gebhart/patrepeval huggingface dataset:
High-throughput microfluidic single-cell RT-qPCR (2011)

A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of (i) miRNA expression in K562 cells, (ii) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (iii) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed.
Affinity chromatography and further characterization of the glucosyltransferases involved in hydroxydocosanoic acid sophoroside production in Candida bogoriensis. (1982)

A simplified purification procedure has been developed for UDP-glucose:13-hydroxydocosanoic acid glucosyltransferase (glucosyltransferase I) and UDP-glucose:13-glucosyloxydocosanoic acid glucosyltransferase (glucosyltransferase 11), enzymes isolated from Candida bogoriemis which are involved in the biosynthesis of hydroxydocosanoic acid sophorosides by this organism (Esders, T.
Identification and characterization of a cDNA encoding mouse CAP: a homolog of the yeast adenylyl cyclase associated protein (1993)

CAP, an adenylyl cyclase associated protein, is present in Saccharomyces cerevisiae and Schizosaccharomyces pombe. In both organisms, CAP is bifunctional: the N-terminal domain binds to adenylyl cyclase, thereby enabling adenylyl cyclase to respond appropriately to upstream regulatory signals, such as RAS in S. cerevisiae; the C-terminal domain is required for cellular morphogenesis. Here, we describe the isolation of a cDNA encoding a CAP homolog from a higher eukaryote. The mouse CAP cDNA contains an open reading frame capable of encoding a 474 amino acid protein. The protein encoded by the mouse CAP cDNA shows extensive homology to the yeast CAP proteins, particularly in the central poly-proline rich region and in the C-terminal domain. By northern analysis, the CAP message appears to be ubiquitous, but not uniform. By indirect immunofluorescence, ectopically expressed mouse CAP protein is found in the cytoplasm of fibroblasts and, in migrating cells, at the leading edge. Expression of the mouse CAP cDNA in S. cerevisiae complements defects associated with loss of the yeast CAP carboxy-terminal domain. Hence, the function of the CAP carboxy-terminal domain has been conserved from yeast to mouse.
Opportunities for New Chemical Libraries: Unnatural Biopolymers and Diversomers (1994)

The search for lead compounds may well be simplified by libraries of unnatural compounds, whose lead compounds may require less extensive modifications for the development of drug candidates than those derived from peptide and oligonucleotide libraries. An oligocarbamate library described by Cho et al. and a benzodiazepine library proposed by Hobbs DeWitt et al. should point the way to a large number of libraries.
Extracellular Invertase Is an Essential Component of Cytokinin-Mediated Delay of Senescence[W] (2004)

Leaf senescence is the final stage of leaf development in which the nutrients invested in the leaf are remobilized to other parts of the plant. Whereas senescence is accompanied by a decline in leaf cytokinin content, exogenous application of cytokinins or an increase of the endogenous concentration delays senescence and causes nutrient mobilization. The finding that extracellular invertase and hexose transporters, as the functionally linked enzymes of an apolasmic phloem unloading pathway, are coinduced by cytokinins suggested that delay of senescence is mediated via an effect on source-sink relations. This hypothesis was further substantiated in this study by the finding that delay of senescence in transgenic tobacco (Nicotiana tabacum) plants with autoregulated cytokinin production correlates with an elevated extracellular invertase activity. The finding that the expression of an extracellular invertase under control of the senescence-induced SAG12 promoter results in a delay of senescence demonstrates that effect of cytokinins may be substituted by these metabolic enzymes. The observation that an increase in extracellular invertase is sufficient to delay leaf senescence was further verified by a complementing functional approach. Localized induction of an extracellular invertase under control of a chemically inducible promoter resulted in ectopic delay of senescence, resembling the naturally occurring green islands in autumn leaves. To establish a causal relationship between cytokinins and extracellular invertase for the delay of senescence, transgenic plants were generated that allowed inhibition of extracellular invertase in the presence of cytokinins. For this purpose, an invertase inhibitor was expressed under control of a cytokinin-inducible promoter. It has been shown that senescence is not any more delayed by cytokinin when the expression of the invertase inhibitor is elevated. This finding demonstrates that extracellular invertase is required for the delay of senescence by cytokinins and that it is a key element of the underlying molecular mechanism.
Cloning and sequence analysis of cDNA species coding for the two subunits of inhibin from bovine follicular fluid. (1986)

The primary amino acid structures of the 43-kDa (A) and 15-kDa (B) subunits of the 58-kDa form of the hormone inhibin have been elucidated by cloning and analysis of cDNA species derived from bovine granulosa cell mRNA. The A subunit (Mr = 32,298) is a protein of 300 amino acids with two potential N-glycosylation sites and two potential proteolytic processing sites and has a pre-pro region of 60 amino acids. The mature B subunit (Mr = 12,977) is a protein of 116 amino acids synthesized from a separate mRNA. These data establish that a 31-kDa form of inhibin also isolated from bovine follicular fluid, with subunits of 20 kDa (Ac) and 15 kDa (B), is derived from the 58-kDa form by proteolytic processing of the A subunit.
Nonlinear optic properties of heterocyclic compounds hyperpolarizability-structure correlation (1991)

Abstract In an attempt towards understanding the relation between molecular structure-nonlinear optic activity (NLO) among heterocycles, with special reference to the identity, number and position of the heteroatom, semiempirical calculations were carried out on a number of nitrogen heterocycles and their thia and carbon analogs using MNDO, AMI and PM3 approaches. The results indicate that given the same number and type of atoms and double bonds in a molecule, linear conjugation excels over cyclic or crossed conjugation in enhancing hyperpolarizabilities and it seems to be far more critical than a chiral center. The data also show that adjacent nitrogens tend to lower second and third order polarizabilities considerably. All the three methods predicted the same correct trends.
Microarray analysis of fiber cell maturation in the lens (2005)

The mammalian lens consists of an aged core of quiescent cells enveloped by layers of mature fully elongated cells and younger, continuously elongating transcriptionally active cells. The fiber cell maturation is initiated when fiber cells cease to elongate. The process of maturation represents a radical switch from active elongation to a life-long quiescence and has not been studied previously. It may also include critical stages of preparation for the organelle removal and denucleation. In the present study, we used laser capture microdisection (LCM) microdissection and RNA amplification to compare global gene expression profiles of young elongating and mature, non-elongating fiber cells. Analysis of microarray data from three independent dye-swap experiments identified 65 differentially expressed genes (FDR<0.1) with greater than 2-fold change in expression levels. Microarray array results for a group of randomly selected genes were confirmed by quantitative RT-PCR. These microarray results provide clues to understanding the molecular pathways underlying lens development. The identified changes in the profile of gene expression reflected a shift in cell physiology characterizing the lens fiber maturation.
Organic Chemistry of Explosives (2006)

Organic Chemistry of Explosives is the first text to bring together the essential methods and routes used for the synthesis of organic explosives in a single volume. Assuming no prior knowledge, the book discusses everything from the simplest mixed acid nitration of toluene, to the complex synthesis of highly energetic caged nitro compounds. Reviews laboratory and industrial methods, which can be used to introduce aliphatic C-nitro, aromatic C-nitro, N-nitro, and nitrate ester functionality into organic compounds Discusses the advantages and disadvantages of each synthetic method or route, with scope, limitations, substrate compatibility and other important considerations Features numerous examples in the form of text, reaction diagrams, and tables.
Chemical complementation: A reaction-independent genetic assay for enzyme catalysis (2002)

A high-throughput assay for enzyme activity has been developed that is reaction independent. In this assay, a small-molecule yeast three-hybrid system is used to link enzyme catalysis to transcription of a reporter gene in vivo. Here we demonstrate the feasibility of this approach by using a well-studied enzyme-catalyzed reaction, cephalosporin hydrolysis by the Enterobacter cloacae P99 cephalosporinase (beta-lactam hydrolase, EC ). We show that the three-hybrid system can be used to read out cephalosporinase activity in vivo as a change in the level of transcription of a lacZ reporter gene and that the wild-type cephalosporinase can be isolated from a pool of inactive mutants by using a lacZ screen. The assay has been designed so that it can be applied to different chemical reactions without changing the components of the three-hybrid system. A reaction-independent high-throughput assay for protein function should be a powerful tool for protein engineering and enzymology, drug discovery, and proteomics.
Iron and Hydrogen Peroxide Detoxification Properties of DNA-binding Protein from Starved Cells (2002)

The DNA-binding proteins from starved cells (Dps) are a family of proteins induced in microorganisms by oxidative or nutritional stress. Escherichia coli Dps, a structural analog of the 12-subunit Listeria innocua ferritin, binds and protects DNA against oxidative damage mediated by H(2)O(2). Dps is shown to be a Fe-binding and storage protein where Fe(II) oxidation is most effectively accomplished by H(2)O(2) rather than by O(2) as in ferritins. Two Fe(2+) ions bind at each of the 12 putative dinuclear ferroxidase sites (P(Z)) in the protein according to the equation, 2Fe(2+) + P(Z) --> [(Fe(II)(2)-P](FS)(Z+2) + 2H(+). The ferroxidase site (FS) bound iron is then oxidized according to the equation, [(Fe(II)(2)-P](FS)(Z+2) + H(2)O(2) + H(2)O --> [Fe(III)(2)O(2)(OH)-P](FS)(Z-1) + 3H(+), where two Fe(II) are oxidized per H(2)O(2) reduced, thus avoiding hydroxyl radical production through Fenton chemistry. Dps acquires a ferric core of approximately 500 Fe(III) according to the mineralization equation, 2Fe(2+) + H(2)O(2) + 2H(2)O --> 2Fe(III)OOH((core)) + 4H(+), again with a 2 Fe(II)/H(2)O(2) stoichiometry. The protein forms a similar ferric core with O(2) as the oxidant, albeit at a slower rate. In the absence of H(2)O(2) and O(2), Dps forms a ferrous core of approximately 400 Fe(II) by the reaction Fe(2+) + H(2)O + Cl(-) --> Fe(II)OHCl((core)) + H(+). The ferrous core also undergoes oxidation with a stoichiometry of 2 Fe(II)/H(2)O(2). Spin trapping experiments demonstrate that Dps greatly attenuates hydroxyl radical production during Fe(II) oxidation by H(2)O(2). These results and in vitro DNA damage assays indicate that the protective effect of Dps on DNA most likely is exerted through a dual action, the physical association with DNA and the ability to nullify the toxic combination of Fe(II) and H(2)O(2). In the latter process a hydrous ferric oxide mineral core is produced within the protein, thus avoiding oxidative damage mediated by Fenton chemistry.
Selective Covalent Conjugation of Phosphorothioate DNA Oligonucleotides with Streptavidin (2011)

Protein-DNA conjugates have found numerous applications in the field of diagnostics and nanobiotechnology, however, their intrinsic susceptibility to DNA degradation by nucleases represents a major obstacle for many applications. We here report the selective covalent conjugation of the protein streptavidin (STV) with phosphorothioate oligonucleotides (psDNA) containing a terminal alkylthiolgroup as the chemically addressable linking unit, using a heterobifunctional NHS-/maleimide crosslinker. The psDNA-STV conjugates were synthesized in about 10% isolated yields. We demonstrate that the terminal alkylthiol group selectively reacts with the maleimide while the backbone sulfur atoms are not engaged in chemical conjugation. The novel psDNA-STV conjugates retain their binding capabilities for both biotinylated macromolecules and the complementary nucleic acid. Moreover, the psDNA-STV conjugate retained its binding capacity for complementary oligomers even after a nuclease digestion step, which effectively degrades deoxyribonucleotide oligomers and thus the binding capability of regular DNA-STV conjugates. The psDNA-STV therefore hold particular promise for applications e.g. in proteome research and novel biosensing devices, where interfering endogenous nucleic acids need to be removed from analytes by nuclease digestion.
Visual Genome: Connecting Language and Vision Using Crowdsourced Dense Image Annotations (2016)

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.
Development of anti‐migraine therapeutics using the capsaicin‐induced dermal blood flow model (2015)

The efficacy of calcitonin gene-related peptide (receptor) (CGRP-(R)) blocking therapeutics in the treatment of acute migraine headache provided proof-of-concept for the involvement of CGRP in the pathophysiology of this disorder. One of the major hurdles for the development of any class of drugs, including CGRP blocking therapeutics, is the early clinical development process during which toxic and inefficacious compounds need to be eliminated as early as possible in order to focus on the most promising molecules. At this stage, human models providing proof of target engagement, combined with safety and tolerability studies, are extremely valuable in focusing on those therapeutics that have the highest engagement from the lowest exposure. They guide the go/no-go decision making, establish confidence in the candidate molecule by de-risking toxicity and safety issues and thereby speed up the early clinical development. In this review the focus is on the so called 'capsaicin model' as a typical example of a target engagement biomarker used as a human model for the development of CGRP blocking therapeutics. By applying capsaicin onto the skin, TRPV1 channels are activated and a CGRP-mediated increase in dermal blood flow can be quantified with laser Doppler perfusion imaging. Effective CGRP blocking therapeutics in turn, display blockade of this response. The translation of this biomarker model from animals to humans is discussed as well as the limitations of the assay in predicting the efficacy of anti-migraine drugs.
Scrapie prion protein accumulation by scrapie-infected neuroblastoma cells abrogated by exposure to a prion protein antibody (2001)

Exposure of susceptible neuroblastoma N2a cells to mouse scrapie prions leads to infection, as evidenced by the continued presence of the scrapie form of the prion protein (PrP(Sc)) and infectivity after 300 or more cell doublings. We find that exposure to phosphatidylinositol-specific phospholipase C (PIPLC) or to the monoclonal anti-prion protein (PrP) antibody 6H4 not only prevents infection of susceptible N2a cells but also cures chronically scrapie-infected cultures, as judged by the long-term abrogation of PrP(Sc) accumulation after cessation of treatment. A nonpassaged, stationary infected culture rapidly loses PrP(Sc) when exposed to the antibody or PIPLC, indicating that the PrP(Sc) level is determined by steady state equilibrium between formation and degradation, and that depletion of the cellular form of PrP can interrupt the propagation of PrP(Sc). These findings encourage the belief that passive immunization may provide a therapeutic approach to prion disease.
Pembrolizumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma (2019)

Among patients with previously untreated advanced renal-cell carcinoma, treatment with pembrolizumab plus axitinib resulted in significantly longer overall survival and progression-free survival, as well as a higher objective response rate, than treatment with sunitinib. (Funded by Merck Sharp & Dohme; KEYNOTE-426 ClinicalTrials.gov number, NCT02853331.).
Identification of Malaria-Infected Red Blood Cells Via Digital Shearing Interferometry and Statistical Inference (2013)

Malaria is one of the most widespread diseases, particularly in Asia and Africa. Correct diagnosis of malaria is necessary for its proper treatment. A compact automated tool for malaria identification will greatly benefit healthcare professionals in these regions. We propose a method that has the potential to automatically detect malaria-infected red blood cells (RBCs). This method combines the simplicity and robustness of lateral shearing interferometry with the flexibility of statistical methods to achieve the classification of diseased RBCs. Shearing interferograms generated using a glass plate in a common path setup were Fourier analyzed to retrieve the gradient phase and amplitude information of the cell. Then, multiple features based on the complex amplitude information of the cells are measured automatically and used to differentiate healthy and malaria-infected cells. Multivariate statistical inference algorithm of the experimental data shows that there is a difference between the populations of healthy and malaria-infected RBCs by using the measured RBC features.
In vitro attachment of mono- and oligosaccharides to surface glycoconjugates of intact cells. (1986)

We have synthesized glycosylhydrazines of various mono- and oligosaccharides and coupled these to periodate- or galactose oxidase-treated human red cells and K562 erythroleukemia cells. The optimal conditions for this carbohydrate modification of cells have been established. This method makes it possible to specifically elongate oligosaccharide chains of cell surface glycoconjugates with desired carbohydrates. In this way, new antigenic and receptor properties can be conferred to cells, and the functional roles of carbohydrates in cell surface glycoconjugates can be studied. The method has been used to make red cells of blood group O reactive with anti-A and anti-B sera, and in rendering K562 cells or red cells of blood group O agglutinable with the alpha-N-acetylgalactosamine-specific Helix pomatia lectin.
alpha 1-ADRENERGIC RECEPTOR SUBTYPES IN HUMAN DETRUSOR (1998)

Human detrusor contained two alpha1AR subtypes (alpha1d > alpha1a), a finding that is different from rat, another commonly used animal model. Since non-subtype selective alpha1AR antagonists ameliorate irritative bladder symptoms (in men and women with/without outlet obstruction), and Rec 15/2739 (alpha1a selective antagonist) does not improve symptom scores in BPH, our findings suggest bladder alpha1dARs may provide a potentially novel mechanism underlying these therapeutic benefits.
Inverse and saturation theorems for radial basis function interpolation (2001)

While direct theorems for interpolation with radial basis functions are intensively investigated, little is known about inverse theorems so far. This paper deals with both inverse and saturation theorems. For an inverse theorem we especially show that a function that can be approximated sufficiently fast must belong to the native space of the basis function in use. In case of thin plate spline interpolation we also give certain saturation theorems.
A simple-design high vacuum infrared cell for in situ studies of supported metal catalysts (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA simple-design high vacuum infrared cell for in situ studies of supported metal catalystsSang H. Moon, Hassan Windawi, and James R. KatzerCite this: Ind. Eng. Chem. Fundamen. 1981, 20, 4, 396–399Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/i100004a018https://doi.org/10.1021/i100004a018research-articleACS PublicationsRequest reuse permissionsArticle Views186Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts