gebhart/patrepeval huggingface dataset:
Convergent Synthesis of Menaquinone-7 (MK-7) (2016)

A practical synthesis of menaquinone-7 (MK-7, vitamin K2) in the all-trans form was designed. Stereoselective synthesis of MK-7 was achieved through a “1 + 6” convergent strategy by condensation of two building blocks, menadione monoprenyl derivative (fragment “1”) with hexaprenyl bromide (fragment “6”, 82%). Pd-catalyzed desulfonation with LiEt3BH (78%) was followed by oxidation of the hydroquinone moiety using ammonium cerium(IV) nitrate (72%). The major challenge in our methodology was the preparation of all-trans hexaprenyl bromide by coupling of two triprenyl units derived from trans,trans-farnesol. Manufacturing on a pilot scale was accomplished through our approach. The scalable method was designed especially for a large, kilogram-scale production from easily available intermediates. Furthermore, the proposed methodology avoids many chromatographic purifications and allows for a relatively cost-effective manufacturing. Moreover, our synthesis yielded high-purity (99.9%) final product MK-7, which can be used as a dietary supplement as well as an active pharmaceutical ingredient.
Novel Diagnosis for Citrus Stubborn Disease by Detection of a <i>Spiroplasma citri</i>-Secreted Protein (2013)

Citrus stubborn disease (CSD), first identified in California, is a widespread bacterial disease found in most arid citrus-producing regions in the United States and the Mediterranean Region. The disease is caused by Spiroplasma citri, an insect-transmitted and phloem-colonizing bacterium. CSD causes significant tree damage resulting in loss of fruit production and quality. Detection of CSD is challenging due to low and fluctuating titer and sporadic distribution of the pathogen in infected trees. In this study, we report the development of a novel diagnostic method for CSD using an S. citri-secreted protein as the detection marker. Microbial pathogens secrete a variety of proteins during infection that can potentially disperse systemically in infected plants with the vascular flow. Therefore, their distribution may not be restricted to the pathogen infection sites and could be used as a biological marker for infection. Using mass spectrometry analysis, we identified a unique secreted protein from S. citri that is highly expressed in the presence of citrus phloem extract. ScCCPP1, an antibody generated against this protein, was able to distinguish S. citri-infected citrus and periwinkle from healthy plants. In addition, the antiserum could be used to detect CSD using a simple direct tissue print assay without the need for sample processing or specialized lab equipment and may be suitable for field surveys. This study provides proof of a novel concept of using pathogen-secreted protein as a marker for diagnosis of a citrus bacterial disease and can probably be applied to other plant diseases.
Color object detection using spatial-color joint probability functions (2006)

Object detection in unconstrained images is an important image understanding problem with many potential applications. There has been little success in creating a single algorithm that can detect arbitrary objects in unconstrained images; instead, algorithms typically must be customized for each specific object. Consequently, it typically requires a large number of exemplars (for rigid objects) or a large amount of human intuition (for nonrigid objects) to develop a robust algorithm. We present a robust algorithm designed to detect a class of compound color objects given a single model image. A compound color object is defined as having a set of multiple, particular colors arranged spatially in a particular way, including flags, logos, cartoon characters, people in uniforms, etc. Our approach is based on a particular type of spatial-color joint probability function called the color edge co-occurrence histogram. In addition, our algorithm employs perceptual color naming to handle color variation, and prescreening to limit the search scope (i.e., size and location) for the object. Experimental results demonstrated that the proposed algorithm is insensitive to object rotation, scaling, partial occlusion, and folding, outperforming a closely related algorithm based on color co-occurrence histograms by a decisive margin.
Development of nondestructive non-contact acousto-thermal evaluation technique for damage detection in materials (2012)

This paper presents the development of a new non-contact acousto-thermal signature (NCATS) nondestructive evaluation technique. The physical basis of the method is the measurement of the efficiency of the material to convert acoustic energy into heat, and a theoretical model has been used to evaluate this. The increase in temperature due to conversion of acoustic energy injected into the material without direct contact was found to depend on the thermal and elastic properties of the material. In addition, it depends on the experimental parameters of the acoustic source power, the distance between sample and acoustic source, and the period of acoustic excitation. Systematic experimental approaches to optimize each of the experimental variables to maximize the observed temperature changes are described. The potential of the NCATS technique to detect microstructural-level changes in materials is demonstrated by evaluating accumulated damage due to plasticity in Ti-6Al-4V and low level thermal damage in polymer matrix composites. The ability of the technique for macroscopic applications in nondestructive evaluation is demonstrated by imaging a crack in an aluminum test sample.
[Pharmacokinetic properties of Bilobalide and Ginkgolides A and B in healthy subjects after intravenous and oral administration of Ginkgo biloba extract (EGb 761)]. (1995)

The pharmacokinetics of Ginkgolide A, Ginkgolide B and Bilobalide, which are compounds extracted from the dried leaves of the Ginkgo biloba tree, were investigated in 12 young healthy volunteers (six men and six women; mean +/- SD age = 25 +/- 5 years) after single-dose administration of Ginkgo biloba extract. Subjects were given, on three occasions, Ginkgo biloba extract as a solution either orally (in fasting conditions and after a standard meal) or intravenously; corresponding to single doses of Ginkgolide A, Ginkgolide B and Bilobalide ranging from 0.90 mg to 3.36 mg. After each dosing, blood and urine samples were collected for up to 36 h and 48 h, for measurements of Ginkgolide A, Ginkgolide B and Bilobalide. Plasma and urine concentrations of these compounds were quantitatively measured by gas chromatography/mass spectrometry using negative chemical ionization, by applying a very sensitive method which allowed plasma concentrations as low as 0.2 ng/ml of each compound to be measured. When given orally, while fasting, the extents of bioavailability are high, as shown by bioavailability coefficients (FAUC) mean (+/- SD) values equal to 0.80 (+/- 0.09), 0.88 (+/- 0.21) and 0.79 (+/- 0.30) for Ginkgolide A, Ginkgolide B and Bilobalide respectively. Food intake does not change AUC quantitatively but increases Tmax. For the three compounds of interest, after oral dosing while fasting, differences can be noted for the elimination half-lives (T1/2Z), which exhibit mean values equal to 4.50, 10.57 and 3.21 h, as well as mean residence times (MRT), equal to 5.86, 11.25 and 4.89 h, for Ginkgolide A, Ginkgolide B and Bilobalide respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Fiber Composites of Metal–Organic Frameworks (2020)

The high chemical and structural diversity of metal–organic frameworks (MOFs), which are porous crystalline materials, has attracted significant academic and industrial interest. However, the poor processability of MOF powders limits their full potential in practical applications. Toward this end, MOF-based composite materials increase the framework robustness and subsequent utility. Among these hybrid materials, MOF composites prepared on commercially available textile fibers offer the high flexibility needed for important applications—such as heterogeneous catalysis, chemical sensing, pollutant removal, and drug release—while maintaining the functional properties of MOFs. The ability to further tailor these composites’ shapes for incorporation into industrial equipment increases their potential in applications such as adsorption devices and protective gears. In this Review, we summarize recently reported MOF/fiber fabrication methods and applications. Our discussion on the advancements and remaining issues of these production methods segues into several highlighted applications of MOF/fiber composites, especially within adsorption devices and protective gears.
Propagation of 1-µm Bubbles in Contiguous Disk Devices (1981)

Propagation margins of contiguous disk devices fabricated on both single- and double-layer garnet films have been measured. These performance measurements for 1-µm diameter magnetic bubble propagation were made on devices with cell sizes of 18 and 30 µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The dependence of bias margin on ion-implantation conditions, material parameters, propagation pattern geometries, and temperature is discussed. Deuterium implantation is introduced, together with a new propagation pattern. Implantation with deuterium induces an anisotropy field change similar to that with hydrogen but with 50% smaller dosage. The new propagation pattern, with sawtooth-shaped tracks, reduces the interaction between charged walls of adjacent propagation tracks, thus resulting in improved performance at low bias fields.
Results of network analyzer measurements with leakage errors-corrected with direct calibration techniques (1997)

Exact calibration procedures to correct two-port measurements with leakage errors are developed for a network analyzer having three or four measurement channels. Many measurement systems including open air devices, such as MMIC wafer probes, contain numerous crosstalk paths which are included in the full models of the direct calibration procedures. These novel 15-term and 22-term procedures are based on closed solutions and need five and six successive measurements of completely known calibration standards. First, both procedures solve these general error models exactly. The reduction of the common 22-term model to a 10-term model describes a network analyzer with three measurement channels in a simple and common manner. In this way one may create a great number of new calibration procedures. The sensitivity and accuracy of a direct 15-term and a direct 22-term error correction procedure is demonstrated by experimental results.
Xylose (glucose) isomerase gene from the thermophile Thermus thermophilus: cloning, sequencing, and comparison with other thermostable xylose isomerases (1991)

The xylose isomerase gene from the thermophile Thermus thermophilus was cloned by using a fragment of the Streptomyces griseofuscus gene as a probe. The complete nucleotide sequence of the gene was determined. T. thermophilus is the most thermophilic organism from which a xylose isomerase gene has been cloned and characterized. The gene codes for a polypeptide of 387 amino acids with a molecular weight of 44,000. The Thermus xylose isomerase is considerably more thermostable than other described xylose isomerases. Production of the enzyme in Escherichia coli, by using the tac promoter, increases the xylose isomerase yield 45-fold compared with production in T. thermophilus. Moreover, the enzyme from E. coli can be purified 20-fold by simply heating the cell extract at 85 degrees C for 10 min. The characteristics of the enzyme made in E. coli are the same as those of enzyme made in T. thermophilus. Comparison of the Thermus xylose isomerase amino acid sequence with xylose isomerase sequences from other organisms showed that amino acids involved in substrate binding and isomerization are well conserved. Analysis of amino acid substitutions that distinguish the Thermus xylose isomerase from other thermostable xylose isomerases suggests that the further increase in thermostability in T. thermophilus is due to substitution of amino acids which react during irreversible inactivation and results also from increased hydrophobicity.
A 2.9mW 53.4&#x2013;79.4GHz frequency-tracking injection-locked frequency divider with 39.2% locking range in 65nm CMOS (2012)

A frequency-tracking technique together with a single-coil distributed differential inductor is proposed to enhance the locking range of mm-Wave injection-locked frequency dividers (ILFDs). Implemented in a 65nm CMOS process, the proposed ILFD measures a locking range of 39.2% from 53.4GHz to 79.4GHz and consumes 2.9mW from a 0.8V supply corresponding to FOM of 8.97 GHz/mW while occupying an area of 0.126 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Survivable resource orchestration for optically interconnected data center networks (2013)

We propose resource orchestration schemes in overlay networks enabled by optical network virtualization. Based on the information from underlying optical networks, our proposed schemes provision the fewest data centers to guarantee K-connect survivability, thus maintaining resource availability for cloud applications under any failure.
Coherent tunneling and giant tunneling magnetoresistance in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mtext>Co</mml:mtext></mml:mrow><mml:mn>2</mml:mn></mml:msub><mml:mtext>FeAl</mml:mtext><mml:mo>/</mml:mo><mml:mtext>MgO</mml:mtext><mml:mo>/</mml:mo><mml:mtext>CoFe</mml:mtext></mml:mrow></mml:math>magnetic tunneling junctions (2010)

Spin-dependent coherent tunneling has been experimentally observed in high-quality sputtered-deposited ${\text{Co}}_{2}\text{FeAl}/\text{MgO}/\text{CoFe}$ epitaxial magnetic tunneling junctions (MTJs). Consequently, the microfabricated MTJs manifest a very large tunnel magnetoresistance (TMR) at room temperature and an unexpectedly TMR oscillation as a function of MgO barrier thickness. First-principles electronic band calculations confirm the pronounced coherent tunneling effect and are in good agreement with the experimental data. The present work demonstrates the importance of coherent tunneling for large TMR with Heusler alloys
Reverse Transcription of Threose Nucleic Acid by a Naturally Occurring DNA Polymerase (2016)

Recent advances in polymerase engineering have enabled the replication of xenonucleic acid (XNA) polymers with backbone structures distinct from those found in nature. By introducing a selective amplification step into the replication cycle, functional XNA molecules have been isolated by in vitro selection with binding and catalytic activity. Despite these successes, coding and decoding genetic information in XNA polymers remains limited by the fidelity and catalytic efficiency of engineered XNA polymerases. In particular, the process of reverse transcribing XNA back into DNA for amplification by PCR has been problematic. Here, we show that Geobacillus stearothermophilus (Bst) DNA polymerase I functions as an efficient and faithful threose nucleic acid (TNA)-dependent DNA polymerase. Bst DNA polymerase generates ∼twofold more cDNA with threefold fewer mutations than Superscript II (SSII), which was previously the best TNA reverse transcriptase. Notably, Bst also functions under standard magnesium-dependent conditions, whereas SSII requires manganese ions to relax the enzyme's substrate specificity. We further demonstrate that Bst DNA polymerase can support the in vitro selection of TNA aptamers by evolving a TNA aptamer to human α-thrombin.
Microwave assisted extraction of curcuminoids from<i>Curcuma longa</i> (2002)

A novel microwave assisted extraction (MAE) technique was investigated for selective and rapid extraction of curcuminoids from Curcuma longa (turmeric) into organic solvents. The degree of extraction and purity of curcuminoids were dependent upon the selected solvent and exposure time to microwaves. The extraction process was optimized using acetone at 20% power level (PL) giving 60% extraction of curcuminoids with 75% purity within 1 min. The dielectric heating of cellular matrix resulted in vaporization of volatile components, increasing internal pressure of the cell leading to remarkable swelling and finally rupturing of the cells. The degradation of cellulosic cell wall at higher temperature when subjected to microwave also increased permeability of solvents into the bio-matrix.
Water Detoxification by a Substrate‐Bound Catecholamine Adsorbent (2012)

A bio-inspired approach for detoxification of water has been investigated. In this approach, three major classes of toxic agents, heavy-metal ions (Cr, Hg, Pb, Cu, and Cd), toxic organic species (4-aminopyridine), and a radioisotope (Lutetium-177) were effectively removed from contaminated water by polydopamine, a mussel-inspired adhesive catecholamine (see figure). In addition, this polydopamine filter was easily regenerated by treatment with acid or hydrogen peroxide. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Abstract 872: APE1/Ref-1 as a serological biomarker for the detection of bladder cancer (2014)

Abstract Apurinic/apyrimidinic endonuclease1/redox factor-1 (APE1/Ref-1) is a DNA repair enzyme whose expression is increased in several forms of cancerous cells. We investigated whether serum APE1/Ref-1 is elevated in patients with bladder cancer. Tumor tissue and serum from patients with bladder cancer who had not received chemotherapy or radiotherapy (n=51) and non-tumor healthy controls (n=55) was used. In immunohistochemistry, and immunoblot analysis, the APE1/Ref-1 protein level of bladder tissues was increased in patients with bladder cancer. The serum APE1/Ref-1 levels were significantly elevated in bladder cancer patients than in those of non-tumor healthy controls and its levels were correlated with tumor staging and grading. The ROC curve of APE1/Ref-1 showed an excellent area under the ROC curve of 0.824. In this study, the optimal combination of sensitivity and specificity were determined as 93% and 59% for a cut-off value of serum APE1/Ref-1 of 2.83 ng/100 μl, respectively. The serum APE1/Ref-1 levels are increased in patients with bladder cancer with recurrence. These data indicate serum APE1/Ref-1 may help to identify patients with bladder cancer and it can be used as a serological marker of bladder cancer. Citation Format: Sunga Choi, Ju Hyun Shin, Yu Ran Lee, Myoung Soo Park, Chang Nam Yim, Young Gil Na, Jae Sung Lim, Byeong Hwa Jeon. APE1/Ref-1 as a serological biomarker for the detection of bladder cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 872. doi:10.1158/1538-7445.AM2014-872
Discovery, characterization, and structural analyses of glucan phosphatases from plants to humans (2012)

We initially demonstrated that the human phosphatase laforin and plant phosphatase S tarch EX cess4 (SEX4) are glucan phosphatases. Mutations in the gene encoding laforin cause glycogen to become hyperphosphorylated, resulting in starch‐like glucans called Lafora bodies (LBs) and the fatal neurodegenerative disorder Lafora's disease. Plant starch contains covalently bound phosphate at the C6‐ and C3‐position of glucosyl residues. Reversible phosphorylation of starch outer glucans renders these glucans accessible to hydrolyzing enzymes. In the absence of starch phosphorylation or dephosphorylation, plants accumulate excessively large starch granules that they are unable to breakdown. SEX4 activity is a necessary step in the starch degradation cycle of glucan phosphorylation, hydrolysis, and dephosphorylation. We utilized X‐ray crystallography to determine the structure of SEX4 and this structure assisted in the identification of L ike S ex F our2 (LSF2). Unlike SEX4, LSF2 lacks a carbohydrate‐binding module yet LSF2 binds starch. We found that SEX4 releases phosphate from the C3‐ and C6‐position, but prefers C6. Alternatively, LSF2 hydrolyzes phosphate from the C3‐position and plants lacking LSF2 have elevated C3‐bound phosphate. Lastly, we determined the crystal structure of LSF2 and utilize site‐directed mutagenesis with in vitro assays to define the structural elements of glucan phosphatases.
Method to determine printability of photomask defects and its use in phase-shift mask evaluations (1998)

Typically all defects found on a photomask are repaired, despite the fact that many of the defects would not cause problems on the wafer. Ideally, if the lithographic process does not image the defect onto the wafer in such a way as to adversely affect the performance of the device, then the mask maker should not be required to repair the defect -- saving time and money. It is difficult to classify defects in this manner, however, as the impact of the defect depends on various factors, including: lithography process parameters, proximity of defect to a critical feature, feature type and the size, shape, phase and transmission of the defect. These effects are further complicated by shrinking critical feature sizes and the use of resolution enhancement techniques, such as PSM and OPC. To address this problem, a new method of determining the printability of defects on all types of photomasks was developed. This method involves characterizing the aerial image of the defect and assigning an equivalent mask CD error to the defect. The equivalent CD error is then compared to the mask CD error specification to determine if the defect should be repaired. This methodology ties the mask defect specification directly to the device performance specifications and accounts for the multitude of factors that influence the defect printability in a real lithography process. This technique has been used to evaluate attenuated and alternating PSM.
Multilayer material characterization using thermographic signal reconstruction (2016)

Active-thermography has become a well-established Nondestructive Testing (NDT) method for detection of subsurface flaws. In its simplest form, flaw detection is based on visual identification of contrast between a flaw and local intact regions in an IR image sequence of the surface temperature as the sample responds to thermal stimulation. However, additional information and insight can be obtained from the sequence, even in the absence of a flaw, through analysis of the logarithmic derivatives of individual pixel time histories using the Thermographic Signal Reconstruction (TSR) method. For example, the response of a flaw-free multilayer sample to thermal stimulation can be viewed as a simple transition between the responses of infinitely thick samples of the individual constituent layers over the lifetime of the thermal diffusion process. The transition is represented compactly and uniquely by the logarithmic derivatives, based on the ratio of thermal effusivities of the layers. A spectrum of derivative responses relative to thermal effusivity ratios allows prediction of the time scale and detectability of the interface, and measurement of the thermophysical properties of one layer if the properties of the other are known. A similar transition between steady diffusion states occurs for flat bottom holes, based on the hole aspect ratio.