gebhart/patrepeval huggingface dataset:
Construction of a novel glucose‐sensing molecule based on a substrate‐binding protein for intracellular sensing (2010)

A novel transcriptional regulator responding to glucose was designed with a substrate-binding protein (SBP) as a probe towards intracellular sensing system for glucose in mammalian cells. A chimeric protein of an SBP for glucose (GBP) and a LacI-type regulator, LacI (SLCP(GL) ), was designed, constructed and characterized using Escherichia coli recombinant protein. We report that SLCP(GL) has a glucose-specific binding ability and an operator-sequence specific DNA-binding ability. The loss of its DNA-binding ability in the presence of glucose suggests a role as a transcriptional regulator in vitro. The glucose-dependent gene regulation function of SLCP(GL) in cells was investigated using mammalian cells co-transfected with SLCP(GL) and Lac operator-fused luciferase gene constructs. The luciferase activity of the transfected cells increased with the glucose concentration in the medium, showing that the expression of the luciferase gene is regulated by SLCP(GL) , which can dissociate from DNA in a glucose concentration-dependent manner. Therefore, we demonstrated that SLCP(GL) functions as a glucose-sensitive transcriptional regulator in mammalian cells. These results reveal the possibility of developing an SBP-based regulator as a probe of intracellular sensing and gene regulation system for mammalian cells in response to a desired ligands depending on the SBP ligand specificity.
O1‐04‐08: C. elegans models of Alzheimer's disease and Parkinson's disease: Systems biology identifies an interaction between tau and LRRK2 (2010)

We have used a systems biology approach to understand the biology of LRRK2, which is a gene that is mutated in Parkinson's disease (PD) and associated with pleiotropic pathology that includes α-synuclein or tau inclusions. We generated lines of C. elegans expressing LRRK2 (WT, G2019S or R1441C), and used gene arrays to identify transcriptional changes associated with mitochondrial toxicity (induced by rotenone). Data from these gene arrays was combined with public transcriptome data of patients with PD. The data were analyzed using two systems biology algorithms, Context Likelihood of Relatedness and Mode-of-action by Network Inference, to identify genes possibly interacting with LRRK2. Identified genes (800) were tested by RNA knockdown using a C. elegans line that expresses LRRK2, GFP (in dopaminergic neurons) and a RNAi hypersensitivity mutation, rrf3 (pk1201). Follow-up studies are being done using C. elegans lines lacking lrk-1, the homologue of LRRK2, and in human tissues. One of the striking networks observed was linked to mcrotubules and tau protein, including ptl-1 (tau protein), cdk-5, coel-1 (tubulin folding cofactor E-like, TBCel) and ebp-1 (microtubule end-plus tracking protein, EB1). RNAi knockdown protected (cdk-5, coel-1, ebp-1) or enhanced (tau) loss of dopaminergic neurons in C. elegans expressing LRRK2. The finding of a systems and RNAi link between tau and LRRK2 prompted us to examine the role of LRRK2 in degeneration induced by tau protein. Knockdown of lrk-1 (the C. elegans homologue of LRRK2) protected against degeneration associated with expression of N337V Tau protein in C. elegans. Conversely, co-expression of LRRK2 (R1441C or G2019S) exacerbated tau-mediated degeneration. Tau is known to be one of the major proteins contributing to degeneration in Alzheimer's disease. Interestingly, GWAS studies of PD consistently rank tau as the second most significant risk factor. However, the relationship between tau and PD is unclear. Our studies raise the possibility that tau might be contributing to the etiology of PD through a mechanism mediated by LRRK2, or vice versa. The identification of other genes known to modify tau function (cdk-5) or microtubule function (coel-1 and ebp-1) supports the putative role of tau in the degenerative pathway.
INITIAL ANIMAL EXPERIENCE WITH THE HEARTWARE VAD (2004)

During the past six years, HeartWare has developed a miniaturized passively magnetically suspended centrifugal VAD. The new pump design was evaluated in a series of 22 animal experiments for a total of 618 cumulative implant days. The animal studies were conducted for a variety of purposes, including anatomical fit, design iteration, and confirmation of hemocompatibility. We report on a study of the five long term sheep implants that led to the final pump design. All experiments were conducted over a mean period of 83 +/−12 days without antico-agulation. Animals were electively terminated after 90 days except one, which had an electrical failure in a controller prototype. Overall pump performance at a rotational speed of 3000 rpm was excellent with a mean pump flow rate of 6.1 +/− 1.4 I/min and a range of 3 to 11 I/min. During the study no pump thrombus formation or pump failures occurred. Hemolysis was low with mean plasma free hemoglobin of 5.1 +/− 5.0 mg/dl. End organ function remained within the physiological range expressed by a mean creatinine-level of 1.O +/− 0.2 mg/dl and mean bilirubin of 0.1 +/− 0.05 mg/dl. Animals necropsy revealed clean pumps and no signs of pump related end organ damage. Initial animal experiments demonstrated excellent performance of the proprietary Heartware pump technology. Based upon these results, pump design was finalized. Further animal experiments with the final design are now underway in preparation for clinical trials.
SIFT Implementation and Optimization for General-Purpose GPU (2007)

With the addition of free programmable components to modern graphics hardware, graphics processing units&#13;\n(GPUs) become increasingly interesting for general purpose computations, especially due to utilizing parallel&#13;\nbuffer processing. In this paper we present methods and techniques that take advantage of modern graphics&#13;\nhardware for real-time tracking and recognition of feature-points. The focus lies on the generation of feature&#13;\nvectors from input images in the various stages. For the generation of feature-vectors the Scale Invariant Feature&#13;\nTransform (SIFT) method [Low04a] is used due to its high stability against rotation, scale and lighting condition&#13;\nchanges of the processed images. We present results of the various stages for feature vector generation of our&#13;\nGPU implementation and compare it to the CPU version of the SIFT algorithm. The approach works well on&#13;\nGeforce6 series graphics board and above and takes advantage of new hardware features, e.g. dynamic&#13;\nbranching and multiple render targets (MRT) in the fragment processor [KF05]. With the presented methods&#13;\nfeature-tracking with real time frame rates can be achieved on the GPU and meanwhile the CPU can be used for&#13;\nother tasks.
Explicit runaway criterion for catalytic reactors with transport limitations (1991)

Abstract Most existing criteria for predicting parametric sensitivity or runaway in a catalytic reactor are based on a single‐phase model that does not account for interparticle heat and mass transfer resistances and intraparticle diffusion. Accounting for these effects, the simple criterion defines the boundary of operating conditions, in which a catalytic reactor is insensitive to small perturbations. Here, r(T f ,C f ) is the intrinsic reaction rate at inlet conditions, d t (d p ) and U(h) are the diameter of reactor tube (catalyst particle) and heat transfer coefficient between the fluid and tube wall (catalyst particle), respectively. The function f(ϕ 0 ), where ϕ 0 is the normalized Thiele modulus at inlet conditions, accounts for the effects of intraparticle diffusion. For the common case of equal coolant and feed temperatures, f(ϕ 0 ) = 1 for ϕ 0 &lt; 0.5 and f(ϕ 0 ) = 2 ϕ 0 for ϕ 0 &gt;0.5. The conservatism associated with the above criterion is comparable to the uncertainty involved in determining the parameters of the packed bed.
<title>Spectroscopic investigations of dithienyl polyenes</title> (1999)

To understand the photophysics of nonlinear absorbers, we have investigated the photophysics of a series of di(2- thienyl-3,3',4,4'-butyl)polyenes. Spectroscopic measurements, including UV/Vis, fluorescence, fluorescence lifetimes, fluorescence quantum yields, triplet state lifetime, solvent effects and two-photon absorption coefficient were obtained as a function of the number of double bonds (n equals 1 - 5). Trends in the data reflected the ordering, energy gap between and mixing of <SUP>1</SUP>B<SUB>u</SUB>* and <SUP>1</SUP>A<SUB>g</SUB>* excited state configurations. We investigated the solvatochromism of a series of (alpha) ,(omega) -di(2- dithienyl 3,3',4,4'-butyl) polyenes. Absorption (n equals 1 - 5 double bonds) were collected in a series of aprotic solvents. The absorption energy dispersion effect sensitivity increased smoothly with n, reaching asymptotic behavior as n approached 5. The emission energy had less solvent sensitivity, giving evidence for a polar <SUP>1</SUP>B<SUB>u</SUB>* absorbing state and a nonpolar <SUP>1</SUP>A<SUB>g</SUB>* emitting state. We observed sensitivity of the absorbing and emitting states to solute-solvent dipole-dipole interactions, suggesting the dithienyl polyenes had a polar syn ground state conformation.
Photonic crystals: a new quasi-optical component for high-power microwaves (1996)

The interaction of a high-power microwave beam with a face-centered-cubic photonic crystal is studied. A Sinus-6 high-power relativistic repetitively pulsed electron beam accelerator was used to drive a slow wave structure in vacuum to generate 450 MW at 9.65 GHz. It is shown that the photonic crystal, comprised of a periodic arrangement of air holes in a dielectric host, is capable of performing as a quasi-optical reflector similar to a metal. The crystals can be designed to operate as efficient frequency-selective reflectors over narrow frequency ranges. We propose that photonic crystals can have many applications in high-power microwave research.
N‐acetylglucosamine and adenosine derivatized surfaces for cell culture: 3T3 fibroblast and chicken hepatocyte response (1994)

3T3 fibroblasts and primary chicken hepatocytes were cultured on derivatized polystyrene surfaces to examine the effect of cell-specific ligands on cellular morphology and growth. Surfaces were prepared by derivatizing chloromethylated polystyrene with N-acetylglucosamine (GlcNAc; recognized by the chicken asialoglycoprotein receptor) and adenosine (not recognized by adult hepatocytes). These surfaces were compared with tissue culture polystyrene (TCPS), acid-cleaned glass, and the unmodified chloromethylated polystyrene. The spreading, cytoskeletal structure and growth of the fibroblasts following attachment to these surfaces were examined. The extent of attachment, total protein levels, and DNA contents for surfaces-attached chicken hepatocytes were also measured. Fibroblast spreading was greatest on polymer surfaces derivatized with GlcNAc, whereas cytoskeletal structure and growth rate were independent of surface chemistry. Although chicken hepatocytes attached most efficiently to the GlcNAc derivatized polymer, the total protein and DNA levels of the surface-attached cells were not affected. In anticipation of the application of these polymers for cell culture and hybrid artificial organ design, the GlcNAc-derivatized polystryrene was fabricated into porous microcarriers. Fibroblasts grew avidly on the microcarriers, whereas chicken hepactocytes adhered well to the formed large aggregates around the microcarriers.
Mongersen (GED-0301) for Active Crohn's Disease: Results of a Phase 3 Study (2019)

GED-0301 did not demonstrate efficacy vs placebo in active CD.
Pharmacokinetics and Safety of PTC596, a Novel Tubulin‐Binding Agent, in Subjects With Advanced Solid Tumors (2021)

PTC596 is a novel, orally bioavailable, small-molecule tubulin-binding agent that reduces B-cell-specific Moloney murine leukemia virus insertion site 1 activity and is being developed for the treatment of solid tumors. A phase 1, open-label, multiple-ascending-dose study was conducted to evaluate the pharmacokinetics and safety of the drug in subjects with advanced solid tumors. PTC596 was administered orally biweekly based on body weight. Dose escalation followed a modified 3 + 3 scheme using doses of 0.65, 1.3, 2.6, 5.2, 7.0, and 10.4 mg/kg. Following oral administration, PTC596 was rapidly absorbed, and between 0.65 and 7.0 mg/kg reached a maximum plasma concentration 2 to 4 hours after dosing. Area under the plasma concentration-time curve increased proportionally with body weight-adjusted doses. Maximum plasma concentration increased with dose, although the increase was less than dose proportional at dose levels >2.6 mg/kg. No accumulation occurred after multiple administrations up to 7.0 mg/kg. PTC596 had a terminal half-life ranging 12 to 15 hours at all doses except for the highest dose of 10.4 mg/kg, where the half-life was approximately 20 hours. Overall, PTC596 was well tolerated. The most frequently reported PTC596-related treatment-emergent adverse events were mild to moderate gastrointestinal symptoms, including diarrhea (54.8%), nausea (45.2%), vomiting (35.5%), and fatigue (35.5%). Only 1 patient treated with 10.4 mg/kg experienced dose-limiting toxicity of neutropenia and thrombocytopenia, both of which were reversible. Stable disease as best overall response was observed among 7 patients, with 2 patients receiving the study drug up to 16 weeks. These results support the further development of PTC596 for the treatment of solid tumors.
(Invited) Linking Ionomer/Electrocatalyst Interactions to Membrane Electrode Assembly Performance and Durability in Proton Exchange Membrane Fuel Cells (2021)

The proper integration of materials to enable high performing low temperature fuel cell operation has never been more crucial to realizing the isolated (e.g. half-cell or ex-situ) improvements of advanced electrocatalysts, supports and ionomers in an effort to maximize efficiency. The integration pathway for oxygen reduction electrocatalysts, from initial testing in a rotating disk electrode (RDE) to their apex form as porous electrodes in a membrane electrode assembly (MEA) is replete with potential pitfalls. Along the route to improving MEA level electrocatalyst kinetics and electrode transport properties are numerous choices relating to ink formulation (i.e. solvents and solvent ratios), ink processing and deposition methodology, ionomer content and chemistry and electrochemical MEA conditioning. Combined with carbon morphology/porosity, such variables can alter the final electrode morphology, influencing active site accessibility and ORR activity as well as oxygen transport resistance and electrode proton conductivity.[1–5]
Comparison of the Effects of Metabolic Acidosis and Acute Uremia on Carbohydrate Tolerance (1972)

In an attempt to assess the role of metabolic acidosis in the glucose intolerance of uremia, we have estimated insulinmediated glucose uptake in normal dogs, in acidotic dogs with normal renal function, and in uremic dogs. Mean steady state plasma glucose and insulin levels were measured in eighteen dogs (pH 7.4 ± .01) during constant infusion of glucose and insulin, while endogenous insulin secretion was suppressed by infusion of propranolol and epinephrine. The dogs were then divided into three groups: moderate acidosis was produced by giving 7 gm. NH4Cl/ day for four days; severe acidosis, 12 gm. NH4Cl/day for four days; and uremia (serum creatinine 15.7 ± 0.2 mg. per cent) by anastomosing both ureters to the vena cava. Duplicate infusions were then performed and the results compared to control values. Plasma insulin levels were identical, despite the presence of either acidosis or uremia. The mean increase in plasma glucose in moderate acidosis (pH 7.2 ± 0.1) over controls was 39 mg./l00 ml. (p &amp;lt; .05); in severe acidosis (pH 7.0 ± .04) plasma glucose increased by 69 mg,/100 ml. (p &amp;lt; .01). However, the mean increase in plasma glucose (149 mg./100 ml.) in uremia (pH 7.3 ± .03) was significantly greater (p &amp;lt; .005) than that following acidosis, although the pH did not significantly fall. Thus, although metabolic acidosis results in deterioration of glucose tolerance, the magnitude of the change does not seem able to account for the carbohydrate intolerance of uremia.
cpmViz: A Web-Based Visualization Tool for Uncertain Spatiotemporal Data (2019)

The goal of the VAST challenge 2019 Mini Challenge 2 was to visualize radioactive contaminations measured by mobile and static sensors and their changes over time, allowing city officials to determine the severity of the leakage at the city's nuclear power plant. We propose cpmViz, a web-based tool that allows for interactive data exploration of the sensor readings in both of the spatial and temporal dimensions. The tool consists out of three views that are connected via linking and scrolling. We visualize static sensor uncertainty by introducing Voronoi cells to illustrate how much space is covered by an individual measurement unit. For mobile sensors, we showcase their activity periods and introduce the concept of sensor streaks as periods of uninterrupted recordings as a temporal uncertainty measure. As for spatial uncertainty, we color individual districts based on the amount of data that was recorded inside the user's selected time window. Using our system, we were able to easily spot major events like the city's initial earthquake in the sensor readings. Certain southern districts are clearly visible as areas of concern that we consider in need of more static sensors. Furthermore, we were also able to identify static as well as moving contaminations.
Characterization of a Molecular Sieve Coating Using Ellipsometric Porosimetry (2007)

Ellipsometric porosimetry was used to determine the adsorption isotherms of toluene, methanol, and water on b-oriented Silicalite-1 coatings with a thickness of less than ca. 250 nm and to obtain adsorption kinetics. The adsorption isotherms are of sufficient quality to reveal several aspects of the pore structure such as the adsorbate capacity and the adsorbate/framework affinity. The use of a combination of different molecular probes in ellipsometric porosimetry to elucidate the molecular accessibility of Silicalite-1 pores is demonstrated. It is shown that ellipsometric porosimetry is an appropriate technique for probing the influence of aging of the Silicalite-1 coating and of planarization polishing on the porosity, pore accessibility, and adsorbate/framework affinity.
Two types of oxygen-deficient centers in synthetic silica glass (1988)

The effects of ArF excimer laser irradiation on dehydrated high-purity silica glass were investigated on both the optical-absorption bands due to oxygen-deficient centers (ODC) and the formation of ${E}^{\ensuremath{'}}$ centers. With an intense uv flux from an excimer laser, an ${E}^{\ensuremath{'}}$-center density of the order of ${10}^{15}$ ${\mathrm{cm}}^{\ensuremath{-}3}$ was created. The 7.6-eV absorption band remains at the original level, while the 5.0-eV absorption band having the 4.3-eV emission band decreased. Both bands were reduced by heat treatment in an ${\mathrm{O}}_{2}$ atmosphere. These results suggest that there exist two types of ODC: ODC(I), which is responsible for the 7.6-eV band, and ODC(II), for the 5.0-eV band. The concentrations of ODC(I) and ODC(II) were evaluated to be 1 \ifmmode\times\else\texttimes\fi{} ${10}^{18}$ ${\mathrm{cm}}^{\ensuremath{-}3}$ through an analysis of the gas treatment data and of the order of ${10}^{14}$ ${\mathrm{cm}}^{\ensuremath{-}3}$ through the growth curve of the ${E}^{\ensuremath{'}}$ centers, respectively. The structural origin of ODC(I) has been attributed to the Si-Si bond, judging from the fact that the peak energy and cross section of the absorption were in close agreement with those of the ${\mathrm{Si}}_{2}$${\mathrm{H}}_{6}$ molecule. Theoretical calculations on defect energy levels by O'Relly and Robertson supported the structural model for IDC(I) and suggested an unrelaxed oxygen vacancy for ODC(II). These assignments were also consistent with the results of a quenching experiment in which the fictive temperature of samples was changed; the equilibrium between concentrations of ODC(I) and ODC(II) shifted in a reasonable manner.
Role of Fluoride Doping in Low-Temperature Combustion-Synthesized ZrOx Dielectric Films (2022)

Zirconium oxide (ZrO<sub><i>x</i></sub>) is an attractive metal oxide dielectric material for low-voltage, optically transparent, and mechanically flexible electronic applications due to the high dielectric constant (κ ∼ 14-30), negligible visible light absorption, and, as a thin film, good mechanical flexibility. In this contribution, we explore the effect of fluoride doping on structure-property-function relationships in low-temperature solution-processed amorphous ZrO<sub><i>x</i></sub>. Fluoride-doped zirconium oxide (F:ZrO<sub><i>x</i></sub>) films with a fluoride content between 1.7 and 3.2 in atomic (at) % were synthesized by a combustion synthesis procedure. Irrespective of the fluoride content, grazing incidence X-ray diffraction, atomic-force microscopy, and UV-vis spectroscopy data indicate that all F:ZrO<sub><i>x</i></sub> films are amorphous, atomically smooth, and transparent in visible light. Impedance spectroscopy measurements reveal that unlike solution-processed fluoride-doped aluminum oxide (F:AlO<sub><i>x</i></sub>), fluoride doping minimally affects the frequency-dependent capacitance instability of solution-processed F:ZrO<sub><i>x</i></sub> films. This result can be rationalized by the relatively weak Zr-F versus Zr-O bonds and the large ionic radius of Zr<sup>+4</sup>, as corroborated by EXAFS analysis and MD simulations. Nevertheless, the performance of pentacene thin-film transistors (TFTs) with F:ZrO<sub><i>x</i></sub> gate dielectrics indicates that fluoride incorporation reduces <i>I</i>-<i>V</i> hysteresis in the transfer curves and enhances bias stress stability versus TFTs fabricated with analogous, but undoped ZrO<sub><i>x</i></sub> films as gate dielectrics, due to reduced trap density.
Palladium-Catalyzed Cross-Coupling of Aryl Chlorides and Triflates with Sodium Cyanate: A Practical Synthesis of Unsymmetrical Ureas (2012)

An efficient method for palladium-catalyzed cross-coupling of aryl chlorides and triflates with sodium cyanate is reported. The protocol allows for the synthesis of unsymmetrical N,N'-di- and N,N,N'-trisubstituted ureas in one pot and is tolerant of a wide range of functional groups. Insight into the mechanism of aryl isocyanate formation was gleaned through studies of the transmetalation and reductive elimination steps of the reaction, including the first demonstration of reductive elimination from an arylpalladium isocyanate complex to produce an aryl isocyanate.
Structural Model and Computer Modeling Study of Allophane (2007)

A model of an allophane nanoball is proposed. The model structure is characterized by a Si/Al ratio of 0.49, has external and internal diameters of 50 and 40 Å, respectively, and contains six holes of about 7 Å size connecting the internal void of the nanoball with external space. The calculated XRD pattern and Raman spectrum of the structure are in a good agreement with the corresponding experimental data. Molecular dynamics calculations of hydrated allophane have shown that the model reproduces the main experimental findings such as the adsorption of water molecules in the void of allophane or the exchange between the "internal" and "external" water. The adsorption of water molecules occurs mostly in the regions with negative electrostatic potential, where the molecules find an environment close to that in bulk liquid water that explains the high water retention by this aluminosilicate. The allophane model can be used as a basis in further refinements of its structure as well as in molecular modeling studies of this aluminosilicate.