gebhart/patrepeval huggingface dataset:
Ion Transport in the Freshwater Zebra Mussel, <i>Dreissena polymorpha</i> (1992)

The blood solute concentration (36 mosm) of pondwater acclimated zebra mussels is among the lowest found in freshwater bivalves. Blood ion concentrations were Na (11-14 mM) and Cl (12-15 mM), with lesser amounts of Ca (4-5 mM), HCO3 (about 2-4 mM), and K (0.5 mM). Sodium, Ca and Cl transport rates were 20-30 μeq (g dry tissue · h)-1 for pondwater acclimated mussels. The influx of both Na and Cl was stimulated by exogenous serotonin (0.1 mM). Sodium transport in zebra mussels was not inhibited by amiloride. Zebra mussels became isosmotic in 30 mM NaCl solutions and did not survive beyond a week in 45 mM NaCl. Zebra mussels are well adapted to their dilute freshwater habitat, but are more stenohaline than other freshwater bivalves as reflected by their intolerance of elevated ion concentrations in the bathing solution.
Sucrose Phosphate Synthase, a Key Enzyme for Sucrose Biosynthesis in Plants (1991)

We have purified the protein for the enzyme sucrose phosphate synthase (SPS) from corn (Zea mays) leaves. Partially purified SPS protein was used to generate specific monoclonal antibodies. The following immunoaffinity chromatography allowed the isolation of pure SPS protein. The apparent molecular mass of the SPS polypeptide is 138 kilodaltons. By immunoblot, an SPS antigen was found to accumulate in mature leaves. SPS protein levels remain constant during the day/night cycle. The observed diurnal fluctuation of extractable enzyme activity, therefore, must be caused by modification of the specific activity of SPS in vivo.
Characterization of a wavelength-tunable surface plasmon resonance microscope (2004)

We have built and characterized the operation and performance of a surface plasmon resonance microscope that uses the rotation of an interference filter to vary the imaging wavelength of the system. The operation of the microscope with respect to signal processing, the dynamic range, and the limit of detection of the system, are described.
Noncontact Rail Monitoring by Ultrasonic Guided Waves (2008)

Abstract Recent train accidents have reaffirmed the need for developing more effective rail defect detection systems than those used today. One of the recent developments in rail inspection is the use of ultrasonic guided waves and noncontact probing techniques to target transverse‐type defects. Besides the obvious advantages of noncontact probing, which include robustness and potential for large inspection speed, such a system can theoretically detect transverse defects under horizontal shelling or head checks. A rail inspection prototype based on these concepts and funded by the Federal Railroad Administration (FRA) is under development at the University of California at San Diego (UCSD). The first field test was carried out in March 2006. The second field test took place in April 2007. This article first presents the main aspects of ultrasonic guided‐wave inspection of rails, including wave propagation modeling and noncontact ultrasound probing. The discussion then focuses on the UCSD/FRA prototype and its defect detection performance as determined in both laboratory tests and field tests.
ChemInform Abstract: Synthesis and Antitumor Activity of New Alkylphospholipids Containing Modifications of the Phosphocholine Moiety. (1990)

Abstract The hydroxyalkylammonium tosylates (III) are prepared either by quaternization of the ω‐dimethylamino alcohols (I) with methyl tosylate (II) or by reaction of the diol monotosylates (VI) with trimethylamine (VII).
Efficient in vivo catheter-based pericardial gene transfer mediated by adenoviral vectors (1999)

Adenoviral vectors are promising agents for a number of in vivo gene therapy applications including diseases of the heart and coronary vessels. Efficient intravascular gene transfer to specific sites has been achieved in occluded vessels, but otherwise is hampered by the effect of blood flow on localized vector uptake in the vessel wall. An alternative delivery approach to coronary arteries is the expression of diffusible gene products into the pericardial space surrounding the heart and coronary arteries. However, in vivo pericardial access is comparatively difficult and has been limited to surgical approaches. We hypothesized that efficient adenovirus-mediated gene expression in pericardial lining mesothelium could be achieved by transmyocardial vector delivery to the pericardium. To evaluate this concept, a hollow, helical-tipped penetrating catheter was used to deliver vector-containing fluid directly into the intrapericardial space. The catheter was introduced percutaneously in anesthetized mongrel dogs, advanced into the right ventricle, and the tip passed through the apical right ventricular myocardium under direct radiographic visualization until the open end of the catheter tip resided in the intrapericardial space. Adenoviral vectors expressing either nuclear-localizing beta-galactosidase, cytoplasmic luciferase, or secreted human alpha 1AT reporters (Av1nBg, Av1Lu, or Av1Aa, respectively) were instilled through the catheter into the intrapericardial space. Three days later the animals were sacrificed and reporter gene expression was evaluated in pericardium, epicardium, and multiple other tissues. In animals receiving Av1nBg, beta-galactosidase activity was evident in most of the pericardial lining endothelium, up to 100% in many areas. In animals receiving Av1Lu, luciferase reporter activity was abundant in pericardial tissues, but near-background levels were observed in other organs. In animals receiving Av1Aa, human alpha 1AT was abundant (16-29 mg/ml) in pericardial fluid, but was undetectable in serum. All animals tolerated the procedure well with no electrocardiographic changes and no clinical sequelae. These observations demonstrate highly efficient adenovirus vector delivery and gene transfer and expression in the pericardium and support the feasibility of localized gene therapy via catheter-based pericardial approaches. We suggest that the pericardial sac may serve as a sustained-release protein delivery system for the generation of desired gene products or their metabolites for diffusion into the epicardial region.
Nucleoside Phosphite, <i>O</i>-Bis(1,1,1,3,3,3-hexafluoro-2-propyl) Deoxyribonucleosid-3′-yl Phosphites. A Versatile Synthetic Intermediate for Phosphonate Modified Nucleotide and Oligonucleotide Synthesis (1992)

Abstract The O-bis(1,1,1,3,3,3-hexa-fluoro-2-propyl) deoxyribonucleosid-3′-yl phosphite units could be converted into the O-nucleosid-3′-yl phosphonate, O-2-cyanoethyl O-nucleosid-3′-yl phosphonate, and O-1,1,1,3,3,3-hexafluoro-2-propyl O-nucleosid-3′-yl phosphonothioate. The phosphite unit reacted with 3′-O-benzoylthymidine in the presence of MeIm to give the dithymidylate derivatives.
In-vivo imaging of inner retinal cellular morphology with adaptive optics - optical coherence tomography: challenges and possible solutions (2012)

Recent progress in retinal image acquisition techniques, including optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO), combined with improved performance of adaptive optics (AO) instrumentation, has resulted in improvement in the quality of in vivo images of cellular structures in the outer layers of the human retina. Despite the significant progress in imaging cone and rod photoreceptor mosaics, visualization of cellular structures in the inner retina has been achieved only with extrinsic contrast agents that have not been approved for use with humans. In this paper we describe the main limiting factors in visualizing inner retinal cells and the methods we implemented to reduce their effects on images acquired with AO-OCT. These include improving the system point spread function (AO performance), monitoring of motion artifacts (retinal motion tracking), and speckle pattern reduction (temporal and spatial averaging). Results of imaging inner retinal morphology and the improvement offered by the new UC Davis AOOCT system with spatio-temporal image averaging are presented.
Real-time chemical recognition of gas mixtures using optoelectronic terahertz waveforms (1997)

A time-domain chemical recognition system for classifying gases and analyzing gas mixtures is presented. The free-induction-decay exhibited by gases excited by far-infrared (terahertz) waveforms is analyzed in time-domain using digital signal processing techniques. A simple geometric picture is used for the classification of the waveforms measured for unknown gas species and for a quantitative pressure analysis of the individual gas species in a mixture. The analysis has have low computational cost and is used for a real-time monitor of gases.
Monitoring Pseudomonas aeruginosa in culture plates using embedded electrochemical sensors (2014)

Described is the fabrication of a disposable electrochemical assay, embedded in solid growth media agar. By applying a unique set of potentials and measuring current change using electrochemical sensors, we were able to selectively detect the presence of Pseudomonas aeruginosa. Bacterial cultures of P. aeruginosa, Escherichia coli, and Staphylococcus aureus were grown on these plates for a period of 48 hours at room temperature. The maximum currents from square-wave voltammetric scans showed the production of redox active molecules by P. aeruginosa after 15 hours of growth. This simple disposable electrochemical approach for detecting P. aeruginosa could have implications for diagnosing the presence of P. aeruginosa infections in limited resource areas.
Measurement of Functional Anti-Meningococcal Serogroup A Activity Using Strain 3125 as the Target Strain for Serum Bactericidal Assay (2011)

Functional anti-N. meningitidis serogroup A (MenA) activity in human serum is detected by serum bactericidal assay (SBA), using either rabbit (rSBA) or human (hSBA) complement, with F8238 as the recommended MenA SBA target strain. However, the F8238 strain may not be optimal for this purpose because, as we show here, it expresses the L11 immunotype, whereas most MenA invasive strains express the L(3,7)9 or L10 immunotype. Moreover, SBA results may be strain dependent, because immunotypes differ in their sensitivity to complement, emphasizing the need to choose the most appropriate strain. Sera from random subsets of infants, toddlers, children, and adolescents in clinical trials of MenA conjugate vaccines were tested by rSBA using strains 3125 (L10) and F8238 (L11). In unvaccinated subjects from all age groups, the percentages of seropositive samples (rSBA-MenA titer, ≥1:8) was lower using strain 3125 than using strain F8238. However, in toddlers and adolescents immunized with a conjugate MenA vaccine, the percentages of seropositive samples generally were similar using either strain in the rSBA. In two studies, sera also were tested with hSBA. Using hSBA, the differences in the percentages of seroprotective samples (hSBA-MenA titer, ≥1:4) between strains 3125 and F8238 was less apparent, and in contrast with rSBA, the percentage of seroprotective samples from unvaccinated subjects was slightly higher using strain 3125 than using strain F8238. In adults vaccinated with plain MenA polysaccharide, the percentage of seroprotective samples was higher using strain 3125 than with strain F8238, and the vaccine response rates using strain 3125 were better aligned with the demonstrated efficacy of MenA vaccination. In conclusion, SBA results obtained using the MenA L10 3125 strain better reflected vaccine-induced immunity.
Trichinella spiralis – New method for sample preparation and objective detection of specific antigens using a chemiluminescence immunoassay (2020)

The parasitic roundworm Trichinella spiralis is most commonly transmitted to humans through consumption of raw or undercooked meat of infected pigs or game. To prevent human infection, slaughterhouses perform meat safety surveillance using the gold standard "Magnetic Stirrer Method". We introduce a fast and objective method using automated detection of specific Trichinella spiralis antigens by a newly developed immunoassay based on chemiluminescence (ChLIA). Panel A comprised muscle tissue samples from non-infected pigs (n=37). Panel B comprised muscle tissue samples from non-infected pigs spiked with different amounts of Trichinella larvae without collagen capsules (n=56). Panel C contained muscle tissue samples from experimentally infected pigs including Trichinella larvae encapsulated in collagen (n=32). Each sample was shredded with PBS buffer in a knife mill, destroying Trichinella larvae. Following centrifugation, the supernatant (muscle tissue extract containing released excretory and secretory Trichinella spiralis antigens) was used for Trichinella-specific antigen detection by the new Trichinella ChLIA. The overall accuracy of the Trichinella ChLIA was 97.6 %. The specificity of the Trichinella ChLIA was 100 % (panel A). The sensitivity in samples from experimentally infected pigs was 100 % representing a detection limit of 0.01 larvae per gram. Cross-reactivity with parasites other than Trichinella spp. was not observed. This new meat inspection method for the detection of Trichinella spiralis antigens presents high specificity and high sensitivity, especially in truly infected samples. In contrast to the gold standard, this new approach to meat safety surveillance does not require longsome digestion or microscopy by trained personnel.
Probabilistic quantum encoder for single-photon qubits (2004)

We describe an experiment in which a physical qubit represented by the polarization state of a single photon was probabilistically encoded in the logical state of two photons. The experiment relied on linear optics, postselection, and three-photon interference effects produced by a parametric down-conversion photon pair and a weak coherent state. An interesting consequence of the encoding operation was the ability to observe entangled three-photon Greenberger-Horne-Zeilinger states.
Gradient Index Polymer Optics: Achromatic Singlet Lens Design (2010)

We have developed an analytic approximation useful for designing achromatic singlet lenses. The designs are based on gradient index lenses fabricated from nanolayered polymer materials. Raytraced results confirm the achromatic performance of the designs.
Textural Mesoporosity and the Catalytic Activity of Mesoporous Molecular Sieves with Wormhole Framework Structures (1999)

Three different water−alcohol cosolvent systems were used to assemble mesoporous molecular sieve silicas with wormhole framework structures (previously denoted HMS silicas) from an electrically neutral amine surfactant (S°) and a silicon alkoxide precursor (I°). The fundamental particle size and associated textural (interparticle) porosity of the disordered structures were correlated with the solubility of the surfactant in the water−alcohol cosolvents used for the S°I° assembly process. Polar cosolvents containing relatively low volume fractions of CnH2n+1OH alcohols (n = 1−3) gave heterogeneous surfactant emulsions that assembled intergrown aggregates of small primary particles with high textural pore volumes (designated HMS−HTx). Conversely, three-dimensional, monolithic particles with little or no textural porosity (designated HMS−LTx) were formed from homogeneous surfactant solutions in lower polarity cosolvents. Aluminum substituted Al-HMS−HTx analogues with high textural porosity and improved framework accessibility also were shown to be much more efficient catalysts than Al-HMS−LTx or monolithic forms of hexagonal Al-MCM-41 for the sterically demanding condensed phase alkylation of 2,4-di-tert-butylphenol with cinnamyl alcohol. Transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) studies verified the textural differences between wormhole HMS and electrostatically assembled hexagonal MCM-41 and SBA-3 molecular sieves. Power law fits to the scattering data indicated a surface fractal (Ds = 2.76) for HMS−HTx, consistent with rough surfaces. A second power law at lower-q indicated the formation of a mass fractal (Dm = 1.83) consistent with branching of small fundamental particles. Hexagonal MCM-41 and SBA-3 silicas, on the other hand, exhibited scattering properties consistent with moderately rough surfaces (Ds = 2.35 and 2.22, respectively) and large particle diameters (≫1 μm). HMS−LTx silicas showed little or no mass fractal character (Dm = 2.87), and no surface fractal scattering.
Surface reconstruction by Voronoi filtering (1998)

We give a simple combinatorial algorithm that computes a piecewlze-linear approximation of a smooth surface from a finite set of sample points. The algorithm uses Voronoi vertices to remove triangles from the Delaunay triangulation. We prove the algorithm correct by showing that for densely sampled surfaces, where density depends on "local feature size", the output is topologically valid and convergent (both point&e and in surface normals) to the original surface. We deocribe an implementation of the algorithm and shorr example outputs.
Direct Formic Acid Fuel Cells with 600 mA cm<sup>–2</sup> at 0.4 V and 22 °C (2004)

Abstract A demonstration of direct formic acid fuel cells (DFAFCs) generating very high power density at ambient temperature is reported. In particular, the performance of the Pd black as an anode catalyst for DFAFCs with different formic acid feed concentrations at different operating temperatures has been evaluated. The Pd black based DFAFCs with dry air and zero backpressure can generate a maximum power density of 248 and 271 mW cm –2 at 22 °C and 30 °C respectively. The open cell potential is 0.90 V. These results show that DFAFCs are potentially excellent alternative power sources for small portable electronic devices.
Development of advanced, non-toxic, synthetic radiation shielding aggregate (2017)

Abstract For the first time in the world, the capability of red mud waste has been explored for the development of advanced synthetic radiation shielding aggregate. Red mud, an aluminium industry waste consists of multi component, multi elemental characteristics. In this study, red mud from two different sources have been utilized. Chemical formulation and mineralogical designing of the red mud has been done by ceramic processing using appropriate reducing agent and additives. The chemical analysis, SEM microphotographs and XRD analysis confirms the presence of multi-component, multi shielding and multi-layered phases in both the different developed advance synthetic radiation shielding aggregate. The mechanical properties, namely aggregate impact value, aggregate crushing value and aggregate abrasion value have also been evaluated and was compared with hematite ore aggregate and found to be an excellent material useful for making advanced radiation shielding concrete for the construction of nuclear power plants and other radiation installations.
Tuning, measurement and prediction of the impact of freezing on product morphology: A step toward improved design of freeze-drying cycles (2019)

The control of freezing is crucial as it can influence the freeze-drying operation as well as the chemical and physical properties of the lyophilized product such as the specific surface area, dissolution rate, and drug stability. In this review article, we focus on two areas related to lyophilization in the pharmaceutical industry: (1) advances in our understanding of the relationship between the freezing conditions, product morphology and drying efficiency, and (2) the control of nucleation in solutions to be frozen. The final objective is to accelerate the transition toward a more robust design of freeze-drying cycles, based on deep knowledge of the phenomena involved rather than on empirical observations. While these topics are not new, they are areas of significant current interest to the community engaged in drying in the pharmaceutical industry.Abbreviations: FDM: freeze-drying microscope; GMP: good manufacturing practice; INA: ice nucleating agent; QbD: quality by design; PRT: pressure rise test; SSA: specific surface area, m2; UIIN: ultrasound-induced ice nucleation; VIN: vacuum induced nucleation; VISF: vacuum induced surface freezing.
Immunological consequences of intragenus conservation of<i>Mycobacterium tuberculosis</i>T-cell epitopes (2014)

A previous unbiased genome-wide analysis of CD4 Mycobacterium tuberculosis (MTB) recognition using peripheral blood mononuclear cells from individuals with latent MTB infection (LTBI) or nonexposed healthy controls (HCs) revealed that certain MTB sequences were unexpectedly recognized by HCs. In the present study, it was found that, based on their pattern of reactivity, epitopes could be divided into LTBI-specific, mixed reactivity, and HC-specific categories. This pattern corresponded to sequence conservation in nontuberculous mycobacteria (NTMs), suggesting environmental exposure as an underlying cause of differential reactivity. LTBI-specific epitopes were found to be hyperconserved, as previously reported, whereas the opposite was true for NTM conserved epitopes, suggesting that intragenus conservation also influences host pathogen adaptation. The biological relevance of this observation was demonstrated further by several observations. First, the T cells elicited by MTB/NTM cross-reactive epitopes in HCs were found mainly in a CCR6(+)CXCR3(+) memory subset, similar to findings in LTBI individuals. Thus, both MTB and NTM appear to elicit a phenotypically similar T-cell response. Second, T cells reactive to MTB/NTM-conserved epitopes responded to naturally processed epitopes from MTB and NTMs, whereas T cells reactive to MTB-specific epitopes responded only to MTB. Third, cross-reactivity could be translated to antigen recognition. Several MTB candidate vaccine antigens were cross-reactive, but others were MTB-specific. Finally, NTM-specific epitopes that elicit T cells that recognize NTMs but not MTB were identified. These epitopes can be used to characterize T-cell responses to NTMs, eliminating the confounding factor of MTB cross-recognition and providing insights into vaccine design and evaluation.
Transmission characteristics of long-period fiber gratings having arbitrary azimuthal/radial refractive index variations (2003)

A numerical method is presented for determining the transmittance of long-period (LP) fiber-gratings having arbitrary azimuthal/radial refractive index variations. The method uses coupled-mode theory and includes both the sine and cosine character of the LP modes. The model treats interactions between the fundamental LP/sub 01/ mode and high-azimuthal-order cladding modes. The method utilizes the transfer matrix method to model cylindrical layers both in the core and the cladding regions.