gebhart/patrepeval huggingface dataset:
Microbial degradation of the morphine alkaloids. Purification and characterization of morphine dehydrogenase from <i>Pseudomonas putida</i> M10 (1991)

The NADP(+)-dependent morphine dehydrogenase that catalyses the oxidation of morphine to morphinone was detected in glucose-grown cells of Pseudomonas putida M10. A rapid and reliable purification procedure involving two consecutive affinity chromatography steps on immobilized dyes was developed for purifying the enzyme 1216-fold to electrophoretic homogeneity from P. putida M10. Morphine dehydrogenase was found to be a monomer of Mr 32,000 and highly specific with regard to substrates, oxidizing only the C-6 hydroxy group of morphine and codeine. The pH optimum of morphine dehydrogenase was 9.5, and at pH 6.5 in the presence of NADPH the enzyme catalyses the reduction of codeinone to codeine. The Km values for morphine and codeine were 0.46 mM and 0.044 mM respectively. The enzyme was inhibited by thiol-blocking reagents and the metal-complexing reagents 1,10-phenanthroline and 2,2'-dipyridyl, suggesting that a metal centre may be necessary for activity of the enzyme.
Molecular and Biochemical Characterization of Novel Polyketide Synthases Likely to Be Involved in the Biosynthesis of Sorgoleone (2007)

Sorgoleone, an oily exudate secreted from the root hairs of sorghum (Sorghum bicolor (L.) Moench), acts as a potent allelochemical. Its phytotoxic properties make the elucidation of the biosynthetic enzymes participating in this pathway desirable. Previous studies suggest that the biosynthetic pathway of sorgoleone involves a polyketide synthase as well as a fatty acid desaturase, an O-methyl transferase, and a cytochrome P450 monooxygenase. This polyketide synthase is proposed to use a novel long chain fatty acyl-CoA (CI6:3) as a starter unit and catalyzes three iterative condensation reactions using malonyl-CoA to form a transient linear tetraketide that cyclizes to form a pentadecatriene resorcinol. To identify the polyketide synthase gene(s) involved in the biosynthesis of these alkylresorcinols, a root-hair specific EST (expressed sequence tag) collection was mined for potential candidates. A total of nine polyketide synthase-like EST's were identified representing five unique contigs, three of which were preferentially expressed in root hairs. The molecular and biochemical characterization of these three candidate polyketide synthases are presented, two of which represent a novel type of type III plant polyketide synthase.
New Structural Insights into Formation of the Key Actin Regulating WIP-WASp Complex Determined by NMR and Molecular Imaging (2017)

Wiskott-Aldrich syndrome protein (WASp) is exclusively expressed in hematopoietic cells and responsible for actin-dependent processes, including cellular activation, migration, and invasiveness. The C-terminal domain of WASp-Interacting Protein (WIP) binds to WASp and regulates its activity by shielding it from degradation in a phosphorylation dependent manner as we previously demonstrated. Mutations in the WAS-encoding gene lead to the primary immunodeficiencies Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT). Here, we shed a first structural light upon this function of WIP using nuclear magnetic resonance (NMR) and in vivo molecular imaging. Coexpression of fragments WASp(20-158) and WIP(442-492) allowed the purification and structural characterization of a natively folded complex, determined to form a characteristic pleckstrin homology domain with a mixed α/β-fold and central two-winged β-sheet. The WIP-derived peptide, unstructured in its free form, wraps around and interacts with WASp through short structural elements. Förster resonance energy transfer (FRET) and biochemical experiments demonstrated that, of these elements, WIP residues 454-456 are the major contributor to WASp affinity, and the previously overlooked residues 449-451 were found to have the largest effect upon WASp ubiquitylation and, presumably, degradation. Results obtained from this complementary combination of technologies link WIP-WASp affinity to protection from degradation. Our findings about the nature of WIP·WASp complex formation are relevant for ongoing efforts to understand hematopoietic cell behavior, paving the way for new therapeutic approaches to WAS and XLT.
<i>In Vitro</i> Bioactive Characteristics of Borate‐Based Glasses with Controllable Degradation Behavior (2006)

Silicate‐based bioactive glasses undergo incomplete conversion to a calcium phosphate material after in vivo implantation, which severely limits their biomedical application. In this communication, novel borate‐based glasses with controllable degradation behavior were developed and their bioactive potential was investigated in vitro . When immersed in a 0.02 M K 2 HPO 4 solution at 37°C, these glasses reacted to form a carbonate‐substituted hydroxyapatite (c‐HA) on their surfaces, indicating their bioactive potential. The conversion rate to c‐HA was controlled by adjusting the B 2 O 3 /SiO 2 ratio in the glass composition. The results indicate the potential application of the borate‐based bioactive glass as scaffold materials for bone tissue engineering.
Factors Controlling the Membrane Efficiency of Shales When Interacting With Water-Based and Oil-Based Muds (2006)

Abstract This paper presents a comprehensive set of experimental data for the membrane efficiency of four shales when interacting with different water-based and oil-based muds. Pressure transmission tests were used to measure the membrane efficiency using three different cations and two different anions at different concentrations (water activities). It was found that the measured membrane efficiencies of shales when exposed to salt solutions were low, ranging from 0.18% to 4.23%. Useful correlations are presented between the membrane efficiency and other shale properties. Results suggest that the membrane efficiency of shales is directly proportional to the ratio of the cation exchange capacity and permeability of shales. Higher cation exchange capacities and lower permeabilities correlate very well with higher membrane efficiencies. Moreover, the ratio of the hydrated solute (ion) size to shale pore throat determines a shale's ability to restrict solutes from entering the pore space and controls its membrane efficiency. Cations and anions with large hydrated radii yielded higher membrane efficiencies, compared to ions with small hydrated diameters. Thus, the formulation of drilling fluids must take into account the types of cation and anion in the water-based fluid. It was also found that the membrane efficiency of oil-based muds was high, however, these membrane efficiencies were not 100 % as postulated by many researchers.
USING PLANT CANOPY TEMPERATURE TO IMPROVE IRRIGATED CROP MANAGEMENT (2012)

Presented at Proceedings of the 24th annual Central Plains irrigation conference held on February 21-22 in Colby, Kansas.
Planar leaky-wave microstrip antenna (2002)

In a single microstripline, the dominant mode is "quasi" TEM, which is a non-radiating surface mode. The higher-order modes, however, become leaky when the propagation constant is less than that of the free-space wave number, k/sub 0/. One of the simplest ways to realize a leaky-wave antenna is to use a regular microstripline properly excited by a coaxial probe. The major problems in this case are input impedance matching and suppression of surface-mode excitations. In the proposed antenna, a double-layer microstrip structure is used to facilitate the impedance variation at the feed. The field distribution at the feed location is altered to match the input impedance by varying the locations and widths of the metallic patches on the two layers. Once the input impedance is matched to a particular leaky mode propagation, the surface modes will be likely to be suppressed because of impedance mismatch to all modes other than the intended leaky mode. Compared with other leaky-wave antennas, the proposed antenna is planar and can be easily implemented in an MMIC environment.
An arrayed hot-film sensor for detection of laminar boundary-layer flow disturbance spatial characteristics (1988)

An arrayed hot-film sensor has been developed for use in laminar boundary-layer research for the detection of crossflow or Goertler vortices. This sensor has been developed to detect spatial variations in heat transfer which are characteristic of crossflow or Goertler vortices. The sensor is ultimately intended for flight research applications. This paper describes the sensor, its priciples of operation, signal analysis techniques, and experimental results illustrating the spatial detection capabilities of this specialized hot-film device. Discretely placed spheres placed in the boundary layer created alternating regions of undisturbed and disturbed laminar flow over a prototype sensor. Flow visualization results were correlated with the sensor output to demonstrate the ability of the sensor to determine the spatial boundaries of localized disturbances in laminar flow. This work represents the initial steps toward the validation and calibration of an arrayed hot-film sensor for the detection of crossflow or Goertler vorticity wavelength and/or wave frequency.
Aqueous Dispersions of Few-Layered and Monolayered Hexagonal Boron Nitride Nanosheets from Sonication-Assisted Hydrolysis: Critical Role of Water (2011)

Hexagonal boron nitride (h-BN) is traditionally considered to be insoluble in water. However, here we demonstrate that water is effective to exfoliate the layered h-BN structures with the assistance of bath sonication, forming “clean” aqueous dispersions of h-BN nanosheets without the use of surfactants or organic functionalization. Besides few-layered h-BN nanosheets, there was also evidence on the presence of monolayered nanosheet and nanoribbon species. Most nanosheets were of reduced lateral sizes, which was attributed to the cutting of parent h-BN sheets induced by the sonication-assisted hydrolysis (evidenced by the ammonia test and spectroscopy results). The hydrolysis effect also assisted in the exfoliation of h-BN nanosheets in addition to the solvent polarity effect. The h-BN nanosheets in such “clean” aqueous dispersions were demonstrated to be conveniently processed via solution methods with retained physical properties. The dispersed h-BN nanosheets in water also exhibited strong affinity toward proteins such as ferritin, suggesting that the nanosheet surfaces were available for further bioconjugations. The above findings may pave the way for the applications of these novel 2-dimensional nanomaterials in various fields such as composites, electronics, and biology.
Cyclotribenzoin (2015)

Using cyanide-assisted benzoin condensation of isophthaldehyde, we prepared cyclotribenzoin: a cone-shaped macrocycle whose three benzene rings define a cuplike cavity, while six of its C–H bonds convergently point in the opposite direction. This combination of convergently oriented cation- and anion-binding groups, coupled with an exceedingly simple synthesis, promises to make cyclotribenzoin an appealing platform for supramolecular chemistry studies.
Resolution enhancement in single-shot imaging using simultaneous acquisition of spatial harmonics (SMASH) (1999)

Spatial resolution in single-shot imaging is limited by signal attenuation due to relaxation of transverse magnetization. This effect can be reduced by minimizing acquisition times through the use of short interecho spacings. However, the minimum interecho spacing is constrained by limits on gradient switching rates, radiofrequency (RF) power deposition and RF pulse length. Recently, simultaneous acquisition of spatial harmonics (SMASH) has been introduced as a method to acquire magnetic resonance images at increased speeds using a reduced number of phase-encoding gradient steps by extracting spatial information contained in an RF coil array. In this study, it is shown that SMASH can be used to reduce the effects of relaxation, resulting in single-shot images with increased spatial resolution without increasing imaging time. After a brief theoretical discussion, two strategies to reduce signal attenuation and increase spatial resolution in single-shot imaging are introduced and their performance is evaluated in phantom studies. In vivo single-shot echoplanar imaging (EPI), BURST, and half-Fourier single-shot turbo spin-echo (HASTE) images are then presented demonstrating the practical implementation of these resolution enhancement strategies. Images acquired with SMASH show increased spatial resolution and improved image quality when compared with images obtained with the conventional acquisitions. The general principles presented for imaging with SMASH can also be applied to other partially parallel imaging techniques.
Self-Interference Cancellation Limits in Full-Duplex Communication Systems (2016)

A good self-interference (SI) cancellation strategy in full-duplex (FD) communication passes first by a proper understanding of the nature of this SI. In this paper, we investigate the basic causes of SI cancellation bottlenecks in FD. To that end, we first classify the known FD architectures based on where the reference signal is taken to cancel the SI. By combining the effects of transceiver impairment, estimation error and SI channel, our analysis reveals that the the main bottleneck to completely cancel the SI turns out to be either the quantization-noise, the phase-noise in the local oscillator or the estimation error, depending on the used architecture.
Moving Object Detection on a Runway Prior to Landing Using an Onboard Infrared Camera (2007)

Determining the status of a runway prior to landing is essential for any aircraft, whether manned or unmanned. In this paper, we present a method that can detect moving objects on the runway from an onboard infrared camera prior to the landing phase. Since the runway is a planar surface, we first locally stabilize the sequence to automatically selected reference frames using feature points in the neighborhood of the runway. Next, we normalize the stabilized sequence to compensate for the global intensity variation caused by the gain control of the infrared camera. We then create a background model to learn an appearance model of the runway. Finally, we identify moving objects by comparing the image sequence with the background model. We have tested our system with both synthetic and real world data and show that it can detect distant moving objects on the runway. We also provide a quantitative analysis of the performance with respect to variations in size, direction and speed of the target.
Solubilization of coal by chemical process (1986)

The invention involves exposing coal to an oxidizing agent such as nitric acid, hydrogen peroxide, or ozone. It is preferable to maximize the surface area of the coal to accelerate oxidation; therefore, coal is broken and crushed into small pieces. The coal is then placed in an oxidizing solution for a sufficient period of time to render it susceptible to solubilization. Exposure to oxidizing agent at 30/sup 0/C for about two days gives good results, although these parameters are not critical. After oxidation, the treated coal is placed in a base solution. Since the original studies were aimed at determining if certain microorganisms could solubilize coal after oxidation pretreatment, the base solutions used for study were organic buffer solutions ordinarily used in biological studies. Although most tests were done with such bases, it was found that a simple sodium hydroxide solution was also very effective, and therefore, it is believed that the critical factor is pH and not the identity of the base; thus, any base would be suitable for use in this solubilization process. The coal can be washed prior to exposure to the base to remove oxidizing agent that might tend to lower the pH of the solubilizingmore » solution. Shaking the coal and base solution can enhance the solubilization process, although it isn't necessary. After two days exposure under ambient conditions, coal is significantly solubilized and can be separated from the solute by centrifugation and filtration.« less
On the guaranteed failing and working frequencies in path delay fault analysis (2003)

When running a set of test vectors to detect path delay faults in a digital system, desired test frequencies are needed. In this paper we determine the guaranteed failure frequency (GFF) and the guaranteed working frequency (GWF) for a given set of test vectors used for path delay testing of a sequential circuit. If the circuit passes the test when the vectors are applied at GFF, then all paths activated by those vectors are guaranteed to be free from delay faults provided the clock frequency does not exceed the GWF. Ambiguity cancellation and minmax-delay or statistical-delay modeling techniques are used in a timing simulation system to determine GFF and GWF. Experiments show that by using the guaranteed failure frequency, we can obtain the best (most reliable) path delay fault coverage provided by the given test vectors.
Flying triangulation—an optical 3D sensor for the motion-robust acquisition of complex objects (2012)

Three-dimensional (3D) shape acquisition is difficult if an all-around measurement of an object is desired or if a relative motion between object and sensor is unavoidable. An optical sensor principle is presented-we call it "flying triangulation"-that enables a motion-robust acquisition of 3D surface topography. It combines a simple handheld sensor with sophisticated registration algorithms. An easy acquisition of complex objects is possible-just by freely hand-guiding the sensor around the object. Real-time feedback of the sequential measurement results enables a comfortable handling for the user. No tracking is necessary. In contrast to most other eligible sensors, the presented sensor generates 3D data from each single camera image.
Algebraic soft-decision decoding of reed-solomon codes (2003)

A polynomial-time soft-decision decoding algorithm for Reed-Solomon codes is developed. This list-decoding algorithm is algebraic in nature and builds upon the interpolation procedure proposed by Guruswami and Sudan(see ibid., vol.45, p.1757-67, Sept. 1999) for hard-decision decoding. Algebraic soft-decision decoding is achieved by means of converting the probabilistic reliability information into a set of interpolation points, along with their multiplicities. The proposed conversion procedure is shown to be asymptotically optimal for a certain probabilistic model. The resulting soft-decoding algorithm significantly outperforms both the Guruswami-Sudan decoding and the generalized minimum distance (GMD) decoding of Reed-Solomon codes, while maintaining a complexity that is polynomial in the length of the code. Asymptotic analysis for alarge number of interpolation points is presented, leading to a geo- metric characterization of the decoding regions of the proposed algorithm. It is then shown that the asymptotic performance can be approached as closely as desired with a list size that does not depend on the length of the code.
Use of KRS-XE positive chemically amplified resist for optical mask manufacturing (2002)

The traditional mask making process uses chain scission-type resists such as PBS, poly(butene-1-sulfone), and ZEP, poly(methyl a-chloroacrylate-co-a-methylstyrene) for making masks with dimensions greater than 180nm. PBS resist requires a wet etch process to produce patterns in chrome. ZEP was employed for dry etch processing to meet the requirements of shrinking dimensions, optical proximity corrections and phase shift masks. However, ZEP offers low contrast, marginal etch resistance, organic solvent development, and concerns regarding resist heating with its high dose requirements1. Chemically Amplified Resist (CAR) systems are a very good choice for dimensions less than 180nm because of their high sensitivity and contrast, high resolution, dry etch resistance, aqueous development, and process latitude2. KRS-XE was developed as a high contrast CA resist based on ketal protecting groups that eliminate the need for post exposure bake (PEB). This resist can be used for a variety of electron beam exposures, and improves the capability to fabricate masks for devices smaller than 180nm. Many factors influence the performance of resists in mask making such as post apply bake, exposure dose, resist develop, and post exposure bake. These items will be discussed as well as the use of reactive ion etching (RIE) selectivity and pattern transfer.
Nanoscale structure and superhydrophobicity of sp<sup>2</sup>-bonded boron nitride aerogels (2015)

Aerogels have much potential in both research and industrial applications due to their high surface area, low density, and fine pore size distribution. Here we report a thorough structural study of three-dimensional aerogels composed of highly crystalline sp(2)-bonded boron nitride (BN) layers synthesized by a carbothermic reduction process. The structure, crystallinity and bonding of the as-prepared BN aerogels are elucidated by X-ray diffraction, (11)B nuclear magnetic resonance, transmission electron microscopy, and resonant soft X-ray scattering. The macroscopic roughness of the aerogel's surface causes it to be superhydrophobic with a contact angle of ∼155° and exhibit high oil uptake capacity (up to 1500 wt%). The oil can be removed from the BN aerogel by oxidizing in air without damaging the crystalline porous structure of the aerogel or diminishing its oil absorption capacity.
Improvement of the Thermostability and Activity of a Pectate Lyase by Single Amino Acid Substitutions, Using a Strategy Based on Melting-Temperature-Guided Sequence Alignment (2007)

In the vast number of random mutagenesis experiments that have targeted protein thermostability, single amino acid substitutions that increase the apparent melting temperature (Tm) of the enzyme more than 1 to 2 degrees C are rare and often require the creation of a large library of mutated genes. Here we present a case where a single beneficial mutation (R236F) of a hemp fiber-processing pectate lyase of Xanthomonas campestris origin (PL(Xc)) produced a 6 degrees C increase in Tm and a 23-fold increase in the half-life at 45 degrees C without compromising the enzyme's catalytic efficiency. This success was based on a variation of sequence alignment strategy where a mesophilic amino acid sequence is matched with the sequences of its thermophilic counterparts that have established Tm values. Altogether, two-thirds of the nine targeted single amino acid substitutions were found to have effects either on the thermostability or on the catalytic activity of the enzyme, evidence of a high success rate of mutation without the creation of a large gene library and subsequent screening of clones. Combination of R236F with another beneficial mutation (A31G) resulted in at least a twofold increase in specific activity while preserving the improved Tm value. To understand the structural basis for the increased thermal stability or activity, the variant R236F and A31G R236F proteins and wild-type PL(Xc) were purified and crystallized. By structure analysis and computational methods, hydrophobic desolvation was found to be the driving force for the increased stability with R236F.