gebhart/patrepeval huggingface dataset:
A New Generation of Stable, Nonantibiotic, Low-Copy-Number Plasmids Improves Immune Responses to Foreign Antigens in <i>Salmonella enterica</i> Serovar Typhi Live Vectors (2009)

We hypothesized that adequately engineered attenuated Salmonella enterica serovar Typhi strains can serve as multivalent mucosal live vector vaccines to immunize against unrelated human pathogens. Toward this ultimate goal, we have developed a novel genetic stabilization system for antigen-expressing plasmids, engineered to encode the single-stranded binding protein (SSB), an essential protein involved in DNA metabolism which was deleted from the live vector chromosome. We utilized full-length protective antigen (PA83) of anthrax toxin from Bacillus anthracis as a foreign antigen and expressed PA83 as a fusion with the ClyA export protein, which allows export of ClyA-PA83 to the surface of S. Typhi live vectors. A series of SSB-encoding multicopy expression plasmids were introduced into reengineered S. Typhi strains previously tested in clinical trials, i.e., CVD 908-htrA and its less attenuated parent CVD 908. Immunogenicity was examined using a mouse model of intranasal immunization with live vector, followed by parenteral boosting with purified PA83. PA-specific antibody responses markedly improved as the copy number of the SSB-encoding plasmids decreased, and this effect was dramatically enhanced when the foreign antigen was delivered by the less attenuated live vector CVD 908ssb. These results suggest that antibody responses to antigens delivered by S. Typhi live vectors are inversely related to the metabolic burden imposed by expression of the foreign antigen and that these responses can be improved when antigens are expressed from low-copy-number plasmids and exported out of the cytoplasm of less attenuated live vectors.
Antigenicity of fullerenes: Antibodies specific for fullerenes and their characteristics (1998)

The recent interest in using Buckminsterfullerene (fullerene) derivatives in biological systems raises the possibility of their assay by immunological procedures. This, in turn, leads to the question of the ability of these unprecedented polygonal structures, made up solely of carbon atoms, to induce the production of specific antibodies. Immunization of mice with a C60 fullerene derivative conjugated to bovine thyroglobulin yielded a population of fullerene-specific antibodies of the IgG isotype, showing that the immune repertoire was diverse enough to recognize and process fullerenes as protein conjugates. The population of antibodies included a subpopulation that crossreacted with a C70 fullerene as determined by immune precipitation and ELISA procedures. These assays were made possible by the synthesis of water-soluble fullerene derivatives, including bovine and rabbit serum albumin conjugates and derivatives of trilysine and pentalysine, all of which were characterized as to the extent of substitution and their UV-Vis spectra. Possible interactions of fullerenes with the combining sites of IgG are discussed based on the physical chemistry of fullerenes and previously described protein-fullerene interactions. They remain to be confirmed by the isolation of mAbs for x-ray crystallographic studies.
Preparation of (4<i>S</i>)-4-Hydroxy-3-methyl-2-(2-propynyl)-2-cyclopenten-1-one by Sequential Combination of Enzymatic Hydrolysis and Mitsunobu Reaction (1991)

(4S)-4-Hydroxy-3-methyl-2-(2-propynyl)-2-cyclopenten-1-one, which is an important alcohol moiety of optically active pyrethroid insecticides, was prepared from the corresponding racemic acetate by the sequential combination of enzymatic hydrolysis and Mitsunobu reaction, in an excellent optical yield.
Broadly Applicable <i>Z</i>‐ and Diastereoselective Ring‐Opening/Cross‐Metathesis Catalyzed by a Dithiolate Ru Complex (2014)

A broadly applicable Ru-catalyzed protocol for Z-selective ring-opening/cross-metathesis (ROCM) is disclosed. In addition to reactions relating to terminal alkenes of different sizes, the first examples of Z-selective ROCM processes involving heteroaryl olefins, 1,3-dienes, and O- and S-substituted alkenes as well as allylic and homoallylic alcohols are reported. Z-Selective transformations with an α-substituted allylic alcohol are shown to afford congested Z alkenes with high diastereoselectivity. Transformations are performed in the presence of 2.0-5.0 mol % of a recently disclosed Ru-based dithiolate complex that can be easily prepared in a single step from commercially available starting materials. Typically, transformations proceed at ambient temperature and are complete within eight hours; products are obtained in up to 97 % yield, >98:2 Z/E, and >98:2 diastereomeric ratio. The present investigations reveal a mechanistically significant attribute of the Ru-based dithiolates that arises from electrostatic interactions with anionic S-based ligands.
Development of acrylamide manufacturing process using microorganism. (1988)

Acrylamide is industrially produced by catalytic hydration of acrylonitrile with reduced copper salts. However, the preparation and regeneration of the catalyst are laborious and the process requires a high temperature. It has therefore been considered very desirable to establish a process for producing acrylamide under moderate conditions, because compounds containing double bonds in the molecule are readily polymerizable.There is a growing interest in the synthesis of useful organic compounds by biological process for its specificity and moderate reaction condition. Therefore, we attempted to produce acrylamide from acrylonitrile using microbial enzyme and we found a bacterium having a high acrylamide producing enzyme (nitrile hydratase).This paper describes the details and merits of the development of microbial production of acrylamide.
Role of Nematode Peptides and Other Small Molecules in Plant Parasitism (2012)

Molecular, genetic, and biochemical studies are demonstrating an increasingly important role of peptide signaling in nematode parasitism of plants. To date, the majority of nematode-secreted peptides identified share similarity with plant CLAVATA3/ESR (CLE) peptides, but bioinformatics analyses of nematode genomes have revealed sequences homologous to other classes of plant peptide hormones that may be utilized by these pests. Extracellular host receptors for secreted nematode peptides are beginning to be identified and their roles in parasitism elucidated. Here, we outline recent advances from studies of biologically active nematode-secreted peptides that function as molecular mimics of endogenous plant peptides to promote parasitism. Several strategies are being used to exploit this information to provide new targets for engineering nematode resistance.
Laser action from <i>s</i> <i>y</i> <i>n</i>-(methyl,chloro) bimane (1987)

Laser action under flashlamp excitation of syn-(methyl,chloro) bimane, dissolved in trifluoroethanol, was observed at 516 nm. This new dye lases about 60% as efficiently as coumarin 30. The heavy atom effect, as related to the laser action properties of syn-(methyl,chloro) bimane, is discussed. The concentration dependence on the laser output of the new laser dye was studied. The spectral location of the fluorescence maximum as a function of the syn-(methyl,chloro) bimane concentration was measured. The effect of solvent mixture ratio on the lasing wavelength of syn-(methyl,chloro) bimane was studied. Different options available for further improving the laser-action properties of syn-bimanes are presented.
Activating Mutations of the Serotonin 5‐HT<sub>2C</sub> Receptor (1997)

Site-directed mutagenesis was performed to create a mutant serotonin 5-HT2C receptor that would mimic the active conformation of the native receptor. Structural alteration of receptor conformation was achieved by changing amino acid no. 312 from serine to phenylalanine (S312F) or lysine (S312K). After expression in COS-7 cells, the binding affinity of 5-HT for [3H]mesulergine-labeled 5-HT2C receptors increased from 203 nM (native) to 76 nM for S312F and 6.6 nM for S312K mutant receptors. 5-HT potency for stimulation of phosphatidylinositol (PI) hydrolysis increased from 70 nM (native) to 28 nM for S312F and 2.7 nM for S312K mutant receptors. The mutant receptors were constitutively active, stimulating PI hydrolysis in the absence of agonist. S312F and S312K mutations resulted in twofold and five-fold increases, respectively, in basal levels of PI hydrolysis. Mianserin and mesulergine displayed inverse agonist activity by decreasing basal levels of PI hydrolysis stimulated by S312K mutant receptors. [3H]5-HT and [3H]mesulergine labeled the same number of S312K mutant receptors and 5'-guanylylimidodiphosphate had no effect on [3H]5-HT binding. These results indicate that serine --> lysine mutation at amino acid no. 312 produces an agonist high-affinity state of the 5-HT2C receptor that spontaneously couples to G proteins and stimulates PI hydrolysis in the absence of agonist.
Diagnosis of human prion disease (2005)

With the discovery of the prion protein (PrP), immunodiagnostic procedures were applied to diagnose Creutzfeldt-Jakob disease (CJD). Before development of the conformation-dependent immunoassay (CDI), all immunoassays for the disease-causing PrP isoform (PrPSc) used limited proteolysis to digest the precursor cellular PrP (PrPC). Because the CDI is the only immunoassay that measures both the protease-resistant and protease-sensitive forms of PrPSc, we used the CDI to diagnose human prion disease. The CDI gave a positive signal for PrPSc in all 10-24 brain regions (100%) examined from 28 CJD patients. A subset of 18 brain regions from 8 patients with sporadic CJD (sCJD) was examined by histology, immunohistochemistry (IHC), and the CDI. Three of the 18 regions (17%) were consistently positive by histology and 4 of 18 (22%) by IHC for the 8 sCJD patients. In contrast, the CDI was positive in all 18 regions (100%) for all 8 sCJD patients. In both gray and white matter, approximately 90% of the total PrPSc was protease-sensitive and, thus, would have been degraded by procedures using proteases to eliminate PrPC. Our findings argue that the CDI should be used to establish or rule out the diagnosis of prion disease when a small number of samples is available as is the case with brain biopsy. Moreover, IHC should not be used as the standard against which all other immunodiagnostic techniques are compared because an immunoassay, such as the CDI, is substantially more sensitive.
Kinetics of Human VWF Cleavage by Human ADAMTS13: Comparison of Recombinant and Plasma-Derived VWF (2008)

Abstract A recombinant human CHO-expressed von Willebrand factor (rVWF) which consists of ultra-high molecular weight (UHMW) multimers resembles the VWF that is stored in Weibel-Palade bodies of endothelial cells. Once secreted into plasma, UHMW multimers are rapidly cleaved by ADAMTS13 and therefore are usually missing in VWF purified from plasma. We analyzed in vitro whether the cleavage of rVWF by ADAMTS13 is similar to the cleavage of plasma VWF by ADAMTS13, using a standard assay that depends on denaturing conditions (1.5 M urea) to expose the ADAMTS13 cleavage site of VWF. We explored the kinetics of ADAMTS13-mediated proteolysis of rVWF over time by exposing 1 VWF:Ag IU/ml of rVWF to various concentrations of recombinant and plasma-derived purified ADAMTS13, ranging from 4 mU/ml to 1 U/ml (corresponding to 0.4 to 100% of the normal human plasma concentration), and to ADAMTS13 present in normal human plasma and VWF-deficient plasma. The multimeric structure and function of VWF were analyzed by multiple assays to compare VWF before, during, and after proteolytic cleavage. In addition, the degradation kinetics of recombinant VWF were compared with those of a plasma-derived VWF product. Recombinant VWF was cleaved rapidly and with the same efficiency using recombinant or plasma-derived ADAMTS13. With 0.5 U/ml pADAMTS13 or rADAMTS13, VWF:RCo activity was below the detection limit of 0.17 IU/ml after 15 s. UHMW multimers disappeared within seconds at physiological concentrations of 0.5–1.0 U/ml ADAMTS13 (50–100% of the normal plasma concentration). Furthermore, UHMW were cleaved within 30 minutes with much lower concentrations of 10–30 mU/ml ADAMTS13 (1–3% of normal plasma concentration). The typical satellite bands appeared very early in an ADAMTS13 dose-dependent manner. Although plasma-derived VWF differs substantially from rVWF in its multimeric structure, the decrease in activity was similar for the recombinant and plasma-derived VWF. Specific cleavage of rVWF (3 IU VWF:Ag/ml) by rADAMTS13 (5 U/ml) was also demonstrated without urea under shear stress in the presence of platelets, detected by a monoclonal antibody (N10) that recognizes VWF only when cleaved by ADAMTS13. The combined data show that ADAMTS13 is able to readily cleave human rVWF even at low concentrations and that the UHMW multimeric fraction of human rVWF is removed within minutes by ADAMTS13 in vitro.
Sepiapterin reverses the changes in gastric nNOS dimerization and function in diabetic gastroparesis (2010)

The above data suggests that supplementation of SEP accelerated gastric emptying and attenuated reduced gastric nNOSα expression, and dimerization. Therefore, SEP supplementation is a potential therapeutic option for female patients of diabetic gastroparesis.
Development of an Onboard Doppler Lidar for Flight Safety (2009)

Air turbulence has become a major cause of significant injuries and aircraft damages. Timely advanced warning of turbulence ahead of an aircraft may allow pilots to take appropriate action to minimize potential damage, such as reducing speed and securing passengers and unsecured objects, or to avoid the turbulence altogether. The aim of our research is to develop a practical, onboard, Lidar-based proactive sensor that will detect air turbulence in clear air at a range of 5 n miles (9.3 km) at cruising altitudes. In February 2007 we successfully measured wind speeds approximately 3 n miles (5.6 km) ahead of an aircraft in low-altitude flight experiments, and in a subsequent experiment in July of the same year, we succeeded in detecting air turbulence before encountering it. An upgraded 5-n-mile Lidar for low altitudes was developed in fiscal year 2007, and has successfully measured wind speeds at ranges up to 5 n miles in ground tests. This paper describes the master development plan of our Lidar turbulence sensor and the results of basic flight and ground experiments.
Theoretical and Experimental Characterisation of Magnetic Microbubbles (2012)

In addition to improving image contrast, microbubbles have shown great potential in molecular imaging and drug/gene delivery. Previous work by the authors showed that considerable improvements in gene transfection efficiency were obtained using microbubbles loaded with magnetic nanoparticles under simultaneous exposure to ultrasound and magnetic fields. The aim of this study was to characterise the effect of nanoparticles on the dynamic and acoustic response of the microbubbles. High-speed video microscopy indicated that the amplitude of oscillation was very similar for magnetic and nonmagnetic microbubbles of the same size for the same ultrasound exposure (0.5 MHz, 100 kPa, 12-cycle pulse) and that this was minimally affected by an imposed magnetic field. The linear scattering to attenuation ratio (STAR) was also similar for suspensions of both bubble types although the nonlinear STAR was ~50% lower for the magnetic microbubbles. Both the video and acoustic data were supported by the results from theoretical modelling.
Production and characterization of rabbit anti‐idiotypic antibodies specific to mouse monoclonal anti‐human IgE and reacting with IgE‐binding factors and lymphocyte receptors for IgE (1986)

A mouse monoclonal antibody specific to human IgE (mAb 75) was employed to immunize a rabbit to obtain anti-idiotypes (aId) bearing the internal image of human IgE determinants and reacting with IgE-binding factors (IgE-BF) and/or lymphocyte receptors for IgE (Fc epsilon R). mAb 75 was selected on the basis of inhibition assays where the binding of mAb 75 to radiolabeled IgE was blocked by IgE-BF. The latter were produced by a lymphoblastoid cell line (RPMI 8866) expressing Fc epsilon R. Sequential samples of rabbit serum, collected during the immunization period, were extensively absorbed on mouse and human Ig-Sepharose 4B. The IgG fractions of the rabbit serum displayed the following activities: (a) they reacted with 125I-labeled mAb 75 but not with other labeled mouse Ig including mAb-aIgE, (b) this binding was inhibited in a dose-dependent fashion by human IgE but not by other human Ig classes nor by heat-inactivated IgE, (c) they reacted with a polyclonal rabbit anti-human IgE and (d) they blocked the binding of 125I-labeled IgE to mAb 75. It was concluded that the rabbit IgG contained aId (RaId) bearing the internal image of heat labile determinants of human IgE. The rosetting of IgE-coated bovine erythrocytes with Fc epsilon R-bearing cells was inhibited by preincubating the receptor-bearing cells with IgG RaId or its F(ab')2 but not with normal rabbit IgG. The ability of RaId to react with IgE-BF as well as with Fc epsilon R was also shown in inhibition experiments where IgE-BF and solubilized Fc epsilon R blocked the binding of mAb 75 to RaId. Finally, Western blot analysis of human colostrum, known to contain IgE-BF, indicated that radioiodinated RaId and IgE identified the same 12-16-kDa molecules corresponding to IgE-BF. It is concluded that RaId expresses the internal image of a heat-labile determinant of IgE which is involved in the binding of IgE to IgE-BF and Fc epsilon R. An alternative interpretation is that RaId reacts with an idiotypic determinant of mAb 75 which is shared by IgE-BF and Fc epsilon R.
From planar to fiber chiral gratings (Invited Paper) (2005)

We describe the development of fiber chiral gratings and discuss salient similarities and differences from planar chiral structures. Planar chiral structures include cholesteric liquid crystals and structured thin films produced by oblique deposition of dielectric materials on a rotating substrate. These are composed of uniform anisotropic planes with 180 degrees rotation symmetry which rotate uniformly with displacement perpendicular to the planes so that the pitch is equal to twice the period. The sinusoidal modulation of the structure which possesses double-helix symmetry results in a single band gap for co-handed light with the same sense of circular polarization as the handedness of the helical structure. Orthogonally polarized light is freely transmitted. Within the band gap the wavelength in the medium equals the structure pitch. Double-helix symmetry may also be implemented into a fiber geometry by twisting glass optical fiber with noncircular core cross section as it passes through a miniature oven. In addition to the polarization-selective resonant band observed in planar chiral gratings, we observe two additional modes of optical interaction when the pitch exceeds the wavelength in the fiber. In chiral long period gratings, dips in transmission are observed at wavelengths associated with coupling of the core mode and distinct cladding modes mediated by the chiral grating. In chiral intermediate period gratings, a broad scattering band is observed due to scattering out of the fiber into a continuum of states. Gratings with uniform pitch as well as with a specially designed pitch profile can be utilized to produce a variety of polarization selective devices. In addition to describing optical chiral gratings, we describe studies of microwave planar and fiber gratings, which played a key role in the development of optical fiber chiral gratings.
MEMS directional acoustic sensor for locating sound sources (2017)

The conventional directional sound sensing systems employ an array of spatially separated microphones to achieve directional sensing. However, there are insects such as <i>Ormia ochracea</i> fly that can determine the direction of sound using a miniature hearing organ much smaller than the wavelength of sound it detects. The MEMS based sensors mimicking the fly’s hearing system was fabricated using SOI substrate with 25 micrometer device layer. The sensor was designed to operate around 1.7 kHz, consists of two 1.2 mm × 1.2 mm wings connected in the middle by a 3 mm × 30 micrometer bridge. The entire structure is connected to the substrate by two torsional legs at the center. The sensor operates at its bending resonance frequency and has cosine directional characteristics similar to that of a pressure gradient microphone. For unambiguously determining the direction of sound, two sensors were assembled with a canted angle and outputs of the two sensors were processed to uniquely locate the bearing. At the bending resonant frequency (1.7 kHz) an output voltage of about 25 V/Pa was measured. The uncertainty of the bearing of sound ranged from less than 0.3 degrees close to the normal axis (0 degree) to 3 degrees at the limits of coverage (± 60 degrees) based on the 30 degree canted angle used. These findings indicate the potential use of a dual MEMS direction finding sensor assembly to locate sound sources with high accuracy.
Characterization of New Organic Nitrate Hybrid Drugs Covalently Bound to Valsartan and Cilostazol (2012)

Our results demonstrate that organic nitrates can be successfully linked to existing therapeutic molecules to create a new class of molecular entities with a potential dual mechanism of action via combining the established pharmacological properties of valsartan or cilostazol with the vasodilating properties of organic nitrates. Future experimental studies have to demonstrate whether the combined action of these compounds translates to superior therapeutic effects.
Petrophysical Implications of Laboratory NMR and Petrographical Investigation on a Shaly Sand Core (1999)

Abstract Nuclear magnetic resonance (NMR) measurements on rocks directly respond to the hydrogen content of the fluids in the pore space. Thus, besides the routine application of NMR in measuring the producible water- and hydrocarbon-filled porosity in the rocks, NMR technology has the potential to characterize the surficial clay-bound water. The exact nature of NMR transverse-relaxation T2 spectra obtainable from the clay-bound water has been discussed in recent studies conducted on both pure clays and reservoir rocks. The paper presents the results of a laboratory investigation on systematically sampled shaly sand rocks. We explore the relationship between the T2 distribution as a function of the rock texture, pore size distribution, clay mineralogy, and clay morphology. A 10-ft conventional core, cut in water-bearing, clay-rich sandstone, was sampled for this study. Mineralogy, texture, pore size distributions, and clay morphology were analyzed by X-ray diffraction (XRD), thin section petrography, scanning-electron microscopy (SEM), and petrographic image analysis (PIA). In addition, fully polarized NMR signals were acquired from brine-saturated and desaturated samples with inter-echo spacings (Te) of 0.3 and 0.6 millisecond. NMR porosity, computed by summing the signal in the T2 spectra, match favorably with the helium porosity, indicating that the full spectrum of pore sizes is included in the NMR porosity. The NMR T2 spectra obtained from brine-saturated samples show three distinct T2 classes: 1 to 3, 5 to 20, and 30 to 200 milliseconds. These appear from core properties to be controlled by pore-size changes, which are primarily influenced by the changes in clay type and morphology. The &lt;5-millisecond components likely correspond with &lt;5-μm sized pores typically trapped within the flakes of detrital illite. Features in the 5- to 20-millisecond range are also likely associated with the authigenic aggregates of kaolinite and chlorite that enclose 5- to 30-μm sized pores. T2 spectra obtained from desaturated rocks support the match of the specific features in the T2 spectra to the clays present in the rocks. Finally, the water in the relatively larger pores (30 to 150 μm) is associated with the signals at about 30 milliseconds and greater.