gebhart/patrepeval huggingface dataset:
Electrokinetically Controlled Microfluidic Analysis Systems (2000)

Electrokinetic forces are emerging as a powerful means to drive microfluidic systems with flow channel cross-sectional dimensions in the tens of micrometers and flow rates in the nanoliter per second range. These systems provide many advantages such as improved analysis speed, improved reproducibility, greatly reduced reagent consumption, and the ability to perform multiple operations in an integrated fashion. Planar microfabrication methods are used to make these analysis chips in materials such as glass or polymers. Many applications of this technology have been demonstrated, such as DNA separations, enzyme assays, immunoassays, and PCR amplification integrated with microfluidic assays. Further development of this technology is expected to yield higher levels of functionality of sample throughput on a single microfluidic analysis chip.
Sequence-selective carbohydrate-DNA interaction: dimeric and monomeric forms of the calicheamicin oligosaccharide interfere with transcription factor function. (1996)

The synthetic oligosaccharide moiety of the antibiotic calicheamicin and the head-to-head dimer of this oligosaccharide are known to bind to the minor groove of DNA in a sequence-selective manner preferring distinct target sequences. We tested these carbohydrates for their ability to interfere with transcription factor function. The oligosaccharides inhibit binding of transcription factors to DNA in a sequence-selective manner, probably by inducing a conformational change in DNA structure. They also interfere with transcription by polymerase II in vitro. The effective concentrations of the oligosaccharides for inhibition of transcription factor binding and for transcriptional inhibition are in the micromolar range. The dimer is a significantly more active inhibitor than is the monomer.
Cholinergic Regulation of Morphine Release from Human White Blood Cells: Evidence for a Novel Nicotinic Receptor via Pharmacological and Micro Array Analysis (2007)

Recent work from our laboratory has demonstrated that human white blood cells make morphine and that substances of abuse, i.e. nicotine, alcohol and cocaine have the ability to release this endogenous substance, suggesting a common mechanism of action. We now demonstrate that the nicotinic process is more complex than formerly envisioned. The incorporation rate of 125I-labeled morphine into PMN and MN are 7.85+/-0.36%, 1.42+/-0.19%, respectfully, suggesting in MN this process is of low activity. Separate incubations of PMN with varying concentrations of nicotine or the nicotine agonist epibatidine resulted in a statistically significant enhancement of 125I-trace labeled morphine released into the extracellular medium. In order to ascertain the specificity of the nicotine stimulated morphine release the following experiments were performed. Co-incubation of hexamethonium dichloride (5 microg/ml and at 10 microg/ml), which preferentially blocks nicotinic receptors at autonomic ganglia, with nicotine, exerted a very weak inhibitory effect. Co-incubation of alpha-BuTx or atropine or chlorisondamine diiodide or dihydro-Beta-erythroidine hydrobromide, an alpha4Beta2 receptor antagonist, did not block nicotine induced morphine release alone or in combination, suggesting either the response was not specific or it was mediated by a novel nicotinic receptor. Human leukocyte total RNA isolated from whole blood were analyzed, using the Human Genome Survey microarray (Applied Biosystems), for cholinergic receptor expression. PMN nicotinic receptor gene expression was present and contained numerous variants (eight). The number of variants suggests that indeed a novel nicotinic receptor may be mediating this effect, while simultaneously demonstrating the significance of the cholinergic receptor expression in these immune cells.
Comparative Genomics of Thiamin Biosynthesis in Procaryotes (2002)

Vitamin B(1) in its active form thiamin pyrophosphate is an essential coenzyme that is synthesized by coupling of pyrimidine (hydroxymethylpyrimidine; HMP) and thiazole (hydroxyethylthiazole) moieties in bacteria. Using comparative analysis of genes, operons, and regulatory elements, we describe the thiamin biosynthetic pathway in available bacterial genomes. The previously detected thiamin-regulatory element, thi box (Miranda-Rios, J., Navarro, M., and Soberon, M. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 9736-9741), was extended, resulting in a new, highly conserved RNA secondary structure, the THI element, which is widely distributed in eubacteria and also occurs in some archaea. Search for THI elements and analysis of operon structures identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms. In particular, we assign the thiamin transporter function to yuaJ in the Bacillus/Clostridium group and the HMP transporter function to an ABC transporter thiXYZ in some proteobacteria and firmicutes. By analogy to the model of regulation of the riboflavin biosynthesis, we suggest thiamin-mediated regulation based on formation of alternative RNA structures involving the THI element. Either transcriptional or translational attenuation mechanism may operate in different taxonomic groups, dependent on the existence of putative hairpins that either act as transcriptional terminators or sequester translation initiation sites. Based on analysis of co-occurrence of the thiamin biosynthetic genes in complete genomes, we predict that eubacteria, archaea, and eukaryota have different pathways for the HMP and hydroxyethylthiazole biosynthesis.
Quantitative profiling of LNCaP prostate cancer cells using isotope‐coded affinity tags and mass spectrometry (2004)

Androgens are involved in the pathogenesis of diseases including adenocarcinoma of the prostate. These hormones are important for growth, maintenance, and integrity of structure and function of the prostate. Androgen-deprivation is currently the only effective systemic therapy for prostate cancer but the effects of androgens on the proteome are still poorly described. Here we quantitatively profile changes in the proteome of LNCaP human prostate cancer cells in response to androgen using the newly developed isotope-coded affinity tag (ICAT) labeling and two-dimensional liquid chromatography-tandem mass spectroscopy (2-D LC-MS/MS). ICAT enables the concurrent identification and comparative quantitative analysis of proteins present in various biological samples including human cell and tissue extracts. Quantification and identification of 139 proteins in complex protein mixtures obtained from androgen-stimulated and unstimulated LNCaP cells were achieved. Changes in levels of 77 proteins in response to androgens were detected. Some of these proteins have been previously reported to be regulated by androgens and include spermine synthase, fatty acid synthase and calreticulin precursor. A large number of proteins that have not been previously reported to be expressed in prostate cells were also quantitatively identified. Examples of these include members of the dual specificity protein phosphatase subfamily, "similar" to hypothetical protein DKFZp434B0328.1, "similar" to 14-3-3 protein zeta and "similar" to hypothetical protein 458, components of the actin cytoskeleton and a range of unknown/uncharacterized proteins. This catalogue of proteins provides an overview of the proteome of prostate cancer cells and the global changes that occur in response to androgens.
Architecture and design of NX-2700: a programmable single-chip HDTV all-format-decode-and-display processor (2001)

This paper describes the architecture, functionality, and design of NX-2700, a digital television and media processor chip from Philips Semiconductors. The NX-2700 is the second generation of an architectural family of programmable multimedia processors targeted at the digital television (DTV) markets, including the United States Advanced Television Systems Committee (ATSC) DTV-standard-based applications. The chip not only supports all of the 18 ATSC formats from standard-definition to wide-angle, high-definition video, but has also the power to handle high-definition television (HDTV) video and audio source decoding (high-level MPEG-5 AC-3 and ProLogic audio, closed captioning, etc.) as well as the flexibility to process advanced interactive services. NX-2700 is a programmable processor with a very powerful, general-purpose very long instruction word (VLIW) central processing unit (CPU) core that implements many nontrivial multimedia algorithms, coordinates all on-chip activities, and runs a small real-time operating system. The CPU core, aided by an array of peripheral devices (multimedia coprocessors and input-output units) and high-performance buses, facilitates concurrent processing of audio, video, graphics, and communication-data.
Chronic lung disease in preterm lambs: effect of daily vitamin A treatment on alveolarization (2010)

Neonatal chronic lung disease is characterized by failed formation of alveoli and capillaries, and excessive deposition of matrix elastin, which are linked to lengthy mechanical ventilation (MV) with O(2)-rich gas. Vitamin A supplementation has improved respiratory outcome of premature infants, but there is little information about the structural and molecular manifestations in the lung that occur with vitamin A treatment. We hypothesized that vitamin A supplementation during prolonged MV, without confounding by antenatal steroid treatment, would improve alveolar secondary septation, decrease thickness of the mesenchymal tissue cores between distal air space walls, and increase alveolar capillary growth. We further hypothesized that these structural advancements would be associated with modulated expression of tropoelastin and deposition of matrix elastin, phosphorylated Smad2 (pSmad2), cleaved caspase 3, proliferating cell nuclear antigen (PCNA), VEGF, VEGF-R2, and midkine in the parenchyma of the immature lung. Eight preterm lambs (125 days' gestation, term approximately 150 days) were managed by MV for 3 wk: four were treated with daily intramuscular Aquasol A (vitamin A), 5,000 IU/kg, starting at birth; four received vehicle alone. Postmortem lung assays included quantitative RT-PCR and in situ hybridization, immunoblot and immunohistochemistry, and morphometry and stereology. Daily vitamin A supplementation increased alveolar secondary septation, decreased thickness of the mesenchymal tissue cores between the distal air space walls, and increased alveolar capillary growth. Associated molecular changes were less tropoelastin mRNA expression, matrix elastin deposition, pSmad2, and PCNA protein localization in the mesenchymal tissue core of the distal air space walls. On the other hand, mRNA expression and protein abundance of VEGF, VEGF-R2, midkine, and cleaved caspase 3 were increased. We conclude that vitamin A treatment partially improves lung development in chronically ventilated preterm neonates by modulating expression of tropoelastin, deposition of elastin, and expression of vascular growth factors.
Deterministically Encoding Quantum Information Using 100-Photon Schrödinger Cat States (2013)

In contrast to a single quantum bit, an oscillator can store multiple excitations and coherences provided one has the ability to generate and manipulate complex multiphoton states. We demonstrate multiphoton control by using a superconducting transmon qubit coupled to a waveguide cavity resonator with a highly ideal off-resonant coupling. This dispersive interaction is much greater than decoherence rates and higher-order nonlinearities to allow simultaneous manipulation of hundreds of photons. With a tool set of conditional qubit-photon logic, we mapped an arbitrary qubit state to a superposition of coherent states, known as a "cat state." We created cat states as large as 111 photons and extended this protocol to create superpositions of up to four coherent states. This control creates a powerful interface between discrete and continuous variable quantum computation and could enable applications in metrology and quantum information processing.
Does fibrin glue cause foreign body reactions? (1993)

The study was performed in 20 Wistar rats. Approximately 4 mm perforations were created in the left colon of ten rats to which fibrin glue was applied (Group D). The control group had the same injury without any therapeutic or surgical measures (Group K). Of the 20 rats in both groups none died during the postoperative period. All animals sacrificed on the 11th postoperative day. All ten rats of Group D displayed inflammatory foreign body reactions. The control group showed no such reaction.
Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region (1996)

In order to develop a diagnostic tool to identify phytoplasmas and classify them according to their phylogenetic group, we took advantage of the sequence diversity of the 16S-23S intergenic spacer regions (SRs) of phytoplasmas. Ten PCR primers were developed from the SR sequences and were shown to amplify in a group-specific fashion. For some groups of phytoplasmas, such as elm yellows, ash yellows, and pear decline, the SR primer was paired with a specific primer from within the 16S rRNA gene. Each of these primer pairs was specific for a specific phytoplasma group, and they did not produce PCR products of the correct size from any other phytoplasma group. One primer was designed to anneal within the conserved tRNA(Ile) and, when paired with a universal primer, amplified all phytoplasmas tested. None of the primers produced PCR amplification products of the correct size from healthy plant DNA. These primers can serve as effective tools for identifying particular phytoplasmas in field samples.
Solubility enhancement studies on lurasidone hydrochloride using mixed hydrotropy (2015)

Low aqueous solubility is a major problem faced during formulation development of new drug molecules. Lurasidone HCl (LRD) is an antipsychotic agent specially used in the treatments of schizophrenia and is a good example of the problems associated with low aqueous solubility. Lurasidone is practically insoluble in water, has poor bioavailability and slow onset of action and therefore cannot be given in emergency clinical situations like schizophrenia. Hence, purpose of this research was to provide a fast dissolving oral dosage form of Lurasidone. This dosage form can provide quick onset of action by using the concept of mixed hydrotropy. Initially, solubility of LRD was determined individually in nicotinamide, sodium citrate, urea and sodium benzoate at concentration of 10, 20, 30 and 40% w/v solutions using purified water as a solvent. Highest solubility was obtained in 40% sodium benzoate solution. In order to decrease the individual hydrotrope concentration mixed hydrotropic agents were used. Highest solubility was obtained in 15:20:5 ratio of Nicotinamide + sodium benzoate + sodium citrate. This optimized combination was utilized in the preparation of solid dispersions by using distilled water as a solvent. Solid dispersions were evaluated for X-ray diffraction, differential scanning calorimetry and Fourier-transform infrared to show no drug-hydrotropes interaction has occurred. This solid dispersion was compressed to form fast dissolving tablets. Dissolution studies of prepared tablets were done using USP Type II apparatus. The batch L3 tablets show 88% cumulative drug release within 14 min and in vitro dispersion time was 32 min. It was concluded that the concept of mixed hydrotropic solid dispersion is novel, safe and cost-effective technique for enhancing the bioavailability of poorly water-soluble drugs. The miraculous enhancement in solubility and bioavailability of Lurasidone is clear indication of the potential of mixed hydrotropy to be used in future for other poorly water-soluble drugs in which low bioavailability is a major concern.
ChemInform Abstract: Chemistry of Oxalyl Derivatives of Methyl Ketones. Part 43. Synthesis of 2‐Imino‐ 2,3‐dihydro‐3‐furanones, Their Hydrolysis and Aminolysis. (1986)

Abstract The thermolytic decarbonylation of the furandiones (I) in the presence of the isocyanides (II) yields the [4 + 1] cycloadducts, i.e. the 2‐imino derivatives (III).
ExoCarta: A compendium of exosomal proteins and RNA (2009)

Exosomes, membrane microvesicles (40-100 nm) secreted by most cell types, can be isolated in several ways while characterizing them is heavily based on electron microscopy and, most importantly, the identification of exosome marker proteins. Researchers rely on the identification of certain exosomal marker proteins including Alix, CD9 and CD63 to confirm the presence of exosomes in their preparations. An evolutionary-conserved set of protein molecules have been identified in most exosomes studied to date. However, with the complexity of tissue/cell type-specific proteins being incorporated in the exosomes, some of these so-called exosomal markers are not always present in all the exosomes. The presence of tissue/cell type-specific proteins in exosomes allows researchers to isolate them using immunoaffinity capture methods. A compendium for exosomal proteomes will aid researchers in identifying proteins that were more commonly found in various exosomes (exosome markers) and those that are specific to certain tissue/cell type-derived exosomes. Here, we describe ExoCarta, a compendium for proteins and RNA molecules identified in exosomes. ExoCarta is first of its kind and the resource is freely available to the scientific community through the web (http://exocarta.ludwig.edu.au). We believe that this community resource will be of great biological importance for any future exosome analyses.
Time-Resolved Fluorescence for Real-Time Monitoring of Both Scale and Corrosion Inhibitors: A Game-Changing Technique (2016)

Abstract Inhibitor products have been widely used to reduce both steel corrosion and scale deposition on pipelines, tubings and safety valves in critical offshore sites. Their simultaneous injection with brine has gradually increased the lifetime of production wells with incontestable benefits for the oil and gas industry. However, the large use of such additives has not been followed by the development of any efficient technique of dosage that considers the strict requirements of an offshore platform. In this paper, we describe a novel method of chemical dosage that takes into account all the on-site technical and practical parameters, such as the quantification thresholds or molecule specificity, the real-time monitoring, the resistance and compactness of measurement device and a user-friendly interface of measurement. Current techniques of inhibitor monitoring that use elemental analysis (ICP, MS, …) for sub-ppm quantifications appear too complex for a successful long-term on-site industrial exploitation due to the bulky dimensions of apparatus and the delay and complexity of analysis. A long-term collaboration between University of Lyon and Total EP has defined a simple and accurate method for inhibitor monitoring based on the use of lanthanide tracers and the Time-Resolved Fluorescence (TRF) technique. We exploited the fact that inhibitor chemicals (i) are good chelators for lanthanide ions and (ii) amplify the luminescence signal of rare-earths. In this way we are able to collect the photon emission signal by TRF apparatus and dosing the inhibitors. The portability of the TRF device as well as the sensitivity of detection have been engineered in order to obtain a sub-ppm quantification threshold via 1-click task. Several carboxylates, phosphonates and sulphonates additives diluted in brine solutions has been easily measured out even in presence of residual oil. More than 20 commercial inhibitor solution samples were quickly prepared and dosed with an impressive linearity of response (R2 test &amp;gt; 0.996) in the 10 – 100 ppm range. Any further extension of range has been possible. In addition, we were able to quantify two inhibitors (scale – scale, scale – corrosion) in the same brine water. This technique certainly opens a new conception of smart chemicals management in oil and gas production for (i) a dramatic minimization of the injected compounds (ii) a reducing delay in pipelines monitoring, and (iii) a shut down of expenses of pipeline maintenance.
Human alpha-galactosidase A: nucleotide sequence of a cDNA clone encoding the mature enzyme. (1986)

The complete nucleotide sequence has been determined for a lambda gt11 cDNA clone (lambda AG18) containing the full-length coding region for the mature lysosomal form of human alpha-galactosidase A (alpha-Gal A; EC 3.2.1.22). The lambda AG18 insert contained a 1226-base-pair sequence with an open reading frame encoding 398 amino acids of the mature polypeptide (predicted Mr = 45,356) and the last 5 amino acids of the propeptide sequence. The poly(A) signals AATACA and ATTAAA occurred 28 and 11 nucleotides prior to the TAA stop codon, respectively. There was no 3' untranslated region as the poly(A) sequence immediately followed the TAA termination codon; a second independently cloned cDNA confirmed this finding. The predicted amino acid sequence was colinear with 86 nonoverlapping residues (22% of the mature subunit) determined by microsequencing amino-terminal, tryptic, and cyanogen bromide peptides of the purified mature enzyme. Four potential N-glycosylation sites were identified, all of which occurred at predicted beta turns in hydrophilic regions of secondary structure. RNA transfer hybridization analysis of HeLa poly(A)+ RNA demonstrated a single 1.45-kilobase band whose signal was decreased by prior immunoabsorption of polysomes with monospecific alpha-Gal A antibodies. Searches of nucleic acid and protein data bases did not reveal significant homology even with the limited sequences available for mammalian lysosomal enzymes.
Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay (2005)

Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP assays using this technology in a population of 30 trios from the Centre d'Etude Polymorphisme Humain family panel as part of the International HapMap project, we established SNP conversion rates of approximately 90% with concordance rates >99.6% and completeness levels >98% for assays multiplexed up to 12,000plex levels. Furthermore, these individual metrics can be "traded off" and, by sacrificing a small fraction of the conversion rate, the accuracy can be increased to very high levels. No loss of performance is seen when scaling from 6,000plex to 12,000plex assays, strongly validating the ability of the technology to suppress cross-reactivity at high multiplex levels. The results of this study demonstrate the suitability of this technology for comprehensive association studies that use targeted SNPs in indirect linkage disequilibrium studies or that directly screen for causative mutations.