gebhart/patrepeval huggingface dataset:
Recombinant <i>E. coli</i> Prototype Strains for <i>in Vivo</i> Glycorandomization (2010)

In vitro glycorandomization is a powerful strategy to alter the glycosylation patterns of natural products and small molecule therapeutics. Yet, such in vitro methods are often difficult to scale and can be costly given the requirement to provide various nucleotides and cofactors. Here, we report the construction of several recombinant E. coli prototype strains that allow the facile production of a range of small molecule glycosides. This strategy relies on the engineered promiscuity of three key enzymes, an anomeric kinase, a sugar-1-phosphate nucleotidyltransferase, and a glycosyltransferase, as well as the ability of diverse small molecules to freely enter E. coli. Subsequently, this work is the first demonstration of "in vivo glycorandomization" and offers vast combinatorial potential by simple fermentation.
Rapid room temperature solubilization and depolymerization of polymeric lignin at high loadings (2016)

The relatively poor solubility of lignin in most pretreatment solvents remains one of the biggest challenges in lignin valorization to improve overall biorefinery economics.
Cardiac Ablation Catheter Guidance by Means of a Single Equivalent Moving Dipole Inverse Algorithm (2013)

Background We developed and evaluated a novel system for guiding radiofrequency catheter ablation therapy of ventricular tachycardia. This guidance system employs an inverse solution guidance algorithm (ISGA) using a single equivalent moving dipole (SEMD) localization method. The method and system were evaluated in both a saline tank phantom model and in vivo animal (swine) experiments. Methods A catheter with two platinum electrodes spaced 3 mm apart was used as the dipole source in the phantom study. A 40‐Hz sinusoidal signal was applied to the electrode pair. In the animal study, four to eight electrodes were sutured onto the right ventricle. These electrodes were connected to a stimulus generator delivering 1‐ms duration pacing pulses. Signals were recorded from 64 electrodes, located either on the inner surface of the saline tank or on the body surface of the pig, and then processed by the ISGA to localize the physical or bioelectrical SEMD. Results In the phantom studies, the guidance algorithm was used to advance a catheter tip to the location of the source dipole. The distance from the final position of the catheter tip to the position of the target dipole was 2.22 ± 0.78 mm in real space and 1.38 ± 0.78 mm in image space (computational space). The ISGA successfully tracked the locations of electrodes sutured on the ventricular myocardium and the movement of an endocardial catheter placed in the animal's right ventricle. Conclusion In conclusion, we successfully demonstrated the feasibility of using an SEMD inverse algorithm to guide a cardiac ablation catheter.
Electrospinning Bioactive Supramolecular Polymers from Water (2014)

Electrospinning is a high-throughput, low-cost technique for manufacturing long fibers from solution. Conventionally, this technique is used with covalent polymers with large molecular weights. We report here the electrospinning of functional peptide-based supramolecular polymers from water at very low concentrations (<4 wt %). Molecules with low molecular weights (<1 kDa) could be electrospun because they self-assembled into one-dimensional supramolecular polymers upon solvation and the critical parameters of viscosity, solution conductivity, and surface tension were optimized for this technique. The supramolecular structure of the electrospun fibers could ensure that certain residues, like bioepitopes, are displayed on the surface even after processing. This system provides an opportunity to electrospin bioactive supramolecular materials from water for biomedical applications.
Zero-reflectivity homogeneous layers and high spatial-frequency surface-relief gratings on lossy materials (1987)

The required thickness and complex refractive index of single homogeneous layers on lossy substrates to produce zero reflectivity are calculated by a rigorous impedance matching approach. The analysis is applicable to both TE and TM polarization and to any angle of incidence. The filling factor and groove depth of a rectangular-groove grating, equivalent to a single homogeneous lossy layer in the long-wavelength limit, are calculated. The method reduces to that previously found for dielectric surface-relief gratings in the limit of no losses. The antireflection behavior of the gratings is verified using the rigorous (without approximations) coupled-wave analysis of metallic surface-relief grating diffraction. It is shown that multiple zeroreflectivity solutions exist for both TE and TM polarizations and for any angle of incidence for an arbitrary complex-refractive-index substrate. Example zero-reflectivity gold gratings for incident free space wavelengths from 0.44 to 12.0 microm are presented.
Hydrocarbon Saturation From Total Organic Carbon Logs Derived From Inelastic and Capture Nuclear Spectroscopy (2013)

Abstract The accurate determination of formation hydrocarbon or water saturation is an essential step in the petrophysical evaluation of petroleum reservoirs. A novel method has been developed for estimating hydrocarbon saturation directly from a total organic carbon (Corg) log and a porosity log. The method is enabled by the recent development of a pulsed-neutron logging tool that combines inelastic and capture gamma ray spectroscopy measurements to provide a robust and accurate total organic carbon estimate. The method differs from the well-known approach of using carbon-to-oxygen ratios that is most often applied in cased-hole evaluation. The main advantages of this new method are that it does not require knowledge of formation water resistivity, it does not rely on a resistivity model, it does not require an extensive calibration database, and it is largely independent of clay or other lithology effects. Calculations are available to explore uncertainties in the saturation estimates arising from uncertainties in the log inputs. The statistical uncertainty in the estimate of hydrocarbon saturation is as good as 10 saturation units (s.u.) in conventional reservoirs with porosities of 15 p.u. or greater. The method has been applied to the determination of hydrocarbon saturation in a variety of formations, including bitumen-filled dolomite, heavy oil sand, and shaly sands with both open-hole and cased-hole wells. The method works equally well in formations drilled and logged with either oil- or water-based mud. The saturation estimates have been benchmarked against a combination of conventional and new logging approaches (e.g., resistivity, magnetic resonance, and dielectric logs) and core measurements, with generally excellent agreement among independent determinations. Hydrocarbon saturations can be determined accurately using the method in a number of formation types where conventional methods and models for estimating fluid saturation commonly fail, such as freshwater and unknown water salinity in formations under enhanced oil recovery. The case studies demonstrate that a Corg log derived from geochemical spectroscopy logs can be used to obtain reliable estimates of hydrocarbon saturation in a wide range of environmental conditions and formations.
Axially uniform resonant cavity modes for potential use in electron paramagnetic resonance spectroscopy (2001)

This article is concerned with cylindrical transverse electric TE011 and rectangular TE102 microwave cavity resonators commonly used in electron paramagnetic resonance (EPR) spectroscopy. In the cylindrical mode geometry considered here, the sample is along the z axis of the cylinder, dielectric disks of 1/4 wavelength thickness are placed at each end wall, and the diameter of the cylinder is set at the cutoff condition for propagation of microwave energy in a cylindrical waveguide at the desired microwave frequency. The microwave magnetic field is exactly uniform along the sample in the region between the dielectric disks and the resonant frequency is independent of the length of the cylinder without limit. The rectangular TE102 geometry is analogous, but here the microwave magnetic field is exactly uniform in a plane. A uniform microwave field along a line sample is highly advantageous in EPR spectroscopy compared with the usual sinusoidal variation, and these geometries are called “uniform field” modes. Extensive theoretical analysis as well as finite element calculation of field patterns are presented. The perturbation of field patterns caused by sample insertion as functions of the overall length of the resonator and diameter of the sample is analyzed. The article is intended to provide a basis for design of practical structures in the range of 10 to 100 GHz.
Palladium‐Catalyzed Formal Cross‐Coupling of Diaryl Ethers with Amines: Slicing the 4‐<i>O</i>‐5 Linkage in Lignin Models (2018)

Lignin is the second most abundant organic matter on Earth, and is an underutilized renewable source for valuable aromatic chemicals. For future sustainable production of aromatic compounds, it is highly desirable to convert lignin into value-added platform chemicals instead of using fossil-based resources. Lignins are aromatic polymers linked by three types of ether bonds (α-O-4, β-O-4, and 4-O-5 linkages) and other C-C bonds. Among the ether bonds, the bond dissociation energy of the 4-O-5 linkage is the highest and the most challenging to cleave. To date, 4-O-5 ether linkage model compounds have been cleaved to obtain phenol, cyclohexane, cyclohexanone, and cyclohexanol. The first example of direct formal cross-coupling of diaryl ether 4-O-5 linkage models with amines is reported, in which dual C(Ar)-O bond cleavages form valuable nitrogen-containing derivatives.
<title>Semiconductor acceleration sensor</title> (1996)

This paper reports a practical semiconductor acceleration sensor especially suited for automotive air bag systems. The acceleration sensor includes four beams arranged in a swastika structure. Two piezoresistors are formed on each beam. These eight piezoresistors constitute a Wheatstone bridge. The swastika structure of the sensing elements, an upper glass plate and a lower glass plate exhibit the squeeze film effect which enhances air dumping, by which the constituent silicon is prevented from breakdown. The present acceleration sensor has the following features. The acceleration force component perpendicular to the sensing direction can be cancelled. The cross-axis sensitivity is less than 3 percent. And, the erroneous offset caused by the differences between the thermal expansion coefficients of the constituent materials can be canceled. The high aspect ratio configuration realized by plasma etching facilitates reducing the dimensions and improving the sensitivity of the acceleration sensor. The present acceleration sensor is 3.9 mm by 3.9 mm in area and 1.2 mm in thickness. The present acceleration sensor can measure from -50 to +50 G with sensitivity of 0.275 mV/G and with non-linearity of less than 1 percent. The acceleration sensor withstands shock of 3000 G.
Multidimensional Correlation of Software Source Code (2008)

Standard ways of calculating the similarity of different computer programs are needed in computer science. Such measurements can be useful in many different areas such as clone detection, refactoring, compiler optimization, and run-time optimization. Such standards are particularly important for uncovering plagiarism, trade secret theft, copyright infringement, and patent infringement. Other uses include locating open source code within a proprietary program and determining the authors of different programs. In a previous paper (R. Zeidman, 2006) I introduced the concept of source code correlation, presented a theoretical basis for such a measure, and described a program, CodeMatchreg, that compares software source code and calculates correlation. That paper compared the described method of source code correlation against existing methods of comparing source code and found it to be significantly superior. This paper refines that definition of source code correlation and presents a new, more robust, definition of multidimensional source code correlation.
Noninvasive Assessment of Retinal Blood Flow Using a Novel Handheld Laser Speckle Contrast Imager (2018)

To our knowledge, this is the first human study of a handheld laser speckle retinal imaging device. Determination of retinal blood flow has applications to ophthalmic and systemic disease and a portable handheld retinal imager that determines blood flow may be widely adopted at the point of care.
Developing a Vacuum Electrospray Source To Implement Efficient Atmospheric Sampling for Miniature Ion Trap Mass Spectrometer (2017)

The performance of a miniature mass spectrometer in atmospheric analysis is closely related to the design of its sampling system. In this study, a simplified vacuum electrospray ionization (VESI) source was developed based on a combination of several techniques, including the discontinuous atmospheric pressure interface, direct capillary sampling, and pneumatic-assisted electrospray. Pulsed air was used as a vital factor to facilitate the operation of electrospray ionization in the vacuum chamber. This VESI device can be used as an efficient atmospheric sampling interface when coupled with a miniature rectilinear ion trap (RIT) mass spectrometer. The developed VESI-RIT instrument enables regular ESI analysis of liquid, and its qualitative and quantitative capabilities have been characterized by using various solution samples. A limit of detection of 8 ppb could be attained for arginine in a methanol solution. In addition, extractive electrospray ionization of organic compounds can be implemented by using the same VESI device, as long as the gas analytes are injected with the pulsed auxiliary air. This methodology can extend the use of the proposed VESI technique to rapid and online analysis of gaseous and volatile samples.
Enhancing the Bandwidth of Low-Dropout Regulators Using Power Transmission Lines for High-Speed I/Os (2017)

Power supply rejection peaking in low-dropout (LDO) voltage regulators can lead to reduced bandwidth and efficiency. This paper presents a new design method by combining power transmission lines (PTLs) with LDOs for enhancing its bandwidth and efficiency. This approach is applicable for LDOs regulating high-speed I/O drivers. The PTL combined with decoupling capacitors on the package or board is used to mitigate the power supply noise (PSN). This methodology is demonstrated using printed circuit board test vehicles with off-the-shelf components. Compared to conventional approaches, the PTL solution showed an ~80% lower PSN.
Alkali-Resistant, Alkaline Endo-l,4-<i>β</i>-glucanase Produced by<i>Bacillus</i>sp. PKM-5430 (1992)

Journal Article Alkali-Resistant, Alkaline Endo-l,4-β-glucanase Produced by Bacillus sp. PKM-5430 Get access Decorosa D Lusterio, Decorosa D Lusterio Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 Philippines Search for other works by this author on: Oxford Academic Google Scholar Franklin G Suizo, Franklin G Suizo Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 Philippines Search for other works by this author on: Oxford Academic Google Scholar Nellie M Labunos, Nellie M Labunos Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 Philippines Search for other works by this author on: Oxford Academic Google Scholar Marietta N Valledor, Marietta N Valledor Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 Philippines Search for other works by this author on: Oxford Academic Google Scholar Shinta Ueda, Shinta Ueda Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 Philippines Search for other works by this author on: Oxford Academic Google Scholar Shuji Kawai, Shuji Kawai Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 PhilippinesTochigi Research Laboratories of Kao Co., 2606 Akabane, Ichikai, Tochigi 321–34, Japan Search for other works by this author on: Oxford Academic Google Scholar Kenzo Koike, Kenzo Koike Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 PhilippinesTochigi Research Laboratories of Kao Co., 2606 Akabane, Ichikai, Tochigi 321–34, Japan Search for other works by this author on: Oxford Academic Google Scholar Shitsuw Shikata, Shitsuw Shikata Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 PhilippinesTochigi Research Laboratories of Kao Co., 2606 Akabane, Ichikai, Tochigi 321–34, Japan Search for other works by this author on: Oxford Academic Google Scholar Tadashi Yoshimatsu, Tadashi Yoshimatsu Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 PhilippinesTochigi Research Laboratories of Kao Co., 2606 Akabane, Ichikai, Tochigi 321–34, Japan Search for other works by this author on: Oxford Academic Google Scholar Susumu Ito Susumu Ito Microbiology Laboratory of Pilipinas Kao, Inc., Jasa-an, Misamis Oriental, 9003 PhilippinesTochigi Research Laboratories of Kao Co., 2606 Akabane, Ichikai, Tochigi 321–34, Japan To whom all correspondence should be addressed. Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 56, Issue 10, 1 January 1992, Pages 1671–1672, https://doi.org/10.1271/bbb.56.1671 Published: 01 January 1992 Article history Published: 01 January 1992 Received: 27 April 1992
Optical Vaginal Biopsy Using Optical Coherence Tomography (2020)

This study establishes feasibility of optical coherence tomography in providing an optical biopsy of the vaginal epithelium and lamina propria. In addition, it demonstrates vaginal changes as women enter menopause. This report is the initial phase of a longitudinal cohort study to evaluate changes in vaginal microstructure after energy-based treatment.
Detection of Viable <i>Mycobacterium tuberculosis</i> by Reverse Transcriptase-Strand Displacement Amplification of mRNA (1999)

Numerous assays have been described for the detection of DNA and rRNA sequences that are specific for the Mycobacterium tuberculosis complex. Although beneficial to initial diagnosis, such assays have proven unsuitable for monitoring therapeutic efficacy owing to the persistence of these nucleic acid targets long after conversion of smears and cultures to negative. However, prokaryotic mRNA has a typical half-life of only a few minutes and we have previously shown that the presence of mRNA is a good indicator of bacterial viability. The purpose of the present study was to develop a novel reverse transcriptase-strand displacement amplification system for the detection of M. tuberculosis alpha-antigen (85B protein) mRNA and to demonstrate the use of this assay in assessing chemotherapeutic efficacy in patients with pulmonary tuberculosis. The assay was applied to sequential, noninduced sputum specimens collected from four patients: 10 of 11 samples (91%) collected prior to the start of therapy were positive for alpha-antigen mRNA, compared with 1 of 8 (13%), 2 of 8 (25%), 2 of 8 (25%), and 0 of 8 collected on days 2, 4, 7, and 14 of treatment, respectively. In contrast, 39 of 44 samples (89%) collected on or before day 14 were positive for alpha-antigen DNA. The loss of detectable mRNA corresponded to a rapid drop over the first 4 days of treatment in the number of viable organisms present in each sputum sample, equivalent to a mean fall of 0.43 log10 CFU/ml/day. Analysis of mRNA is a potentially useful method for monitoring therapeutic efficacy and for rapid in vitro determination of drug susceptibility.
Development of Superhigh Strength Valve Spring Coexisting with both Easiness of Coiling Operation and High Fatigue Strength (2000)

A way of improving the fatigue strength of valve springs is to increase the tensile strength of oil tempered wire. However, the more the tensile strength increases, the more coiling operation becomes difficult. Therefore it has been difficult to make a great progress in fatigue strength depending on enhanced tensile strength only. In order that the high fatigue strength coexists with the easiness of coiling, high strength wire with controlled hardness on its surface is developed. Further more, the valve spring is treated by nitriding process at higher temperatures than usual, and the optimized triple hard shot peening is performed. As a result, the developed valve spring seems to exhibit the excellent performance of the world highest level
Identification of lactose fermentation plasmids of streptococcal dairy starter strains by Southern hybridization (1986)

Twenty‐two strains of Streptococcus cremoris, seven strains of Streptococcus lactis and three strains of Streptococcus lactis subsp. diacetilactis, each with a different plasmid complement, were isolated from a starter culture used in a Finnish dairy plant. By using DNA‐DNA hybridization, with cloned 6‐P‐ß‐galactosidase gene of the Strep, lactis plasmid pLP712 as a probe, the lactose fermentation genes were located, in each strain, in the large ( 30 MD) plasmid.
New Ionic Liquids Based on Alkylsulfate and Alkyl Oligoether Sulfate Anions: Synthesis and Applications (2003)

Typical ionic liquids consist of halogen containing anions such as [AlCl4]-, [PF6]-, [BF4]-, [CF3SO3]- or [(CF3SO2)2N]-. However, for many technical applications the presence of halogen atoms in the ionic liquid's anion may cause concerns if the hydrolytic stability of the anion is poor (e. g. for chloroaluminate and hexafluorophosphate systems) or if a thermal treatment of the spent ionic liquid is desired. In this contribution, synthesis, properties and application of several new alkylsulfate and alkyloligoethersulfate ionic liquids are presented. The described systems are easily available from technical raw materials. Some candidates combine low melting points with high hydrolytic stability and acceptable viscosity. Some of the new ionic liquids have been tested as catalyst layer in the Rh-catalyzed hydroformylation of 1-octene.
Experimental Results From Performance Improvement and Radiation Hardening of Inverted Metamorphic Multijunction Solar Cells (2012)

This paper discusses results from continued development of inverted metamorphic multijunction (IMM) solar cells with air mass zero (AM0) conversion efficiencies greater than 34%. An experimental best four-junction IMM (IMM4J) design is presented. In an effort to improve IMM performance in space radiation environments, 1-MeV electron irradiation studies are conducted on the individual IMM4J subcells. These data are used to engineer an IMM4J structure with beginning of life AM0 conversion efficiency of approximately 34% and an end of life (EOL) remaining factor greater than 82%, where EOL is defined as performance after exposure to 1-MeV electron irradiation at 1E15 e/cm <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$^2$</tex></formula> fluence. Next-generation IMM designs are explored and an avenue toward AM0 conversion efficiencies of greater than 35% is presented.