gebhart/patrepeval huggingface dataset:
General assay for phosphoproteins in cerebrospinal fluid: A candidate market for paraneoplastic cerebellar degeneration (1990)

The components of protein phosphorylation systems (protein kinases, protein phosphatases, and their phosphoprotein substrates) are highly enriched in neuronal cells compared with other cell types. We exploited this relative neuronal enrichment of protein phosphorylation system components to develop a general assay technique for putative protein kinase substrates (phosphoproteins) in human cerebrospinal fluid. Using this cerebrospinal fluid phosphoprotein assay, we have detected a putative protein kinase C substrate protein of apparent Mr 60 kd in 6 of 14 patients with paraneoplastic cerebellar degeneration but not in any of 55 patients with a variety of other neurological diseases. Phosphoproteins in cerebrospinal fluid may provide novel and unique markers for the diagnosis or staging of neuronal diseases as well as offer potential insights into the biochemical characterization of affected neuronal populations.
Modeling the performance limits of novel microcantilever heaters for volatile organic compound detection (2016)

We present a theoretical model estimating the performance limits of novel AlGaN/GaN heterostructure based microcantilever heater sensors to perform advanced volatile organic compound (VOC) detection and mixture analysis. Operating without any specific surface functionalization or treatment; these devices utilize the strong surface polarization of AlGaN as well as the unique device geometries, to perform selective detection of analytes based on their latent heat of evaporation and molecular dipole moment over a wide concentration range. The presented model incorporates heat transfer, Joule heating, thermal expansion and evaporative heat loss mechanisms, to predict device behaviors such as temperature profiles and sensing performance limits under various steady-state and transient test conditions. In addition, the versatility of the proposed model enables us to successfully predict the capability of the device to perform mixture analysis, and provides guidelines to further optimize the device properties to achieve a limit of detection in sub-ppm concentration.
Intramolecular capture of Pummerer rearrangement intermediates. IV. Preparation of pyrrolo[2,1-b][1,3]benzothiazin-9-ones via intramolecular sulfenylation of an N-acylpyrrole (1992)

Pyrrolo[2,1-6][1,3]benzothiazin-9-one (6a) was synthesized in 45% overall yield from thiosalicylic acid in six steps. The title compound (88%) and its 1-trifluoroacetyl (83%) and 1-formyl derivatives were synthesized via intramolecular reaction of 1-(2-ethylsulfinyl) benzoylpyrrole (5) by thermal cyclization or treatment with trifluoroacetic anhydride or DMF/POCl3, respectively. The key step in each case is formation of the heterocycle by sulfoxide activation followed by C-S bond formation via attack of sulfur. Reaction of 6a with common electrophiles (trifluoroacetic anhydride (86%), POCl3/DMF (75%), and acetyl nitrate) indicates that C-1 is the predominant site of electrophilic substitution. © 1992, American Chemical Society. All rights reserved.
Structure−Activity Relationships in a Series of Orally Active γ-Hydroxy Butenolide Endothelin Antagonists (1997)

The design of potent and selective non-peptide antagonists of endothelin-1 (ET-1) and its related isopeptides are important tools defining the role of ET in human diseases. In this report we will describe the detailed structure-activity relationship (SAR) studies that led to the discovery of a potent series of butenolide ETA selective antagonists. Starting from a micromolar screening hit, PD012527, use of Topliss decision tree analysis led to the discovery of the nanomolar ET(A) selective antagonist PD155080. Further structural modifications around the butenolide ring led directly to the subnanomolar ETA selective antagonist PD156707, IC50's = 0.3 (ET(A)) and 780 nM (ET(B)). This series of compounds exhibited functional activity exemplified by PD156707. This derivative inhibited the ETA receptor mediated release of arachidonic acid from rabbit renal artery vascular smooth muscle cells with an IC50 = 1.1 nM and also inhibited the ET-1 induced contraction of rabbit femoral artery rings (ETA mediated) with a pA2 = 7.6. PD156707 also displayed in vivo functional activity inhibiting the hemodynamic responses due to exogenous administration of ET-1 in rats in a dose dependent fashion. Evidence for the pH dependence of the open and closed tautomerization forms of PD156707 was demonstrated by an NMR study. X-ray crystallographic analysis of the closed butenolide form of PD156707 shows the benzylic group located on the same side of the butenolide ring as the gamma-hydroxyl and the remaining two phenyl groups on the butenolide ring essentially orthogonal to the butenolide ring. Pharmacokinetic parameters for PD156707 in dogs are also presented.
Toward Selective Lignin Liquefaction: Synergistic Effect of Hetero- and Homogeneous Catalysis in Sub- and Supercritical Fluids (2016)

Selective liquefaction of lignin is important for synthesis of value-added phenolic monomers contributing to green chemistry and sustainable energy applications. In the present study, a synergistic effect of a supercritical carbon dioxide (scCO2) acidic catalyst in combination with a heterogeneous metal oxide catalyst, specifically nickel oxide (NiO) or ceria-doped scandia-stabilized zirconia (CeScSZ), in sub- or supercritical water (sbcr/scH2O) for selective liquefaction of alkali lignin is demonstrated for the first time. The scCO2-assisted hydrothermal process in the temperature range of 100–400 °C resulted in highly selective synthesis of the phenolic monomers. On the basis of the total organic carbon (TOC) and gas chromatography–mass spectroscopy (GC–MS) analysis, it is evident that the scCO2 catalyst is essential for enhancing the reaction selectivity in the presence of a heterogeneous catalyst. A combination of homogeneous scCO2 and heterogeneous NiO catalysts resulted in the highest total relative yield of the phenolic monomers, reaching ∼97% at 200 °C. It is confirmed that the scCO2-assisted hydrothermal depolymerization of the alkali lignin in the presence of both scCO2 and a heterogeneous catalyst is superior to that of the each of these catalysts alone and in comparison of the systems where scCO2 is replaced by inert nitrogen.
Genetic and Biochemical Characterization of Fructose Accumulation: A Strategy to Improve Fruit Quality (2000)

The goal of the research project was to evaluate the potential to genetically modify or engineer carbohydrate metabolism in tomato fruit to enhance levels of fructose, a sugar with nearly twice the sweetness value of other sugars. The specific research objectives to achieve that goal were to: 1. Establish the inheritance of a fructose-accumulating trait identified in F1 hybrids of an inferspecific cross between L. hirsutum XL. esculentum and identify linked molecular markers to facilitate its introgression into tomato cultivars. This objective was completed with the genetic data indicating a single major gene, termed Fgr (Fructose glucose ratio), that controlled the partitioning of hexose in the mature fruit. Molecular markers for the gene, were developed to aid introgression of this gene into cultivated tomato. In addition, a second major gene encoding fructokinase 2 (FK2) was found to be a determinant of the fructose to glucose ratio in fruit. The relationship between FK2 and Fgr is epistatic with a combined synergistic effect of the two hirsutum-derived genes on fructose/glucose ratios. 2. Characterize the metabolic and transport properties responsible for high fructose/glucose ratios in fructose-accumulating genotypes. The effect of both the Fgr and FK2 genes on the developmental accumulation of hexoses was studied in a wide range of genetic backgrounds. In all backgrounds the trait is a developmental one and that the increase in fructose to glucose ratio occurs at the breaker stage of fruit development. The following enzymes were assayed, none of which showed differences between genotypes, at either the breaker or ripe stage: invertase, sucrose synthase, FK1, FK2, hexokinase, PGI and PGM. The lack of effect of the FK2 gene on fructokinase activity is surprising and at present we have no explanation for the phenomenon. However, the hirsutum derived Fgr allele was associated with significantly lower levels of phosphorylated glucose, G1c-1-P and G1c-6-P and concomitantly higher levels of the phosphorylated fructose, Fru-6-P, in both the breaker and ripe stage. This suggests a significant role for the isomerase reaction. 3. Develop and implement molecular genetic strategies for the production of transgenic plants with altered levels of enzymes that potentially control fructose/glucose ratios in fruit. This objective focused on manipulating hexokinase and fructokinase expression in transgenic plants. Two highly divergent cDNA clones (Frk1 and Frk2), encoding fructokinase (EC 2.7.1.4), were isolated from tomato (Lycopersicon esculentum) and a potato fructokinase cDNA clone was obtained from Dr. Howard Davies. Following expression in yeast, each fructokinase was identified to code for one of the tomato or potato fructokinase isoforms Transgenic tomato plants were generated with the fructokinase cDNA clone in both sense and antisense orientations and the effect of the gene on tomato plants is currently being studied.
Rational Design, Synthesis, Purification, and Activation of Metal−Organic Framework Materials (2010)

The emergence of metal-organic frameworks (MOFs) as functional ultrahigh surface area materials is one of the most exciting recent developments in solid-state chemistry. Now constituting thousands of distinct examples, MOFs are an intriguing class of hybrid materials that exist as infinite crystalline lattices with inorganic vertices and molecular-scale organic connectors. Useful properties such as large internal surface areas, ultralow densities, and the availability of uniformly structured cavities and portals of molecular dimensions characterize functional MOFs. Researchers have effectively exploited these unusual properties in applications such as hydrogen and methane storage, chemical separations, and selective chemical catalysis. In principle, one of the most attractive features of MOFs is the simplicity of their synthesis. Typically they are obtained via one-pot solvothermal preparations. However, with the simplicity come challenges. In particular, MOF materials, especially more complex ones, can be difficult to obtain in pure form and with the optimal degree of catenation, the interpenetration or interweaving of identical independent networks. Once these two issues are satisfied, the removal of the guest molecules (solvent from synthesis) without damaging the structural integrity of the material is often an additional challenge. In this Account, we review recent advances in the synthetic design, purification, and activation of metal-organic framework materials. We describe the rational design of a series of organic struts to limit framework catenation and thereby produce large pores. In addition, we demonstrate the rapid separation of desired MOFs from crystalline and amorphous contaminants cogenerated during synthesis based on their different densities. Finally, we discuss the mild and efficient activation of initially solvent-filled pores with supercritical carbon dioxide, yielding usable channels and high internal surface areas. We expect that the advances in the synthesis, separation, and activation of metal-organic frameworks could lead to MOFs with new structures and functions, better and faster separation and purification of these materials, and processing methods that avoid pore blockage and pore collapse.
Expeditious synthesis of porphyrin–cobaltacarborane conjugates (2005)

Two porphyrin-cobaltacarborane conjugates and were prepared in high yields via a nucleophilic ring-opening reaction of . These novel boron-rich and fluorescent compounds have potential application as boron delivery agents for the boron neutron capture therapy of tumors.
Phase I Malaria Vaccine Trial with a Long Synthetic Peptide Derived from the Merozoite Surface Protein 3 Antigen (2005)

The C-terminal conserved region of Plasmodium falciparum merozoite surface protein 3 (MSP3) is the trigger antigen of a protective immune response mediated by cytophilic antibodies. In an open, randomized, two-adjuvant (Montanide ISA 720, aluminum hydroxide) phase I clinical trial we evaluated the safety and immunogenicity of increasing doses of a long synthetic peptide construct spanning the conserved region of MSP3 targeted by biologically active antibodies (MSP3-LSP). Thirty-five healthy volunteers were randomized to receive three subcutaneous injections on days 0, 30, and 120. Of the 100 injections given, 10 caused severe local reactions, 62 caused transient mild to moderate local reactions, and 28 caused no reaction. On the basis of preestablished exclusion criteria, use of the Montanide formulation led to withdrawal of five volunteers after the second injection. This led to a reduction in the subsequent vaccine doses in four of the groups. No vaccine-related serious adverse events occurred throughout the trial. After the third injection, volunteers displayed a marked specific anti-MSP3-LSP antibody response (23/30 individuals, compared with 29/34 individuals for plasma from an area where malaria is endemic), an anti-native MSP3 antibody response (19/30 individuals), a T-cell-antigen-specific proliferative response (26/30 individuals), and gamma interferon production (25/30 individuals). In conclusion, the MSP3-LSP vaccine was immunogenic with both adjuvants, although it was unacceptably reactogenic when it was combined with Montanide. The potential usefulness of the candidate vaccine is supported by the induction of a strong cytophilic response (i.e., the type of anti-MSP3 antibodies involved in antibody-dependent, monocyte-mediated protective mechanisms in areas where malaria is endemic).
Enzyme-Mediated Assimilation of DNA-Functionalized Single-Walled Carbon Nanotubes (2009)

When pyrimidine-functionalized carbon nanotubes were incubated with single-stranded DNA ligase, formations of macroscopic aggregates were observed. Wet-cell transmission electron microscopy imaging revealed that the nanotubes were radially bound to form a 3D latticelike structure. These structures were not observed in control reactions lacking ligase or adenosine triphosphate. Raman spectroscopy analysis revealed no spectra indicative of carbon nanotubes in ligase-unamended controls; however, spectra were observed in radial breathing mode and in the G and G' bands in reactions containing ligase. Furthermore, the addition of deoxyribonuclease to the ligated reactions dispersed the aggregates, and a reduction in Raman spectral intensity was observed.
Carbon aerogel evolution: Allotrope, graphene-inspired, and 3D-printed aerogels (2017)

Abstract
Integrating Carbon Capture and Storage with Energy Production from Saline Aquifers: A Strategy to Offset the Energy Cost of CCS (2014)

Extraction of brine containing methane and geothermal energy from saline aquifers has been considered as a method to offset the cost of carbon capture and storage. This study estimates the potential of power generation from methane and heat and compares it with the power required for capture and storage. Nine aquifer models were prepared from average conditions of several wells in the Gulf Coast at depths from 8,000 to 16,000 ft. Reservoir simulation study was performed to estimate the amounts of stored carbon dioxide and produced methane and heat. The study found that the power generation potential from below the depth of 11,000 ft offsets the power required for capture and storage processes.
Ultrasensitive Electrocatalytic DNA Detection at Two- and Three-Dimensional Nanoelectrodes (2004)

Electrochemical DNA detection systems are an attractive approach to the development of multiplexed, high-throughput DNA analysis systems for clinical and research applications. We have engineered a new class of nanoelectrode ensembles (NEEs) that constitute a useful platform for biomolecular electrochemical sensing. High-sensitivity DNA detection was achieved at oligonucleotide-functionalized NEEs using a label-free electrocatalytic assay. Attomole levels of DNA were detected using the NEEs, validating the promise of nanoarchitectures for ultrasensitive biosensing.
Integrated link adaptation and power control to improve error and throughput performance in broadband wireless packet networks (2002)

In this paper, we prove that the problem of maximizing data throughput by adaptive modulation and power control while meeting packet error requirements is NP-complete. A heuristic algorithm for integrated link adaptation and power control is, thus, proposed to achieve specified error rates and to improve overall throughput for real-time applications in broadband wireless packet networks. The algorithm divides terminals into groups according to their signal path gains and periodically adapts transmissions based on the required error rates, actual error statistics, and average transmission power of each terminal group. Transmission power is adjusted by an enhanced Kalman-filter method to ensure successful reception. Extensive simulation results reveal that the algorithm consistently delivers the specified error performance and attempts to maximize network throughput for a wide range of parameter settings.
Magnetic nanoparticles for targeted vascular delivery (2011)

Magnetic targeting has shown promise to improve the efficacy and safety of different classes of therapeutic agents by enabling their active guidance to the site of disease and minimizing dissemination to nontarget tissues. However, its translation into clinic has proven difficult because of inherent limitations of traditional approaches inapplicable for deep tissue targeting in human subjects and a need for developing well-characterized and fully biocompatible magnetic carrier formulations. A novel magnetic targeting scheme based on the magnetizing effect of deep-penetrating uniform fields is presented as an example of a strategy providing a potentially clinically viable solution for preventing injury-triggered reobstruction of stented blood vessels (in-stent restenosis). The design of optimized magnetic carrier formulations and experimental results showing the feasibility of uniform field-controlled targeting for site-specific vascular delivery of small-molecule pharmaceuticals, biotherapeutics, and cells are discussed in the context of antirestenotic therapy. The versatility of this approach applicable to different classes of therapeutic agents exerting their antirestenotic effects through distinct mechanisms prompts exploring the utility of uniform field-mediated magnetic stent targeting for combination therapies with enhanced efficiencies and improved safety profiles. Additional improvements in terms of site specificity and protracted carrier retention at the site of injury may be expected from the development and use of magnetic carriers exhibiting affinity for arterial wall-specific antigens.
Pressure-Reduction Technique for Crystal Growth (1981)

Large crystals grown by varying rather than temperature. In constant temerature pressure-reduction process crystal growth promoted as solubility decreases by factor of more than 10. Technique used to study crystal growth kinetics by pressure analog of conventional thermal wave experiments. Technique has advantages of faster response and freedom from convective interference.
Point Diffraction Interferometry at EUV Wavelengths (1994)

Point diffraction interferometry is a common-path technique that is suitable for at-wavelength testing of EUV lithography optics. We have constructed and successfully tested such a device at the Advanced Light Source at Lawrence Berkeley Laboratory. Preliminary results on the characterization of the wavefront produced by a Fresnel zone plate lens are presented. Reference wavefront quality and thermal effects are also discussed.
Synergistic Glycosylation as Key to the Chemical Synthesis of an Outer Core Octasaccharide of <i>Helicobacter pylori</i> (2018)

Helicobacter pylori, a widespread gastric bacterial pathogen that infects 90 % of the population in developing countries, causes chronic gastritis, peptic ulcers and gastric cancer. Battling H. pylori infection is a serious challenge due to the increased resistance to antibiotics and the lack of vaccines. The lipopolysaccharide covering the H. pylori cell-surface outer membrane is an attractive target for the development of a glycoconjugate vaccine. Here, we report a [3+5] convergent synthesis of an outer core octasaccharide of H. pylori employing just three orthogonally protected building blocks. A synergistic glycosylation strategy enables the creation of five pivotal 1,2-cis-α-glucosidic bonds consist of four types of linkages using just three monomers. This strategy can be expanded to many 1,2-cis-α-gluoside-containing oligosaccharides both in solution and solid phase.
A planarization process for multilayer lithography applications (2004)

Multi-layer lithography processes have been introduced to fabricate very fine structures over a topographic surface for advanced semiconductor device production. The first layer formed on the topographic surface is the planarization layer to provide surface planarity for additional thin layer(s) of material. Such materials could be a photoresist, a hardmask, or both with uniform film thickness for the lithography step to image the structures. However, the large size and distribution variation of the topography structures across the substrate surface have a major impact on the performance of the lithography processes. A new planarization process, contact planarization (CP), has been introduced to improve thickness uniformity and to provide global surface planarity for multi-layer lithography applications. This study focuses on planarizing an experimental organic 193-nm BARC layer on via wafers to minimize iso-dense film thickness bias and provide improved global surface planarity for the bilayer photolithography process. In addition, minimum thickness bias improves control of downstream processes such as plasma etching. This paper will discuss this unique planarization process and its performance with various thicknesses of the experimental 193-nm BARC on via wafers. The photolithography performance of the material and process will be discussed.
ChemInform Abstract: POTENTIAL ANTIHYPERTENSIVES. SYNTHESIS OF 6‐SUBSTITUTED‐N‐(4H‐1,2,4‐TRIAZOL‐4‐YL)‐3‐PYRIDAZINAMINES AND 3‐SUBSTITUTED‐6‐(3,5‐DIMETHYL‐1H‐1,2,4‐TRIAZOL‐1‐YL)PYRIDAZINES (1985)

A series of 6-substituted-N-(4H-1,2,4-triazol-4-yl)-3-pyridazinamines [(II), Scheme 1] and 3-substituted-6-(3,5-dimethyl-1H-1,2,4-triazol-1-yl) pyridazines [(XII), Scheme 3-5] were synthesized. The compounds were evaluated for their oral antihypertensive activity in rats (SHR) and only some compounds of structure (XII) induced a moderate decrease in systolic blood pressure.