective was to calibrate canopy reflectance sensors to predict economically optimal N rate (EONR) in support of variable‐rate fertilization. Nitrogen rate experiments were conducted on three soils in 2006 and 2007. Reflectance was measured with three sensors (Crop Circle, GreenSeeker, and Cropscan) at three growth stages (early square, mid‐square, and early flower) and at three heights above the canopy (25, 50, and 100 cm). Economically optimal N rate ranged from 0 to 220 kg N ha −1 , suggesting that the need to diagnose EONR is great. Relative reflectance for all three sensors was weakly related to EONR at the early square stage but was related more strongly at the mid‐square and early flower stages. Regression equations were not significantly different between mid‐square and early flower stages, suggesting that a single equation could be used to translate reflectance measurements to N rates over this period. Relationship to EONR was best for all sensors when placed 50 cm above the canopy. For these stages and height, all three sensors were similarly related to EONR ( r 2 = 0.59 to 0.62). These relationships could feasibly support successful variable‐rate N applications to cotton.
Treatment of Produced Water Using a Surfactant Modified Zeolite/Vapor Phase Bioreactor System (2006)

Co-produced water from the oil and gas industry accounts for a significant waste stream in the United States. Produced waters typically contain a high total dissolved solids content, dissolved organic constituents such as benzene and toluene, an oil and grease component as well as chemicals added during the oil-production process. It has been estimated that a total of 14 billion barrels of produced water were generated in 2002 from onshore operations (Veil, 2004). Although much of this produced water is disposed via reinjection, environmental and cost considerations can make surface discharge of this water a more practical means of disposal. In addition, reinjection is not always a feasible option because of geographic, economic, or regulatory considerations. In these situations, it may be desirable, and often necessary from a regulatory viewpoint, to treat produced water before discharge. It may also be feasible to treat waters that slightly exceed regulatory limits for re-use in arid or drought-prone areas, rather than losing them to reinjection. A previous project conducted under DOE Contract DE-AC26-99BC15221 demonstrated that surfactant modified zeolite (SMZ) represents a potential treatment technology for produced water containing BTEX. Laboratory and field experiments suggest that: (1) sorption of benzene, toluene, ethylbenzene and xylenes (BTEX) to SMZ follows linear isotherms in which sorption increases with increasing solute hydrophobicity; (2) the presence of high salt concentrations substantially increases the capacity of the SMZ for BTEX; (3) competitive sorption among the BTEX compounds is negligible; and, (4) complete recovery of the SMZ sorption capacity for BTEX can be achieved by air sparging the SMZ. This report summarizes research for a follow on project to optimize the regeneration process for multiple sorption/regeneration cycles, and to develop and incorporate a vapor phase bioreactor (VPB) system for treatment of the off-gas generated during air sparging. To this end, we conducted batch and column laboratory SMZ and VPB experiments with synthetic and actual produced waters. Based on the results of the laboratory testing, a pilot scale study was designed and conducted to evaluate the combined SMZ/VPB process. An economic and regulatory feasibility analysis was also completed as part of the current study to assess the viability of the process for various water re-use options.
Chinese Ink: A Powerful Photothermal Material for Solar Steam Generation (2018)

Abstract Solar steam generation holds great promise in alleviating fresh water crises, particularly in regions with accessible seawater and abundant insolation. Affordable, efficient, and environmentally friendly photothermal materials are needed to fabricate sunlight‐driven evaporation devices. Herein, Chinese ink, a carbon‐based paint used in traditional painting and calligraphy, is readily coated on diverse substrates and stabilized by atomic layer deposition (ALD) for solar steam generation. The ALD/Chinese ink coating exhibits strong and broad light absorption from the NIR to UV regions. Both ALD/Chinese‐ink‐coated membranes and wood display excellent photothermal properties and superior evaporation performance under simulated sunlight. This study demonstrates the potential of ALD/Chinese ink coating to achieve higher evaporation rate and efficiency by utilizing substrates with rough, structured surfaces and low thermal conductivity.
Planar very high aspect ratio microstructures for large loading forces (1996)

We report on a novel technology called Scream for High Aspect Ratio proportions (SHARP) which adds a new dimension to the Single Crystal Reactive Etching And Metallization (SCREAM) process. The fabrication technology increases the height and capacitive area of mechanical beams to improve the planarity and further extend the loading capabilities of very deep actuator structures. The process is based on a repeated sequence of thermal oxidations and reactive ion etches (RIE). Part of the technique consists of oxidizing through single crystal silicon (SCS) structural beams of a device by thermally growing a thick silicon dioxide (SiO2) layer (H2O2 precursors) after the first trench RIE etch, thus yielding an ultra-thick (>30 μm) SiO2 etch mask for further deep vertical etching (>100 μm) to form high aspect ratio structures.
[Cross-mixing test to detect lupus anticoagulant for diagnosis of antiphospholipid syndrome]. (2009)

The activated partial thromboplastin time (APTT) is generally used to screen for intrinsic coagulation factor deficiency. APTT prolongation suggests a bleeding tendency, although it can also reveal the presence of lupus anticoagulant (LA), which is one of the antiphospholipid antibodies associated with a high risk of thrombosis. Therefore, differential diagnosis in patients with a prolonged APTT is important. Recently, a cross mixing test has been proposed as a useful laboratory examination for differential diagnosis in these patients. When a cross-mixing test utilizes a mixture of patient and normal plasma at various ratios, the APTT value of the control plasma is prolonged by the addition of a small amount (10-20%) of the plasma from a patient with LA, while a prolonged APTT in a patient with an intrinsic coagulation factor deficiency is shortened by the addition of control plasma(50%). We obtained more favorable results for LA detection with a cross mixing test by measuring APTT in 5 different mixtures of control plasma and 0, 10, 20, 50, and 100% concentrations of patient plasma with an LA-sensitive APTT reagent such as PTT-LA. Also, we utilized a 0.2 microm filter unit to remove residual platelets from both patient and control plasma samples, which we recommend as useful. We found that a cross-mixing examination with appropriate samples and reagents contributed to the detection of LA. However, some problems remain regarding the final determination and quantitative measurements of LA.
Insights into the Mechanism of Tandem Alkene Hydroformylation over a Nanostructured Catalyst with Multiple Interfaces (2016)

The concept of tandem catalysis, where sequential reactions catalyzed by different interfaces in single nanostructure give desirable product selectively, has previously been applied effectively in the production of propanal from methanol (via carbon monoxide and hydrogen) and ethylene via tandem hydroformylation. However, the underlying mechanism leading to enhanced product selectivity has remained elusive due to the lack of stable, well-defined catalyst suitable for in-depth comprehensive study. Accordingly, we present the design and synthesis of a three-dimensional (3D) catalyst CeO2-Pt@mSiO2 with well-defined metal-oxide interfaces and stable architecture and investigate the selective conversion of ethylene to propanal via tandem hydroformylation. The effective production of aldehyde through the tandem hydroformylation was also observed on propylene and 1-butene. A thorough study of the CeO2-Pt@mSiO2 under different reaction and control conditions reveals that the ethylene present for the hydroformylation step slows down initial methanol decomposition, preventing the accumulation of hydrogen (H2) and favoring propanal formation to achieve up to 80% selectivity. The selectivity is also promoted by the fact that the reaction intermediates produced from methanol decomposition are poised to directly undergo hydroformylation upon migration from one catalytic interface to another. This synergistic effect between the two sequential reactions and the corresponding altered reaction pathway, compared to the single-step reaction, constitute the key advantages of this tandem catalysis. Ultimately, this in-depth study unravels the principles of tandem catalysis related to hydroformylation and represents a key step toward the rational design of new heterogeneous catalysts.