gebhart/patrepeval huggingface dataset:
Pentacoordinate Organoaluminum Chemistry:  Catalytic Efficiency of Me<sub>3</sub>Al in the Epoxide Cleavage with Alkynyllithiums (1999)

A new and highly effective catalytic method for epoxide alkynylations has been developed that involves the chelation-controlled alkylation of heterosubstituted epoxides with Me3Al via pentacoordinate organoaluminum complexes by taking advantage of the exceedingly high affinity of aluminum to oxygen. For example, reaction of epoxy ether, (1-benzyloxy)-3-butene oxide (1), in toluene with PhC⋮CLi under the influence of catalytic Me3Al (10 mol%) proceeded smoothly at 0 °C for 5 h to furnish the alkynylation product, 1-(benzyloxy)-6-phenylhex-5-yn-3-ol, in 76% yield [cf. 3% without Me3Al catalyst; 78% with stoichiometric Me3Al under similar conditions]. This represents the first catalytic procedure for the amphiphilic alkylation of epoxides. The participation of pentacoordinate Me3Al complexes of epoxy ethers of type 1 is emphasized by comparing the reactivity with the corresponding simple epoxide, 5-phenyl-1-pentene oxide, which was not susceptible to nucleophile attack of PhC⋮CLi with catalytic Me3Al under similar conditions. The pentacoordinate complex formation of Me3Al with epoxy ether 1 is characterized by low-temperature 13C and 27Al NMR spectroscopy. This approach is also applicable to the selective alkynylation of tosyl aziridines with adjacent ether functionality, which provides a promising method for amino alcohol synthesis.
Interaction between zeolites and cluster compounds. Part 2.—Thermal decomposition of iron pentacarbonyl on zeolites (1984)

Thermal decomposition in a thermobalance of Fe(CO)5 adsorbed on alkali-metal, hydrogen-Y, dealuminated Y, L and omega zeolites proceeds stepwise via slow decarbonylation at low and high temperatures, separated by a fast endothermic reaction. Average CO/Fe ratios have been determined after each step. From i.r. results the former intermediates are assigned to species bearing bridging CO, whereas reaction products with CO/Fe < 1 are associated with highly unsaturated carbonyl clusters in strong interaction with the zeolite.The thermal stability of zeolite/Fe(CO)5 adducts as well as of the intermediates increases with the electron-donor properties of the matrix and can be rationalized using the Sanderson electronegativity concept. Iron loadings ranging from 2.4 wt % in zeolite L up to 10 wt % with NaY and HY are obtained by decomposition in inert atmosphere. Under vacuum conditions loss of metal up to 50% is observed. Metallic iron clusters are the final decomposition products in alkali-metal zeolites, as probed by NO adsorption. In HY part of the metallic iron is oxidized to FeII ions, which are located at cation positions.
Beyond Classical Reactivity Patterns: Hydroformylation of Vinyl and Allyl Arenes to Valuable β- and γ-Aldehyde Intermediates Using Supramolecular Catalysis (2014)

In this study, we report on properties of a series of rhodium complexes of bisphosphine and bisphosphite L1-L7 ligands, which are equipped with an integral anion binding site (the DIM pocket), and their application in the regioselective hydroformylation of vinyl and allyl arenes bearing an anionic group. In principle, the binding site of the ligand is used to preorganize a substrate molecule through noncovalent interactions with its anionic group to promote otherwise unfavorable reaction pathways. We demonstrate that this strategy allows for unprecedented reversal of selectivity to form otherwise disfavored β-aldehyde products in the hydroformylation of vinyl 2- and 3-carboxyarenes, with chemo- and regioselectivity up to 100%. The catalyst has a wide substrate scope, including the most challenging substrates with internal double bonds. Coordination studies of the catalysts under catalytically relevant conditions reveal the formation of the hydridobiscarbonyl rhodium complexes [Rh(Ln)(CO)2H]. The titration studies confirm that the rhodium complexes can bind anionic species in the DIM binding site of the ligand. Furthermore, kinetic studies and in situ spectroscopic investigations for the most active catalyst give insight into the operational mode of the system, and reveal that the catalytically active species are involved in complex equilibria with unusual dormant (reversibly inactivated) species. In principle, this involves the competitive inhibition of the recognition center by product binding, as well as the inhibition of the metal center via reversible coordination of either a substrate or a product molecule. Despite the inhibition effects, the substrate preorganization gives rise to very high activities and efficiencies (TON > 18,000 and TOF > 6000 mol mol(-1) h(-1)), which are adequate for commercial applications.
Construction of a Genomic Map of H. pylori by Pulsed-Field Gel Electrophoresis (PFGE) (2003)

The inability of conventional gel electrophoresis to separate DNA molecules exceeding 50 kb in size led to the development of pulsed-field gel electrophoresis (PFGE) by Schwartz et al, (1)in 1982. He introduced the concept of applying two alternating electric fields (i.e., pulsed-field) to separate DNA molecules greater than 50 kb embedded in an agarose gel matrix. Since then, many instruments based on this principle have been developed. For a discussion of various pulsed-field applications, see review articles by Lai et al. (2) and Crété et al. (3). It was shown that, under the influence of an electric field, a DNA molecule embedded in a gel matrix undergoes reorientation, elongation, and migration along the field toward the anode. When a second field is applied in an alternate direction, the DNA molecule must reorientate, elongate, and migrate along the direction of the new field. Larger DNA molecules will take longer to reorientate than smaller molecules; therefore the larger ones spend less time migrating down the gel than the smaller per pulse time. Consequently, larger DNA molecules will appear near the origin while the smaller molecules will migrate furthest. This principle becomes important when different fragment sizes of DNA are to be separated. PFGE has become an important tool for determining genome sizes, physical mapping of the chromosome, and localization of genes on the chromosome of prokaryotic micro-organisms.
Immobilization of Functional Light Antenna Structures Derived from the Filamentous Green Bacterium Chloroflexus aurantiacus (2008)

The integration of highly efficient, natural photosynthetic light antenna structures into engineered systems while their biophotonic capabilities are maintained has been an elusive goal in the design of biohybrid photonic devices. In this study, we report a novel technique to covalently immobilize nanoscaled bacterial light antenna structures known as chlorosomes from Chloroflexus aurantiacus on both conductive and nonconductive glass while their energy transducing functionality was maintained. Chlorosomes without their reaction centers (RCs) were covalently immobilized on 3-aminoproyltriethoxysilane (APTES) treated surfaces using a glutaraldehyde linker. AFM techniques verified that the chlorosomes maintained their native ellipsoidal ultrastructure upon immobilization. Results from absorbance and fluorescence spectral analysis (where the Stokes shift to 808/810 nm was observed upon 470 nm blue light excitation) in conjunction with confocal microscopy confirm that the functional integrity of immobilized chlorosomes was also preserved. In addition, experiments with electrochemical impedance spectroscopy (EIS) suggested that the presence of chlorosomes in the electrical double layer of the electrode enhanced the electron transfer capacity of the electrochemical cell. Further, chronoamperometric studies suggested that the reduced form of the Bchl-c pigments found within the chlorosome modulate the conduction properties of the electrochemical cell, where the oxidized form of Bchl-c pigments impeded any current transduction at a bias of 0.4 V within the electrochemical cell. The results therefore demonstrate that the intact chlorosomes can be successfully immobilized while their biophotonic transduction capabilities are preserved through the immobilization process. These findings indicate that it is feasible to design biophotonic devices incorporating fully functional light antenna structures, which may offer significant performance enhancements to current silicon-based photonic devices for diverse technological applications ranging from CCD devices used in retinal implants to terrestrial and space fuel cell applications.
NOSIP, a novel modulator of endothelial nitric oxide synthase activity (2001)

Production of nitric oxide (NO) in endothelial cells is regulated by direct interactions of endothelial nitric oxide synthase (eNOS) with effector proteins such as Ca2+-calmodulin, by posttranslational modifications such as phosphorylation via protein kinase B, and by translocation of the enzyme from the plasma membrane caveolae to intracellular compartments. Reversible acylation of eNOS is thought to contribute to the intracellular trafficking of the enzyme; however, protein factor(s) that govern the translocation of the enzyme are still unknown. Here we have used the yeast two-hybrid system and identified a novel 34 kDa protein, termed NOSIP (eNOS interacting protein), which avidly binds to the carboxyl-terminal region of the eNOS oxygenase domain. Coimmunoprecipitation studies demonstrated the specific interaction of eNOS and NOSIP in vitro and in vivo, and complex formation was inhibited by a synthetic peptide of the caveolin-1 scaffolding domain. NO production was significantly reduced in eNOS-expressing CHO cells (CHO-eNOS) that transiently overexpressed NOSIP. Stimulation with the calcium ionophore A23187 induced the reversible translocation of eNOS from the detergent-insoluble to the detergent-soluble fractions of CHO-eNOS, and this translocation was completely prevented by transient coexpression of NOSIP in CHO-eNOS. Immunofluorescence studies revealed a prominent plasma membrane staining for eNOS in CHO-eNOS that was abolished in the presence of NOSIP. Subcellular fractionation studies identified eNOS in the caveolin-rich membrane fractions of CHO-eNOS, and coexpression of NOSIP caused a shift of eNOS to intracellular compartments. We conclude that NOSIP is a novel type of modulator that promotes translocation of eNOS from the plasma membrane to intracellular sites, thereby uncoupling eNOS from plasma membrane caveolae and inhibiting NO synthesis.
Retrospective assessment of the utility of an iron‐based agent for contrast‐enhanced magnetic resonance venography in patients with endstage renal diseases (2013)

ceMRV can be performed with ferumoxytol, yielding similar image quality to a blood pool gadolinium-based contrast agent.
Application of sebomics for the analysis of residual skin surface components to detect potential biomarkers of type-1 diabetes mellitus (2017)

Metabolic imbalance in chronic diseases such as type-1 diabetes may lead to detectable perturbations in the molecular composition of residual skin surface components (RSSC). This study compared the accumulation rate and the composition of RSSC in type-1 diabetic patients with those in matched controls in order to identify potential biomarkers of the disease. Samples of RSSC were collected from the foreheads of type-1 diabetic (n = 55) and non-diabetic (n = 58) volunteers. Samples were subsequently analysed to identify individual components (sebomic analysis). There was no significant difference in the rate of accumulation of RSSC between type-1 diabetics and controls. In terms of molecular composition, 171 RSSC components were common to both groups, 27 were more common in non-diabetics and 18 were more common in type-1 diabetic patients. Statistically significant (P < 0.05) differences between diabetic and non-diabetic volunteers were observed in the recovered amounts of one diacylglyceride (m/z 594), six triacylglycerides (m/z 726-860) and six free fatty acids (m/z 271-345). These findings indicate that sebomic analysis can identify differences in the molecular composition of RSSC components between type-1 diabetic and non-diabetic individuals. Further work is required to determine the practical utility and identity of these potential biomarkers.
Allele-specific increase in basal transcription of the plasminogen-activator inhibitor 1 gene is associated with myocardial infarction. (1995)

Increased plasminogen-activator inhibitor 1 (PAI-1) activity is a common finding in patients with coronary heart disease. Here we provide evidence for an independent, etiological role of PAI-1 in myocardial infarction. The 4G allele of a recently described common 4/5-guanine-tract (4G/5G) polymorphism in the PAI-1 promoter is associated with higher plasma PAI-1 activity. The prevalence of the 4G allele is significantly higher in patients with myocardial infarction before the age of 45 than in population-based controls (allele frequencies of 0.63 vs. 0.53). Both alleles bind a transcriptional activator, whereas the 5G allele also binds a repressor protein to an overlapping binding site. In the absence of bound repressor, the basal level of PAI-1 transcription is increased.
Dense Structure Inference for Object Classification in Aerial LIDAR Dataset (2010)

We present a framework to classify small freeform objects in 3D aerial scans of a large urban area. The system first identifies large structures such as the ground surface and roofs of buildings densely built in the scene, by fitting planar patches and grouping adjacent patches similar in pose together. Then, it segments initial object candidates which represent the visible surface of an object using the identified structures. To deal with sparse density in points representing each candidate, we also propose a novel method to infer a dense 3D structure from the given sparse and noisy points without any meshes and iterations. To label object candidates, we build a tree-structure database of object classes, which captures latent patterns in shape of 3D objects in a hierarchical manner. We demonstrate our system on the aerial LIDAR dataset acquired from a few square kilometers of Ottawa.
An adjustable output driver with a self-recovering Vpp generator for a 4M×16 DRAM (1994)

This paper describes an adjustable output driver with a self-recovering Vpp generator for a 4M/spl times/16 DRAM. Its driver characteristics can easily be switched between fast and slow modes in the assembly process. With a small inductance load, the driver operates 2.5 ns faster in fast mode than in slow mode. In slow mode, this driver reduces the initial drive current and prevents ringing waveforms even with a large inductance load. For example, with a 5-pF capacitance load and a 20-cm wire, the ringing amplitude in slow mode is reduced to 1/3 of fast mode. Users can select the output driver operating mode that best suits their application. The self-recovering Vpp generators feed 16 output drivers and control the generator capacity according to the data pattern to supply the exact amount of Vpp charge consumed by the output drivers. The Vpp generator saves 3.9 mA on average in 25-ns read cycle.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Altered microRNA expression profile with miR-146a upregulation in CD4+T cells from patients with rheumatoid arthritis (2010)

We have detected increased miR-146a in CD4+ T cells of RA patients and its close correlation with TNF-alpha levels. Our findings that miR-146a overexpression suppresses T cell apoptosis indicate a role of miR-146a in RA pathogenesis and provide potential novel therapeutic targets.
Post-tyrosine intermediates in the biosynthesis of mesembrine alkaloids and stereochemistry of protonation at C-7 in the formation of the octahydroindole skeleton (1976)

The biosynthesis of (–)-mesembrenol is shown to involve the sequential intermediates, tyrosine → tyramine →N-methyltyramine, which when labelled at their symmetry equivalent 3,5-positions lead to a 50% loss of tritium leaving the remaining tritium equally distributed between the H-5 and H-7α positions; this result indicates that a stereospecific protonation at C-7 occurs from the β-face during the late stages of the biosynthesis.
Capacitive transducers with curved electrodes (2006)

The design, performance, and potential applications are described for capacitive transducers with curved electrodes. A curved electrode governs the deflection of a compliant electrode under applied stress. A dielectric film on one electrode provides a variable region of fixed electrode spacing. The sensitivity and linear dynamic range of the transducers are higher and wider than devices with parallel electrodes. An electrical advantage is obtained from the permittivity of the dielectric film and a mechanical advantage from its thinness. Transducers have been constructed with silicon diaphragms that bend and polymer membranes that stretch in response to uniform pressure. The silicon sensors measured dynamic pressure changes over a linear range of 125 dB. An 885% change in capacitance was obtained for a sensor with a thin silicon diaphragm. Sensors with polycarbonate membranes demonstrated the ability of a low-cost transducer to measure pressure, fluid flow, displacement, and tilt. An active capacitive bridge circuit was developed to linearly measure capacitance changes up to 1000% and to control electrostatic actuators by force-balanced feedback. Methods and materials to construct microscale transducers are discussed along with the performance limitations of electrostatic actuation.
Investigation of turbulent melt flow in a crystal growth system (2004)

Melt flows associated with a Czochralski crystal growth process was investigated to better understand the transition from a steady laminar regime to an unsteady one as the Grashof number increases. The kinetic energy of the flow as a function of time was examined as an indication of stability. Three-dimensional solutions were interpolated onto a two-dimensional unstructured mesh to compute the Reynolds average mean flow and its fluctuations. Our simulations showed that the transition to unsteady three-dimensional flow begins at a Grashof number of approximately 3.0 million. At higher Grashof numbers (e.g., 6.6 million), the melt flow is fully unsteady, three-dimensional turbulent flow. The simulations further indicated that the melt flow at a Grashof number of 6.6 million is statistically stable, which suggested the Reynolds quasi-steady assumption is valid in this case.
Essentials from cells : a laboratory manual (2003)

Cell Culture and Analysis Subcellular Fractionation Preparation of Macromolecules and Introduction into Cells Light and Epifluorescence Microscopy Confocal Microscopy, Multiphoton Microscopy and Deconvolution Visualization of Organelles, Proteins and Gene Expression In Situ Hybridization Electron Microscopy
All-optical nano modulator, sensor, wavelength converter, logic gate, and flip flop based on a manipulated gold nanoparticle (2010)

We developed a device in which one can shift and control the position of a gold nanoparticle by using special type of optical tweezers realized by guiding and confining light in a nanosize void structure in which the nanoparticle is placed. The nanosize void is positioned inside a multimode interference (MMI) region of a silicon waveguide. The coupling of light from two opposite sides of the optical device generates standing interference waves in the MMI region. The relative phase between the two coupled beams is controllable and therefore also the position of the fringes of the standing waves. Evanescent tails coming from the guided standing waves interfere in the void and allow control the position of the trapped nanoparticle. A nanoparticle with diameter of 30 nm was experimentally implanted in the void. The particle was trapped by one of the high intensity evanescent fringes. Changing the relative phase between the two inputs to the chip allowed us experimentally to modify the location of the fringes and the position of the particle (similarly to what happens in optical tweezers). This experimentally demonstrated capability may be useful for all-optical nano modulators, sensors, wavelength converters, logic gates and even a state machine (e.g. a flip flop).
The Importance of Neighborhood Scheme Selection in Agent-based Tumor Growth Modeling (2015)

Modeling tumor growth has proven a very challenging problem, mainly due to the fact that tumors are highly complex systems that involve dynamic interactions spanning multiple scales both in time and space. The desire to describe interactions in various scales has given rise to modeling approaches that use both continuous and discrete variables, known as hybrid approaches. This work refers to a hybrid model on a 2D square lattice focusing on cell movement dynamics as they play an important role in tumor morphology, invasion and metastasis and are considered as indicators for the stage of malignancy used for early prognosis and effective treatment. Considering various distributions of the microenvironment, we explore how Neumann vs. Moore neighborhood schemes affects tumor growth and morphology. The results indicate that the importance of neighborhood selection is critical under specific conditions that include i) increased hapto/chemo-tactic coefficient, ii) a rugged microenvironment and iii) ECM degradation.
Automated Technique to Measure Noise in Clinical CT Examinations (2015)

The global noise level provides an accurate, robust, and automated method to measure CT noise in clinical examinations for quality assurance programs. The significant difference in noise across scanner models indicates the unexploited potential to efficiently assess and subsequently improve protocol consistency. Combined with other automated characterization of imaging performance (e.g., dose monitoring), the global noise level may offer a promising platform for the standardization and optimization of CT protocols.
Immersion disinfection of irreversible hydrocolloid impressions with sodium hypochlorite. Part II: Effect on gypsum. (1995)

This study investigated the effects of various immersion times and concentrations of sodium hypochlorite on irreversible hydrocolloid impressions and resultant gypsum casts. Irreversible hydrocolloid impressions of a test die were immersed for 1, 5, or 10 minutes in water (control), 5.25%, 0.525%, and 0.0525% sodium hypochlorite and then cast in a Type III stone and a Type V stone. Each stone specimen was evaluated for detail reproduction, dimensional change, surface roughness, and surface hardness. The results indicated that impressions may be immersed in sodium hypochlorite for any of the experimental times and concentrations without negative effects on Type V stone casts. However, immersion of impressions in 5.25% sodium hypochlorite causes some surface deterioration on Type III stone casts.