gebhart/patrepeval huggingface dataset:
Altering Toluene 4-Monooxygenase by Active-Site Engineering for the Synthesis of 3-Methoxycatechol, Methoxyhydroquinone, and Methylhydroquinone (2004)

Wild-type toluene 4-monooxygenase (T4MO) of Pseudomonas mendocina KR1 oxidizes toluene to p-cresol (96%) and oxidizes benzene sequentially to phenol, to catechol, and to 1,2,3-trihydroxybenzene. In this study T4MO was found to oxidize o-cresol to 3-methylcatechol (91%) and methylhydroquinone (9%), to oxidize m-cresol and p-cresol to 4-methylcatechol (100%), and to oxidize o-methoxyphenol to 4-methoxyresorcinol (87%), 3-methoxycatechol (11%), and methoxyhydroquinone (2%). Apparent Vmax values of 6.6 +/- 0.9 to 10.7 +/- 0.1 nmol/min/ mg of protein were obtained for o-, m-, and p-cresol oxidation by wild-type T4MO, which are comparable to the toluene oxidation rate (15.1 +/- 0.8 nmol/min/mg of protein). After these new reactions were discovered, saturation mutagenesis was performed near the diiron catalytic center at positions I100, G103, and A107 of the alpha subunit of the hydroxylase (TmoA) based on directed evolution of the related toluene o-monooxygenase of Burkholderia cepacia G4 (K. A. Canada, S. Iwashita, H. Shim, and T. K. Wood, J. Bacteriol. 184:344-349, 2002) and a previously reported T4MO G103L regiospecific mutant (K. H. Mitchell, J. M. Studts, and B. G. Fox, Biochemistry 41:3176-3188, 2002). By using o-cresol and o-methoxyphenol as model substrates, regiospecific mutants of T4MO were created; for example, TmoA variant G103A/A107S produced 3-methylcatechol (98%) from o-cresol twofold faster and produced 3-methoxycatechol (82%) from 1 mM o-methoxyphenol seven times faster than the wild-type T4MO (1.5 +/- 0.2 versus 0.21 +/- 0.01 nmol/min/mg of protein). Variant I100L produced 3-methoxycatechol from o-methoxyphenol four times faster than wild-type T4MO, and G103S/A107T produced methylhydroquinone (92%) from o-cresol fourfold faster than wild-type T4MO and there was 10 times more in terms of the percentage of the product. Variant G103S produced 40-fold more methoxyhydroquinone from o-methoxyphenol than the wild-type enzyme produced (80 versus 2%) and produced methylhydroquinone (80%) from o-cresol. Hence, the regiospecific oxidation of o-methoxyphenol and o-cresol was changed for significant synthesis of 3-methoxycatechol, methoxyhydroquinone, 3-methylcatechol, and methylhydroquinone. The enzyme variants also demonstrated altered monohydroxylation regiospecificity for toluene; for example, G103S/A107G formed 82% o-cresol, so saturation mutagenesis converted T4MO into an ortho-hydroxylating enzyme. Furthermore, G103S/A107T formed 100% p-cresol from toluene; hence, a better para-hydroxylating enzyme than wild-type T4MO was formed. Structure homology modeling suggested that hydrogen bonding interactions of the hydroxyl groups of altered residues S103, S107, and T107 influence the regiospecificity of the oxygenase reaction.
Low-cost Ku to Ka band MMICs using a commercially available Si/SiGe HBT process (2002)

Using modifications to the lateral layout of a commercially available Si/SiGe heterojunction bipolar process only, we demonstrate significant performance improvements in terms of the maximum frequency of oscillation, as well as the microwave noise performance. The optimized HBTs are then used in prototype MMICs in the Ku and lower Ka band. The mature Si/SiGe technology, combined with extremely compact circuit design and layout techniques, results in low-cost integrated circuits enabling consumer-oriented systems up to Ka band.
Langmuir−Blodgett Films Formed by Continuously Varying Surface Pressure. Characterization by IR Spectroscopy and Epifluorescence Microscopy (2007)

Monolayer films of phospholipids at the air-water interface have been transferred to solid substrates under conditions of continuously varying surface pressure, an approach termed COVASP. The molecular and supramolecular properties of the film constituents have been characterized with two complementary techniques. IR spectroscopy was used to monitor chain conformation as a function of transfer surface pressure. Results were compared to those from Langmuir films determined directly at the A/W interface by IR reflection-absorption spectroscopy (IRRAS). The methylene stretching frequencies for both proteated and acyl chain perdeuterated 1,2-dipalmitoylphosphatidylcholine (DPPC and DPPC-d62) in the transferred molecules indicate that the phospholipids retain at least, in part, their surface pressure-dependent chain-conformational order characteristics. The line widths of these modes are somewhat reduced, suggestive of slower rates of reorientational motion in the Langmuir-Blodgett (LB) films. Epifluorescence microscopy reveals a progressive condensation gradient, including nucleation and growth of probe-excluding condensed domains along the transfer line. DPPC condensation, observed along a single LB film, was qualitatively comparable to compression-driven condensation as observed in situ or in conventional LB films transferred at constant pressures. However, condensation along the compression isotherm in COVASP-LB films was reduced by 15-20% as compared to films equilibrated at different constant pressures, probably the result of kinetic differences in equilibration processes. As a preliminary demonstration of the utility of this new approach, the monolayer --> multilayer transition known to occur (Eur. Biophys. J. 2005, 34, 243) in a four-component model for pulmonary surfactant has been examined. IR parameters from both the lipid and the protein constituents of the film all indicate that the transition persists during the transfer process. This new approach for the study of transferred films will permit the efficient characterization of lipid-protein interactions and structural transitions occurring in pulmonary surfactant films subjected to dynamic compression.
Enzymically mediated bioprecipitation of uranium by a Citrobacter sp.: a concerted role for exocellular lipopolysaccharide and associated phosphatase in biomineral formation (2000)

A Citrobacter sp. accumulated uranyl ion (UO2(2+)) via precipitation with phosphate ligand liberated by phosphatase activity. The onset and rate of uranyl phosphate deposition were promoted by NH4(+), forming NH(4)UO(2)PO(4), which has a lower solubility product than NaUO(2)PO(4). This acceleration decoupled the rate-limiting chemical crystallization process from the biochemical phosphate ligand generation. This provided a novel approach to monitor the cell-surface-associated changes using atomic-force microscopy in conjunction with transmission electron microscopy and electron-probe X-ray microanalysis, to visualize deposition of uranyl phosphate at the cell surface. Analysis of extracted surface materials by (31)P NMR spectroscopy showed phosphorus resonances at chemical shifts of 0.3 and 2.0 p.p.m., consistent with monophosphate groups of the lipid A backbone of the lipopolysaccharide (LPS). Addition of fUO2(2+) to the extract gave a yellow precipitate which contained uranyl phosphate, while addition of Cd(2+) gave a chemical shift of both resonances to a single new resonance at 3 p.p.m. Acid-phosphatase-mediated crystal growth exocellularly was suggested by the presence of acid phosphatase, localized by immunogold labelling, on the outer membrane and on material exuded from the cells. Metal deposition is proposed to occur via an initial nucleation with phosphate groups localized within the LPS, shown by other workers to be produced exocellularly in association with phosphatase. The crystals are further consolidated with additional, enzymically generated phosphate in close juxtaposition, giving high loads of LPS-bound uranyl phosphate without loss of activity and distinguishing this from simple biosorption, or periplasmic or cellular metal accumulation mechanisms. Accumulation of 'tethered' metal phosphate within the LPS is suggested to prevent fouling of the cell surface by the accumulated precipitate and localization of phosphatase exocellularly is consistent with its possible functions in homeostatis and metal resistance.
Infection patterns of trematode parasites among Joseon people (2014)

While paleoparasitologists in Korea reported scientific evidences for the infection patterns of various parasite species among the pre-modern Joseon people, historical study is also needed for understanding the socio-cultural aspects of parasitic infections of the past. In this study on the historical documents, we revealed the socio-cultural environment of Joseon society by which people were easily infected by trematode parasites. The historical records showed that Joseon people enjoyed raw fish cuisines, that might have caused Clonorchis sinensis and Metagonimus yokogawai infection, much more frequently than originally expected. It is also proven that Joseon people ate raw crab and crayfish, the intermediate host of Paragonimus westermani, as the seasonal delicacy or miracle cure drug for incurable diseases. We also found many Joseon records on raw-oyster dishes, possibly having caused Gymnophalloides seoi infection among the people. By this study, we could get the historical clues on how Joseon people could have been infected by various trematode parasites.
Relational metric: A new metric for network service and in-network resource control (2012)

This paper discusses a new paradigm of network service and in-network resource control: relational metric based control. The relational metrics indicate the closeness relationship between objects in the real world, and these objects could be people, locations, things, and content. Closeness is measured by using a fusion of online and physical sensing. We will describe the system model and discuss possible service applications of this technology.
Reduced PWM harmonic distortion for multilevel inverters operating over a wide modulation range (2006)

It is known that the optimal carrier based approach for modulating a multilevel converter is to use a phase disposition (PD) carrier arrangement with a common mode offset added to the reference waveforms to centre the implicitly selected space vectors. However, this strategy does not fully utilize all available voltage levels at lower modulation depths, with an odd level system only using odd voltage levels and an even level system only using even voltage levels as the modulation depth varies. Recent work has suggested that this is not the harmonically optimal approach at reduced modulation depths. This paper shows how up to a 40% reduction in harmonic distortion can be achieved if all available voltage levels are used throughout the linear modulation range. The improvement is achieved by adding a simple (1/2) carrier magnitude common mode dc offset in key modulation regions, which allows the converter to use all available voltage levels. The paper uses analytical spectral decomposition and harmonic flux trajectory analysis to propose a theoretical basis for this improvement, and to determine the precise points at which the (1/2) carrier magnitude offset should be added to achieve the harmonic improvement.
Triazines: Efficient Corrosion Inhibitors for Mild Steel in Hydrochloric Acid Solution (2012)

Five triazines namely Hexahydro-1,3,5-triphenyl-s-triazine (Inh-1), Hexahydro-1,3,5-p-tolyl-s-triazine (Inh-2), Hexahydro-1,3,5-p-methoxyphenyl-s-triazine (Inh-3), Hexahydro-1,3,5-p-aminophenyl-s-triazine (Inh-4) and Hexahydro-1,3,5-p-nitrophenyl-s-triazine (Inh-5) were synthesized and investigated as corrosion inhibitors of mild steel in 1N HCl solution using weight loss, polarization resistance, Tafel polarization and electrochemical Impedance spectroscopy techniques. The inhibition efficiency of the synthesized inhibitors followed the order Inh4 > Inh3 > Inh2 > Inh1 > Inh5. The inhibiting action of triazines was found to depend on electronic nature of functional groups present in triazines. Potentiodynamic polarizations suggest that triazines are mixed type in nature. Electrochemical Impedance spectroscopy was also used to investigate the mechanism of corrosion inhibition. Thermodynamic parameters were also calculated to know the mechanism of the inhibition. AFM is used to know the surface roughness of the mild steel sample with and without inhibitors.
Saquinavir pharmacokinetics alone and in combination with nelfinavir in HIV-infected patients (1997)

NLF increases the oral bioavailability of SQV (hard gel) approximately fivefold. For some patients the addition of NLF to SQV will increase the drug levels from subtherapeutic to the therapeutic range. In one of our patients the addition of NLF resulted in SQV levels that were much higher than previous work suggests are necessary for maximum antiviral effect. The variability in SQV concentrations both at baseline and following addition of NLF suggest that dosing may best be adjusted by individual therapeutic drug monitoring.
Abstract 1577: Lactobacilli secreting a tumor antigen and IL15 activates neutrophils and dendritic cells and generates cytotoxic T lymphocytes against cancer cells (2012)

Abstract Introduction and Objective Lactobacillus rhamnosus GG (LGG) are lactic acid bacteria, which were found to be better than BCG at inducing cell death in human bladder cancer cell lines. This study compares both LGG and BCG in vivo in an orthopic model and further evaluates the potential of recombinant LGG to induce a directed anti-tumor response. Methods MB49-PSA (murine bladder cancer cells secreting human PSA) cells were implanted orthotopically in C57BL/6 mice and either LGG or BCG was instilled weekly for 6 weeks. Tumor cure rates were noted and an immnohistochemical examination was performed on the tumors. The human prostate specific antigen (PSA) PSA was cloned into pLP500-slpAp vector under the control of S-layer promoter of L. acidophilus. The murine IL-15 cDNA minus its termination codon was cloned upstream of the PSA protein sequence. Lactobacilli were transformed with the plasmids to generate LGG-IL15-PSA, LGG-PSA and LGG-S (pLP500-slpAp) respectively. PSA and IL15 secretion was 16-19 ng/2x109 CFU/ml. Bone marrow cells were isolated from the tibia and femur of 8-10 weeks old female C57BL/6 mice. Neutrophils were isolated by positive selection with anti-Ly6G microbead kit (Miltenyi Biotech, Germany). To generate DCs, bone marrow derived cells were cultured for 9 days in media with 40ng/ml of GM-CSF (BD Bioscience) which was replaced every other day. Neutrophils and DC were exposed to the recombinant LGG for 2h and used to stimulate T cells to generate CTL against the murine bladder cancer cell lines expressing PSA (MB49-PSA). Results LGG was as effective as BCG in the mice. Analysis of tumors after repeated weekly LGG instillations showed increased infiltration of neutrophils and macrophages into the tumor mass after therapy. In vitro, recombinant LGG activated neutrophils (elevated MHC class I expression) induced DC maturation (increased expression of CD86, CD80, CD40, MHC II and CD83), T cell proliferation and PSA specific cytotoxic T lymphocytes (CTL) activity. Activated DC were more efficient than activated neutrophils in inducing T cell IL2 and IFNα production. DC activated with LGG for 2 h or with LGG treated neutrophils were re-isolated and plated with naïve T cells for 5 days to generate PSA specific T cells. Then PSA secreting or control MB49 cells were added to the wells. IL15 enhanced DC generation of CTL. Conclusions Intravesical instillation of LGG cured mice of tumors. LGG secreting tumor antigens and cytokines could be used to activate DC in vitro for DC therapy in patients or used as intravesical therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1577. doi:1538-7445.AM2012-1577
Solubilities of Flavone and 3-Hydroxyflavone in Supercritical Carbon Dioxide (1997)

The solubilities of flavone and 3-hydroxyflavone in supercritical carbon dioxide (SC-CO2) were measured at 308.2 K and 318.2 K over the pressure range from 9.1 MPa to 25.3 MPa by a flow type apparatus, which can detect the concentrations of the solutes in a supercritical fluid. The solubilities were determined from the mass of solute trapped by decompressing and the volume of CO2. Solubility data were correlated by a solution model based on the regular solution model.
Plasma Polymerized Films for Sensor Devices (2000)

Miniaturization with semiconductor microfabrication or micromachining techniques is one of the main concerns in sensor technologies. For the combination of sensor and microelectronics technology, polymers should be fabricated in a mass-producible and miniaturization-conscious manner as an interface. The polymers fabricated in conventional manners could have potential problems, e.g., obtaining thin (<1 µm) and homogeneous films. Plasma-polymerized films, which are made in a glow discharge or plasma in a vapor phase, offer a new alternative. This review describes the several characteristics, properties, and applications of plasma-polymerized films in both chemical and biological fields.
Macrolide-Resistant <i>Streptococcus pneumoniae</i> and <i>Streptococcus pyogenes</i> in the Pediatric Population in Germany during 2000-2001 (2003)

In a nationwide study in Germany covering 13 clinical microbiology laboratories, a total of 307 Streptococcus pyogenes (mainly pharyngitis) and 333 Streptococcus pneumoniae (respiratory tract infections) strains were collected from outpatients less than 16 years of age. The MICs of penicillin G, amoxicillin, cefotaxime, erythromycin A, clindamycin, levofloxacin, and telithromycin were determined by the microdilution method. In S. pyogenes isolates, resistance rates were as follows: penicillin, 0%; erythromycin A, 13.7%; and levofloxacin, 0%. Telithromycin showed good activity against S. pyogenes isolates (MIC(90) = 0.25 micro g/ml; MIC range, 0.016 to 16 micro g/ml). Three strains were found to be telithromycin-resistant (MIC >/= 4 micro g/ml). Erythromycin-resistant strains were characterized for the underlying resistance genotype, with 40.5% having the efflux type mef(A), 38.1% having the erm(A), and 9.5% having the erm(B) genotypes. emm typing of macrolide-resistant S. pyogenes isolates showed emm types 4 (45.2%), 77 (26.2%), and 12 (11.9%) to be predominant. In S. pneumoniae, resistance rates were as follows: penicillin intermediate, 7.5%; penicillin resistant, 0%; erythromycin A, 17.4%; and levofloxacin, 0%. Telithromycin was highly active against pneumococcal isolates (MIC(90) </= 0.016 micro g/ml; range, 0.016 to 0.5 micro g/ml). The overall resistance profile of streptococcal respiratory tract isolates is still favorable, but macrolide resistance is of growing concern in Germany.
Cellular states in a boundary-layer model of directional solidification (1985)

We use a boundary-layer model to study the cellular states in directional solidification. Away from threshold a gap develops in the center of the band of allowed states, and the boundaries of the Eckhaus instability move toward longer wavelength.
A quasi-monoclonal anti-HBs response can lead to immune escape of ‘wild-type’ hepatitis B virus (2005)

Hepatitis B virus (HBV) infections can be prevented or controlled by the host humoral immune response (anti-HBs) directed against the major surface antigen (HBsAg), elicited either naturally or by vaccination. A chronic HBV carrier was found to have high levels of both virus and anti-HBs. Full-length HBV genomes were amplified from the patient's serum, sequenced and cloned. The genome was 'wild-type' HBV of genotype C and serotype adr. The sequence has remained stable, with no signs of emergence of an immune-escape mutant population. To study what was recognized by the patient's serum, viral particles were 35S-labelled and then immunoprecipitated by using the patient's serum or control sera. The patient's serum immunoprecipitated the adr HBsAg encoded by his HBV genome poorly, but efficiently recognized HBsAg of serotype ayw. When his HBV genome was modified by a point mutation to express HBsAg of serotype ayr, the patient's serum could recognize the antigen, as well as the control anti-HBs-positive serum. The patient appeared to have made a quasi-monoclonal humoral response to the y epitope. By switching to the d epitope, which requires only a point mutation, the virus could replicate, despite the high levels of anti-HBs. This study underlines the subtleties of virus-host interactions. Implications for HBV vaccination are discussed.
Hierarchical High Sigma Monte Carlo Simulation of SRAM Vmin Shift by Parts for Automotive Grade Fail Rate Projection (2020)

We developed an infrastructure to simulate SRAM Vmin shift from time-zero (TO) to end-of-life (EOL) by parts utilizing the Hierarchical Monte Carlo tool under Mentor's Solido Variation Designer environment. This tool applies machine learning (ML) to rapidly verify full-chip memories with perfect SPICE accuracy. This allows us to simulate a large number of SRAM parts and obtain a better description of the statistics. The TO Vmin and Vmin shift distribution, obtained from the simulation, provide a way to project SRAM fail rate up to the stringent requirement of <; 1 defective-parts-per-million (dppm) for automotive-grade applications. Furthermore, we used this tool to assess the improvement in SRAM fail rate utilizing TO screening with negative read assist.
Recent experience measuring breeder fresh fuel assemblies (1987)

The International Atomic Energy Agency (IAEA) is required to conduct independent on-site verification of nuclear material held under safeguards agreements with member states. The nuclear material contained in liquid-metal fast breeder reactor (LMFBR) fresh fuel assemblies presents unique safeguards and measurement problems. Since LMFBR fresh fuel may contain uranium of various enrichments, plutonium, or mixtures of uranium and plutonium, a combination of nondestructive assay (NDA) methods and equipment must be used to achieve independent verification of the nuclear material contained in LMFBR fresh fuel assemblies. During 1985 and 1986, a number of measurements were carried out at the BOR-60 LMFBR facility near Dimitrovgrad, USSR to train IAEA inspectors in the use of standard NDA equipment and measurement procedures that can be employed to verify the nuclear material content of LMFBR fresh fuel. Since these measurements were conducted at an operation LMFBR facility, agency inspectors had an opportunity to receive training under actual field conditions. These activities also presented the first opportunity for the agency to test NDA measurement methods on LMFBR fresh fuel of the BOR-60 design. The measurements conducted at the BOR-60 site established that standard agency NDA equipment and procedures can be employed to independently verify the nuclearmore » material content of LMFBR fresh fuel assemblies.« less
<title>Coherent Pulse Laser Holography</title> (1968)

The beam of light emitted by a conven-tional pulse laser is a summation of a number of transverse and axial resonance frequency modes. This type of laser is not suitable for making holograms except with a very specific arrangement of the laser light, object, and photographic plate (Ref. 1-3). In this arrangement, the object is illuminated from behind. Thus, an observer looking through the hologram plate at the reconstructed image sees only the outline or shadow of the object. Obviously, this technique is inadequate when the observer desires to discern surface detail on the holographed object.