gebhart/patrepeval huggingface dataset:
Photoaddition to DNA by Nonintercalated Chlorpromazine Molecules (1998)

Chlorpromazine (CPZ) forms photoadducts with DNA and photosensitizes DNA strand breaks. These reactions may be responsible for the reported photomutagenicity of CPZ and for the well-known cutaneous and ocular phototoxicity associated with this drug. We have investigated whether CPZ molecules that are intercalated between base pairs in double-stranded (ds) DNA are the absorbing species for the photoaddition reaction. Quenching of CPZ fluorescence by ds-DNA gave nonlinear Stern-Volmer plots, indicating that more than one type of complex is formed. Linear dichroism spectra of CPZ in the presence of ds-DNA showed a minimum at 345 nm, indicating that the absorption maxima of intercalation complex(es) are red-shifted compared to the absorption maximum of free CPZ at 307 nm. The sum of the absorption of all CPZ complexes with ds-DNA, obtained from dialysis experiments, was broadened and maximized at about 315 nm, indicating that complexes not involving intercalation dominate the absorption spectrum at lambda < 350 nm. The wavelength dependence for covalent binding of CPZ to DNA was determined by irradiating 3H-CPZ in the presence of ds-DNA at 310, 322, 334, 346, 358 and 370 nm. The resulting spectrum correlated closely with the absorption spectrum of nonintercalated CPZ rather than with the spectrum of intercalated CPZ, indicating that the latter species is not the chromophore for the photoaddition reaction.
Purified and porous poly(vinylidene fluoride-trifluoroethylene) thin films for pyroelectric infrared sensing and energy harvesting (2010)

This paper aims at improving the performance of the poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] copolymer for pyroelectric infrared detection and direct thermal to electrical energy conversion. Three different types of samples were prepared and examined: commercial, purified and porous films. Here, full characterization of the thermophysical and electrical properties relevant to pyroelectric infrared detection and energy conversion of both purified and porous P(VDF-TrFE) thin films is presented. Properties measured include (1) density, (2) ferroelectric to paraelectric phase transition temperature, (3) enthalpy of change of phase, (4) electrical resistivity and (5) ferroelectric hysteresis, as well as (6) specific heat, (7) dielectric constant, (8) loss tangent and (9) pyroelectric coefficient as a function of temperature. The figures of merit for infrared detection FV, FI and FD were improved by 47.0, 59.6 and 51.6%, respectively, for the purified films while the porous films with a porosity of 33% showed an improvement of 52.8, 66.3 and 62.6%, respectively, when compared to those of dense commercial P(VDF-TrFE) films. In addition, figures of merit for energy harvesting, FE and k2, indicate that the purified and porous films are attractive for thermal to electrical energy conversion as well.
Investigational developments for the treatment of progesterone-dependent diseases (2008)

Preclinical and clinical evidence demonstrated that PR antagonists and SPRMs are effective for the treatment of progesterone-dependent diseases. Future development will demonstrate if they can become important drugs.
Endoscopic Ultrasonography-Guided Fine-Needle Cytodiagnosis of Mediastinal Metastases from Renal Cell Cancer (2000)

EUS-FNA diagnosis of metastatic RCC is safe and feasible. It is especially useful in the evaluation of the mediastinum for suspected metastases. Cytology examination results in combination with clinical features could suggest the site of origin of the primary, assisting in further management.
Role of B Cells and Antibodies in Acquired Immunity against Mycobacterium tuberculosis (2014)

Accumulating evidence has documented a role for B cells and antibodies (Abs) in the immunity against Mycobacterium tuberculosis (Mtb). Passive transfer studies with monoclonal antibodies (mAbs) against mycobacterial antigens have shown protection against the tubercle bacillus. B cells and Abs are believed to contribute to an enhanced immune response against Mtb by modulating various immunological components in the infected host including the T-cell compartment. Nevertheless, the extent and contribution of B cells and Abs to protection against Mtb remains uncertain. In this article we summarize the most relevant findings supporting the role of B cells and Abs in the defense against Mtb and discuss the potential mechanisms of protection.
Finite-SNR Bounds on the Sum-Rate Capacity of Rayleigh Block-Fading Multiple-Access Channels With No A Priori CSI (2015)

We provide nonasymptotic upper and lower bounds on the sum-rate capacity of Rayleigh block-fading multiple-access channels for the set up where a priori channel state information is not available. The upper bound relies on a dual formula for channel capacity and on the assumption that the users can cooperate perfectly. The lower bound is derived assuming a noncooperative scenario where each user employs unitary space-time modulation (independently from the other users). Numerical results show that the gap between the upper and the lower bound is small already at moderate SNR values. This suggests that the sum-rate capacity gains obtainable through user cooperation are minimal for the scenarios considered in the paper.
Liquid Injection Atomic Layer Deposition of Metallic Ru Thin Films from Ru(tmhd)3 and of High-k TiO2 Thin Films from Ti(O-i-Pr)2(tmhd)2 (2009)

Unique features of liquid delivery atomic layer deposition (LIALD) are considered in this paper in comparison to standard bubbler-type thermal ALD processes. The first part deals with the LIALD growth of metallic Ru thin films using tris(2,2,6,6-tetra-methyl-3,heptanedionato)ruthenium(III) dissolved in ethylcyclo hexane (ECH) and oxygen as metal and oxidation sources. We will show that LIALD is effective in reducing the contents of the corresponding oxides in the noble metal films. The second case deals with LIALD of TiO 2 thin films with a smooth morphology from Ti(O-i-Pr) 2 (thd) 2 dissolved in ECH as a Ti source and H 2 O as an oxidant. The self-saturation growth behavior of the TiO 2 films was confirmed up to 390 oC. The differences in the surface roughness of the nanocrystalline LIALD TiO 2 thin films obtained from Ti(O-i-Pr) 2 (thd) 2 compared to nanocrystalline ALD TiO 2 thin films from Ti(O-i-Pr) 4 are discussed with respect to the differences in the nucleation behavior.
Transformation of Unipolar Single-Walled Carbon Nanotube Field Effect Transistors to Ambipolar Induced by Polystyrene Nanosphere Assembly (2008)

We have fabricated single-walled carbon nanotube (SWNT) field effect transistors (FETs) with molybdenum source and drain contacts. Normally, these devices operate only as p-channel transistors, however, after polystyrene latex nanospheres were attached to the nanotubes close to the contacts, they changed to ambipolar operation. This strategy provides a simple method to modify the electrical behavior of unipolar SWNT-FETs by influencing the gate-channel electric field distribution and offset charge, so enabling complementary circuits to be fabricated.
Directing self-assembly in macromolecular systems: Hydrogen bonding in ordered polymers (2004)

Abstract Hydrogen-bonded side-chain liquid-crystalline block copolymers (SCLCBCPs) containing block segments with proton donors were combined with functionalized mesogenic pendent groups. Studies of a wide range of mesogen and polymer combinations were carried out to study the relationship between morphology and mesophase behavior. The thermal behaviors of the resulting self-assembled microstructures were also examined. A model of the assembly process leading to mesogenic group organization corresponding to different compositions was proposed.
New Approaches for Validation of Lethal Phenotypes and Genetic Reversion in Helicobacter pylori (2001)

Abstract Background. Because of limited genetic tools for use in Helicobacter pylori , tests routinely applied in other bacteria for demonstrating a gene’s role in viability and other phenotypes have not been applied to this organism. In a mutational study of putative response regulator genes, we aimed to develop such tools for H. pylori . Materials and Methods. We attempted to mutate five response regulator genes by allelic exchange insertional mutagenesis. For genes that yielded no viable mutants, a second copy of the gene was inserted into the chromosome via a suicide vector, and it was seen if providing the second copy would permit the gene’s disruption. For genes that yielded mutants with selectable phenotypes, a strategy was developed for reversion whereby an intact copy of the gene is introduced to the organism by transformation with PCR products. Following this procedure, revertants were selected by phenotypic tests then tested for genetic reversion. Results. After failure to attain transformants upon attempted mutation of genes HP0166 and HP1365, we inserted a second copy of each gene within the H. pylori chromosome. In each case the second copy relieved the block of transformation. Mutation of genes HP0703 and HP1021 gave non‐motile and small‐colony phenotypes, respectively. Following transformation with PCR products containing intact copies of the genes, both phenotype and genotype had reverted following phenotypic selections. Conclusions. The methods used in this study provide new approaches for confirming suspected genotype/phenotype associations and should be widely applicable in the study of H. pylori .
Fundamental studies comparing nanobubbles and microbubbles as vascular disrupting agents: Elucidating on the mechanism of action using photoacoustic imaging (Conference Presentation) (2020)

In this work, we examine the potential of photoacoustic imaging for understanding the biophysical mechanism of nanobubble and microbubble-based vascular disrupting therapies. We present for the first time, a direct in-vivo comparison between sub-micron nanobubbles and the commercially available microbubbles. Our results show that PA imaging of tumor oxygenation is capable of measuring the nanobubble-induced almost 40% cell death as a result of vascular disruption.
Figure S1 from Pharmacologic Properties and Preclinical Activity of Sasanlimab, A High-affinity Engineered Anti-Human PD-1 Antibody (2023)

&lt;p&gt;Supplementary Figure 1 shows the complete, confirmed amino acid sequence of sasanlimab&lt;/p&gt;
EVIDENCE THAT RAPAMYCIN HAS DIFFERENTIAL EFFECTS ON IL-4 FUNCTION (1993)

The immunosuppressive drug rapamycin, which inhibits the response of T cells to growth-promoting lymphokines, has been considered to act as a general inhibitor of cytokine action. Our investigations into the effect of rapamycin on human IL-4, a cytokine controlling B and T cell function, show this not to be the case. Unexpectedly, rapamycin actually synergized with IL-4 in both the upregulation of CD23 expression and the down-regulation of the type II (p75) TNF receptor, while in the same B cell line, rapamycin simultaneously inhibited the IL-4-dependent production of TNFα and β. These results raise the possibility that multiple IL-4 signaling pathways may be responsible for the pleiotropic effects of IL-4, and have important implications for both the experimental and possible clinical in vivo use of rapamycin as a selective immunosuppressant.
Synthesis strategies to control the Al distribution in zeolites: thermodynamic and kinetic aspects (2022)

The activity and selectivity of acid-catalyzed chemistry is highly dependent on the Brønsted and Lewis acid sites generated by Al substitutions in a zeolite framework with the desired pore architecture. The siting of two Al atoms in close proximity in the framework of high-silica zeolites can also play a decisive role in improving the performance of redox catalysts by producing exchangeable positions for extra-framework multivalent cations. Thus, considerable attention has been devoted to controlling the Al incorporation through direct synthesis approaches and post-synthesis treatments to optimize the performance as (industrial) solid catalysts and to develop new acid- and redox-catalyzed reactions. This Feature Article highlights bottom-up synthetic strategies to fine-tune the Al incorporation in zeolites, interpreted with respect to thermodynamic and kinetic aspects. They include (i) variation in extra-framework components in zeolite synthesis, (ii) isomorphous substitution of other heteroatoms in the zeolite framework, and (iii) control over the (alumino)silicate network in the initial synthesis mixture <i>via in situ</i> and <i>ex situ</i> methods. Most synthetic approaches introduced here tentatively showed that the energy barriers associated with Al incorporation in zeolites can be variable during zeolite crystallization processes, occurring in complex media with multiple chemical interactions. Although the generic interpretation of each strategy and underlying crystallization mechanism remains largely unknown (and often limited to a specific framework), this review will provide guidance on more efficient methods to prepare fine-tuned zeolites with desired chemical properties.
Millimeter-Wave Radio-Over-Fiber Network for Linear Cell Systems (2017)

We discuss and propose millimeter-wave linear cell systems for signal distribution on railway radiocommunication systems between train and trackside, and a foreign object debris detection system for airport runways using the radio-over-fiber network technology. Linear cell configurations based on wavelength-division multiplexing (WDM) and power-splitter-based distribution networks are discussed and demonstrated experimentally. A single-sideband modulation for data transmission in an intermediate frequency over a fiber system is successfully transmitted with an ultrafast wavelength-tunable laser diode for WDM routing to track the train car within 3 μs. Radar signal distribution by an optical double-sideband suppressed-carrier modulation mitigates the dispersion effect of the fiber cable to transmit a 32-GHz signal into the remote radar heads.
Uncertainty Quantification of Pull-In Phenomenon in Capacitive RF-MEMS (2011)

The goal of this paper is to elucidate the effects of device geometry and fabrication process variations on the statistical pull-in performance of an electrostatically-actuated capacitive radio frequency micro electro-mechanical system (RF-MEMS) switch through the use of uncertainty quantification. The prediction of switch dynamics and pull-in voltage involves the coupled interaction of elastodynamics, fluid dynamics, and electrostatics. A comprehensive computational framework based on the finite volume method (FVM) is developed to account for these effects. The immersed boundary method (IBM) is employed to couple the fluid, structure and electrostatics. A population of switches is fabricated, and geometry and material properties measured; these measurements provide the probabilistic input information needed for uncertainty quantification. Deterministic simulations are first made for a specific device, and the gap-versus-voltage and pull-in voltage predicted compare favorably with measurements and theoretical estimation. Uncertainty quantification of dynamic pull-in is performed next, using the stochastic collocation method for uncertainty propagation. Probability density functions (PDFs) of pull-in voltage and gap-versus-time are computed. The primary determinants of uncertainty in pull-in voltage are found to be the membrane thickness and gap size, with uncertainty in residual stress having a relatively small effect.
Designing siRNA that distinguish between genes that differ by a single nucleotide (2005)

Small interfering RNAs (siRNAs), the guides that direct RNA interference (RNAi), provide a powerful tool to reduce the expression of a single gene in human cells.Ideally, dominant, gain-of-function human diseases could be treated using siRNAs that specifically silence the mutant disease allele, while leaving expression of the wild-type allele unperturbed.Previous reports suggest that siRNAs can be designed with single nucleotide specificity, but no rational basis for the design of siRNAs with single nucleotide discrimination has been proposed.We systematically identified siRNAs that discriminate between the wild-type and mutant alleles of two disease genes: the human Cu, Zn superoxide dismutase (SOD1) gene, which contributes to the progression of hereditary amyotrophic lateral sclerosis through the gain of a toxic property, and the huntingtin (HTT) gene, which causes Huntington disease when its CAG-repeat region expands beyond approximately 35 repeats.Using cell-free RNAi reactions in Drosophila embryo lysate and reporter assays and microarray analysis of off-target effects in cultured human cells, we identified positions within an siRNA that are most sensitive to mismatches.We also show that purine:purine mismatches imbue an siRNA with greater discriminatory power than other types of base mismatches.siRNAs in which either a G:U wobble or a mismatch is located in the ''seed'' sequence, the specialized siRNA guide region responsible for target binding, displayed lower levels of selectivity than those in which the mismatch was located 39 to the seed; this region of an siRNA is critical for target cleavage but not siRNA binding.Our data suggest that siRNAs can be designed to discriminate between the wild-type and mutant alleles of many genes that differ by just a single nucleotide.
Steady‐state imaging for visualization of endovascular interventions (2003)

Steady-state imaging techniques offer the potential to couple high spatial and temporal resolution with good signal-to-noise ratio (SNR), which makes them ideally suited for fluoroscopic applications. However, disturbance of the steady state can result in artifacts and substantially reduced signal levels. In this study the use of steady-state imaging techniques was investigated as a means of guiding endovascular interventions with fluoroscopic MRI. Devices containing localized susceptibility defects were shown to disturb the steady-state signal of spins that pass through the magnetic field disturbances. It was demonstrated that these effects are appreciable and can make delineation of interventional devices difficult in the presence of flow. T(1)-shortening contrast agents were shown to dramatically reduce these effects by reducing the time taken to achieve steady state. The addition of a blood pool agent in an in vivo model was found to be necessary for adequate visualization of a dysprosium-marked catheter.
Prozesse im Grundwasser und ihre Modellierung; Geologische Ansätze zur Bestimmung der Heterogenität des Untergrundes — geologisch-hydraulische Charakteristika (1996)

Geologische Strukturen beeinflussen in vielfältiger Weise den Transport von Stoffen im Grundwasser. In der Literatur sind verschiedene Konzepte der Aquifer-Sedimentologie vorgeschlagen worden. Kombinierte sedimentologisch-geophysikalische Studien von Schottergrundwasserleitern stellen eine Möglichkeit dar, solche Konzepte zu konkretisieren. Die Resultate eines solchen Ansatzes bilden die Grundlage für konzeptionelle Modelle des Stofftransportes in verschiedenen Massstabsbereichen.
<title>Density of states and lasing at the edge of a photonic stop band in dye-doped cholesteric liquid crystals</title> (1999)

We present simulations of optical propagation in cholesteric liquid crystal (CLC) films and find a stop band in which the wave is evanescent and the density of states is zero. Sharp structure is found in the calculated transmission spectra near the band edge. This corresponds to enhanced residence times and lower group velocities, as well as to significant enhancements of the energy density and of the density of states within the samples. These simulation are consistent with our measurements of suppressed emission within the stop band and of enhanced emission at the band edge for dye molecules doped into CLCs. We also observe spatially coherent emission from the CLC sample with narrow spectral lines at the edge of the stop band and a distinct threshold behavior for the coherent emission. The results of computer simulations together with observations of emission and lasing demonstrate that the optical properties of CLCs, including laser action at the modes closest to the band edge, are consequences of its band gap structure. The compact nature of these structures and the ease with which they ca be fabricated suggest that they may be useful for producing integrated lasers and photonic devices.
Preclinical Studies of Amixicile, a Systemic Therapeutic Developed for Treatment of Clostridium difficile Infections That Also Shows Efficacy against Helicobacter pylori (2014)

Amixicile shows efficacy in the treatment of Clostridium difficile infections (CDI) in a mouse model, with no recurrence of CDI. Since amixicile selectively inhibits the action of a B vitamin (thiamine pyrophosphate) cofactor of pyruvate:ferredoxin oxidoreductase (PFOR), it may both escape mutation-based drug resistance and spare beneficial probiotic gut bacteria that do not express this enzyme. Amixicile is a water-soluble derivative of nitazoxanide (NTZ), an antiparasitic therapeutic that also shows efficacy against CDI in humans. In comparative studies, amixicile showed no toxicity to hepatocytes at 200 μM (NTZ was toxic above 10 μM); was not metabolized by human, dog, or rat liver microsomes; showed equivalence or superiority to NTZ in cytochrome P450 assays; and did not activate efflux pumps (breast cancer resistance protein, P glycoprotein). A maximum dose (300 mg/kg) of amixicile given by the oral or intraperitoneal route was well tolerated by mice and rats. Plasma exposure (rats) based on the area under the plasma concentration-time curve was 79.3 h · μg/ml (30 mg/kg dose) to 328 h · μg/ml (100 mg/kg dose), the maximum concentration of the drug in serum was 20 μg/ml, the time to the maximum concentration of the drug in serum was 0.5 to 1 h, and the half-life was 5.6 h. Amixicile did not concentrate in mouse feces or adversely affect gut populations of Bacteroides species, Firmicutes, segmented filamentous bacteria, or Lactobacillus species. Systemic bioavailability was demonstrated through eradication of Helicobacter pylori in a mouse infection model. In summary, the efficacy of amixicile in treating CDI and other infections, together with low toxicity, an absence of mutation-based drug resistance, and excellent drug metabolism and pharmacokinetic metrics, suggests a potential for broad application in the treatment of infections caused by PFOR-expressing microbial pathogens in addition to CDI.
Supplementary Data from Covalent Targeting of Fibroblast Growth Factor Receptor Inhibits Metastatic Breast Cancer (2023)

&lt;p&gt;This file includes supplementary figures S1-S8 and supplementary tables S1-S3.&lt;/p&gt;