gebhart/patrepeval huggingface dataset:
Self‐assembling protein arrays on DNA chips by auto‐labeling fusion proteins with a single DNA address (2006)

The high-throughput deposition of recombinant proteins on chips, beads or biosensor devices would be greatly facilitated by the implementation of self-assembly concepts. DNA-directed immobilization via conjugation of proteins to an oligonucleotide would be preeminently suited for this purpose. Here, we present a unique method to attach a single DNA address to proteins in one step during the purification from the E. coli lysate by fusion to human O6-alkylguanine-DNA-alkyltransferase (SNAP-tag) and the Avitag. Use of the conjugates in converting a DNA chip into a protein chip by self assembly is demonstrated.
Analysis of protein–nucleic acid interactions by photochemical cross‐linking and mass spectrometry (2002)

Photochemical cross-linking is a commonly used method for studying the molecular details of protein-nucleic acid interactions. Photochemical cross-linking aids in defining nucleic acid binding sites of proteins via subsequent identification of cross-linked protein domains and amino acid residues. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross-linking sites in proteins. The present review of the field describes a number of MS-based approaches for the characterization of cross-linked protein-nucleic acid complexes and for sequencing of peptide-nucleic acid heteroconjugates. The combination of photochemical cross-linking and MS provides a fast screening method to gain insights into the overall structure and formation of protein-oligonucleotide complexes. Because the analytical methods are continuously refined and protein structural data are rapidly accumulating in databases, we envision that many protein-nucleic acid assemblies will be initially characterized by combinations of cross-linking methods, MS, and computational molecular modeling.
Quinoxaline studies. XVI. Unequivocal synthesis of (S)-2-methyl-1,2,3,4-tetrahydroquinoxaline (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuinoxaline studies. XVI. Unequivocal synthesis of (S)-2-methyl-1,2,3,4-tetrahydroquinoxalineGeorge H. Fisher, Peter J. Whitman, and Harry P. SchultzCite this: J. Org. Chem. 1970, 35, 7, 2240–2242Publication Date (Print):July 1, 1970Publication History Published online1 May 2002Published inissue 1 July 1970https://pubs.acs.org/doi/10.1021/jo00832a029https://doi.org/10.1021/jo00832a029research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations12LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Conserved enzymes mediate the early reactions of carotenoid biosynthesis in nonphotosynthetic and photosynthetic prokaryotes. (1990)

Carotenoids comprise one of the most widespread classes of pigments found in nature. The first reactions of C40 carotenoid biosynthesis proceed through common intermediates in all organisms, suggesting the evolutionary conservation of early enzymes from this pathway. We report here the nucleotide sequence of three genes from the carotenoid biosynthesis gene cluster of Erwinia herbicola, a nonphotosynthetic epiphytic bacterium, which encode homologs of the CrtB, CrtE, and CrtI proteins of Rhodobacter capsulatus, a purple nonsulfur photosynthetic bacterium. CrtB (prephytoene pyrophosphate synthase), CrtE (phytoene synthase), and CrtI (phytoene dehydrogenase) are required for the first three reactions specific to the carotenoid branch of general isoprenoid metabolism. The homologous proteins from E. herbicola and R. capsulatus show sequence identities of 41.7% for CrtI, 33.7% for CrtB, and 30.8% for CrtE. E. herbicola and R. capsulatus CrtI also display 27.2% and 27.9% sequence identity, respectively, with R. capsulatus CrtD (methoxyneurosporene dehydrogenase). All three dehydrogenases possess a hydrophobic N-terminal domain containing a putative ADP-binding beta alpha beta fold characteristic of enzymes known to bind FAD or NAD(P) cofactors. In addition, E. herbicola and R. capsulatus CrtB show 25.2% and 23.3% respective sequence identities with the protein product of pTOM5, a tomato cDNA of unknown function that is differentially expressed during fruit ripening. These data indicate the structural conservation of early carotenoid biosynthesis enzymes in evolutionarily diverse organisms.
Evaluation of lipid oxidative stress status and inflammation in atopic ocular surface disease. (2010)

The ocular surface disease in AKC was characterized by marked tear instability, ocular surface epithelial damage, increase in inflammatory infiltrates and presence of increased lipid oxidation.
Relationship Between Coefficient of Parentage and Genetic Similarity Indices in the Soybean1 (1985)

Estimates of genetic similarity or distance between populations or strains of plants are useful in planning crosses for hybrid or pureline cultivar development. We compared coefficients of parentage ( r ) and similarity indices ( s , s z , and s M , based on 20, 13, and 7 genetic loci, respectively) for combinations of 115 soybean [ Glycine max (L.) Merr.] cultivars and ancestral introductions. Correlations between r and s were higher than those between r and s z or s M , primarily because s includes information from more loci. The correlation between r and s was higher for the group of soybean cultivars released in the 1970s than for earlier cultivar groups, primarily because of the greater importance of identity by descent relative to identity in phenotype in determining s . The most useful estimate of genetic relationship is a composite index that includes both r and s .
Using domain-specific languages for analytic graph databases (2016)

Recently graph has been drawing lots of attention both as a natural data model that captures fine-grained relationships between data entities and as a tool for powerful data analysis that considers such relationships. In this paper, we present a new graph database system that integrates a robust graph storage with an efficient graph analytics engine. Primarily, our system adopts two domain-specific languages (DSLs), one for describing graph analysis algorithms and the other for graph pattern matching queries. Compared to the API-based approaches in conventional graph processing systems, the DSL-based approach provides users with more flexible and intuitive ways of expressing algorithms and queries. Moreover, the DSL-based approach has significant performance benefits as well, (1) by skipping (remote) API invocation overhead and (2) by applying high-level optimization from the compiler.
The Many Faces of G Protein Signaling (1998)

Progress in areas of research that once might have seemed distant from the field of G protein signaling now shows that G proteins are involved in a broad range of cellular regulatory activities. The understanding of how the proteins interact (receptors, G proteins, and effectors, as well as other regulatory proteins) thus has enormous implications for physiology. The rapid progress in determining three-dimensional structures of G proteins, and more recently their regulators and effectors, has illuminated the search for mechanisms of activation and regulation and has allowed structure-based mutagenesis to test these ideas. The structural and mechanistic studies will in the future also hopefully provide opportunities to alter those interactions in pathological situations.
Expression of gene MAGE-A4 in Reed-Sternberg cells. (2000)

Genes of the MAGE-A family are expressed in several types of solid tumors but are silent in normal tissues with the exception of male germline cells, which do not carry HLA molecules.Therefore, peptides encoded by MAGE-A genes are strictly tumor-specific antigens that can be recognized by CTL and constitute promising targets for immunotherapy. The expression of 6 genes of the MAGE-A family was tested with reverse transcriptase-polymerase chain reaction in lymphoma samples. Among 38 samples of non-Hodgkin lymphoma, 1 anaplastic large cell lymphoma expressed genes MAGE-A1, -A2, -A3, -A4, and -A12, and 1 lymphoepithelioid T-cell lymphoma expressed gene MAGE-A4. Five of 18 samples (28%) from patients with Hodgkin disease expressed gene MAGE-A4. In tissue sections, staining by a monoclonal antibody that recognizes the MAGE-A4 protein was observed in 11 of 53 samples (21%) from patients with Hodgkin disease. In the positive samples, the Reed-Sternberg cells were strongly stained whereas the surrounding cells were not. These results indicate that Hodgkin disease may be a target for specific immunotherapy involving MAGE-A4 antigens.
The identification of a novel synaptosomal-associated protein, SNAP-25, differentially expressed by neuronal subpopulations. (1989)

cDNA clones of a neuronal-specific mRNA encoding a novel 25-kD synaptosomal protein, SNAP-25, that is widely, but differentially expressed by diverse neuronal subpopulations of the mammalian nervous system have been isolated and characterized. The sequence of the SNAP-25 cDNA revealed a single open reading frame that encodes a primary translation product of 206 amino acids. Antisera elicited against a 12-amino acid peptide, corresponding to the carboxy-terminal residues of the predicted polypeptide sequence, recognized a single 25-kD protein that is associated with synaptosomal fractions of hippocampal preparations. The SNAP-25 polypeptide remains associated with synaptosomal membrane components after hypoosmotic lysis and is released by nonionic detergent but not high salt extraction. Although the SNAP-25 polypeptide lacks a hydrophobic stretch of residues compatible with a transmembrane region, the amino terminus may form an amphiphilic helix that may facilitate alignment with membranes. The predicted amino acid sequence also includes a cluster of four closely spaced cysteine residues, similar to the metal binding domains of some metalloproteins, suggesting that the SNAP-25 polypeptide may have the potential to coordinately bind metal ions. Consistent with the protein fractionation, light and electron microscopic immunocytochemistry indicated that SNAP-25 is located within the presynaptic terminals of hippocampal mossy fibers and the inner molecular layer of the dentate gyrus. The mRNA was found to be enriched within neurons of the neocortex, hippocampus, piriform cortex, anterior thalamic nuclei, pontine nuclei, and granule cells of the cerebellum. The distribution of the SNAP-25 mRNA and the association of the protein with presynaptic elements suggest that SNAP-25 may play an important role in the synaptic function of specific neuronal systems.
Bread wheat: improvement and production. (2002)

Bread wheat :improvement and production , Bread wheat :improvement and production , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Evidence for a Commensal, Symbiotic Relationship between Gardnerella vaginalis and Prevotella bivia Involving Ammonia: Potential Significance for Bacterial Vaginosis (1997)

Six strains of Prevotella bivia and 4 of Gardnerella vaginalis were examined for nutrient substrate utilization as part of ongoing studies on the pathogenesis of bacterial vaginosis. Addition of single amino acids to vaginal defined medium (VDM) was stimulatory to the growth of P. bivia but not to G. vaginalis. However, peptides significantly promoted the growth of both organisms. Growth of P. bivia in VDM and VDM supplemented with either amino acids or peptone was accompanied by net ammonia production, while growth of G. vaginalis under the same conditions resulted in net ammonia utilization. Ammonia-enriched supernatants from the growth of P. bivia in peptone-supplemented VDM were stimulatory to G. vaginalis growth. However, ammonia-reduced supernatants from G. vaginalis growth in peptone-supplemented VDM had a neutral effect on P. bivia growth. A commensal relationship between P. bivia to G. vaginalis is proposed, with ammonia flow as a mechanism to support this hypothesis.
Neutrophil heterogeneity in health and disease: a revitalized avenue in inflammation and immunity (2012)

Leucocytes form the principal cellular components of immunity and inflammation, existing as multiple subsets defined by distinct phenotypic and functional profiles. To date, this has most notably been documented for lymphocytes and monocytes. In contrast, as neutrophils are traditionally considered, to be short-lived, terminally differentiated cells that do not re-circulate, the potential existence of distinct neutrophil subsets with functional and phenotypic heterogeneity has not been widely considered or explored. A growing body of evidence is now challenging this scenario, and there is significant evidence for the existence of different neutrophil subsets under both physiological and pathological conditions. This review will summarize the key findings that have triggered a renewed interest in neutrophil phenotypic changes, both in terms of functional implications and consequences within disease models. Special emphasis will be placed on the potential pro- and anti-inflammatory roles of neutrophil subsets, as indicated by the recent works in models of ischaemia-reperfusion injury, trauma, cancer and sepsis.
Coreceptors--Implications for HIV Pathogenesis and Therapy (1997)

Last year, the second of the two receptors that HIV uses to enter and infect human cells was identified. In his Perspective, Moore discusses the resulting revolution in thought about how these coreceptor molecules can influence the progress of AIDS and what their existence means for future therapies.
THE CARDIAC FIBROBLAST: Therapeutic Target in Myocardial Remodeling and Failure (2005)

Cardiac fibroblasts play a central role in the maintenance of extracellular matrix in the normal heart and as mediators of inflammatory and fibrotic myocardial remodeling in the injured and failing heart. In this review, we evaluate the cardiac fibroblast as a therapeutic target in heart disease. Unique features of cardiac fibroblast cell biology are discussed in relation to normal and pathophysiological cardiac function. The contribution of cardiac fibrosis as an independent risk factor in the outcome of heart failure is considered. Candidate drug therapies that derive benefit from actions on cardiac fibroblasts are summarized, including inhibitors of angiotensin-aldosterone systems, endothelin receptor antagonists, statins, anticytokine therapies, matrix metalloproteinase inhibitors, and novel antifibrotic/anti-inflammatory agents. These findings point the way to future challenges in cardiac fibroblast biology and pharmacotherapy.
Four Genetic Polymorphisms of Lymphotoxin-Alpha Gene and Cancer Risk: A Systematic Review and Meta-Analysis (2013)

Lymphotoxin-alpha (LTA) is a pro-inflammatory cytokine that plays an important role in the inflammatory and immunologic response. Numerous studies have shown LTA polymorphisms as risk factors for cancers, but the results remain inconclusive. The goal of the present meta-analyses is to establish the associations between cancers and four LTA variants (rs1041981, rs2239704, rs2229094 and rs746868). A total of 30 case-control studies involving 58,649 participants were included in the current meta-analyses. Our results showed significant associations with increased cancer risk for rs1041981 (odd ratio (OR) = 1.15, 99% confidential interval (CI) = 1.07-1.25, P < 0.0001, I(2) = 12.2%), rs2239704 (OR = 1.08, 99% CI = 1.01-1.16, P = 0.021, I(2) = 0.0%) and rs2229094 (OR = 1.28, 99% CI = 1.09-1.50, P = 0.003, I(2) = 0.0%). No evidence was found for the association between rs746868 and cancer risk (OR = 1.01, 99% CI = 0.93-1.10, P = 0.771, I(2) = 0.0%). Subgroup meta-analysis suggested that rs2239704 was likely to increase the risk of hematological malignancy (OR = 1.10, 99% CI = 1.01-1.20, P = 0.023, I(2) = 0.0%), and rs2229094 was specific for the increased risk of adenocarcinoma (OR = 1.33, 99% CI = 1.11-1.59, P = 0.002, I(2) = 0.0%). In conclusion, our meta-analyses suggested that the LTA rs1041981, rs2239704 and rs2229094 polymorphisms contributed to the increased risk of cancers. Future functional studies were needed to clarify the mechanistic roles of the three variants in the cancer risk.
Phage display-derived human antibodies in clinical development and therapy (2016)

Over the last 3 decades, monoclonal antibodies have become the most important class of therapeutic biologicals on the market. Development of therapeutic antibodies was accelerated by recombinant DNA technologies, which allowed the humanization of murine monoclonal antibodies to make them more similar to those of the human body and suitable for a broad range of chronic diseases like cancer and autoimmune diseases. In the early 1990s in vitro antibody selection technologies were developed that enabled the discovery of "fully" human antibodies with potentially superior clinical efficacy and lowest immunogenicity. Antibody phage display is the first and most widely used of the in vitro selection technologies. It has proven to be a robust, versatile platform technology for the discovery of human antibodies and a powerful engineering tool to improve antibody properties. As of the beginning of 2016, 6 human antibodies discovered or further developed by phage display were approved for therapy. In 2002, adalimumab (Humira®) became the first phage display-derived antibody granted a marketing approval. Humira® was also the first approved human antibody, and it is currently the best-selling antibody drug on the market. Numerous phage display-derived antibodies are currently under advanced clinical investigation, and, despite the availability of other technologies such as human antibody-producing transgenic mice, phage display has not lost its importance for the discovery and engineering of therapeutic antibodies. Here, we provide a comprehensive overview about phage display-derived antibodies that are approved for therapy or in clinical development. A selection of these antibodies is described in more detail to demonstrate different aspects of the phage display technology and its development over the last 25 years.
Integrated transversal equalizers in high-speed fiber-optic systems (2003)

Intersymbol interference (ISI) caused by intermodal dispersion in multimode fibers is the major limiting factor in the achievable data rate or transmission distance in high-speed multimode fiber-optic links for local area networks applications. Compared with optical-domain and other electrical-domain dispersion compensation methods, equalization with transversal filters based on distributed circuit techniques presents a cost-effective and low-power solution. The design of integrated distributed transversal equalizers is described in detail with focus on delay lines and gain stages. This seven-tap distributed transversal equalizer prototype has been implemented in a commercial 0.18-μm SiGe BiCMOS process for 10-Gb/s multimode fiber-optic links. A seven-tap distributed transversal equalizer reduces the ISI of a 10-Gb/s signal after 800 m of 50-μm multimode fiber from 5 to 1.38 dB, and improves the bit-error rate from about 10/sup -5/ to less than 10/sup -12/.
A Succinct Synthesis of the Vaulted Biaryl Ligand Vanol via a Dienone–Phenol Rearrangement (2011)

Vanol is a member of the vaulted biaryl family of ligands and it has been proven to be very effective in a number of asymmetric catalytic reactions. The previous synthesis of vanol, while effective, is limited by the cost of reagents involved. The present work evaluates three different approaches to the synthesis of 3-phenyl-1-naphthol, a key intermediate in the synthesis of vanol. The first approach has its key step as the Michael addition of a benzyl Grignard to methyl cinnamate. In the second approach the key step is the first step, a Reformatsky reaction of ethyl bromoacetate and deoxybenzoin. The final and most-efficient approach involves a dienone-phenol rearrangement of a 4-aryl-1-tetralenone generated in-situ from the reaction of 4-chloro-1-naphthol with AlCl(3) and benzene, and preliminary results are reported on the extension of this method to substituted vanol derivatives.
Thin films of Pd/Ni alloys for detection of high hydrogen concentrations (1992)

Thin alloy films of Pd and Ni (8%&amp;lt;Ni&amp;lt;20% in at. %) formed by dual-electron-beam evaporation techniques have been found to give durable and quickly reversible detectors of high H2 concentrations (pH2 0.1%–100%, 0.7–700 Torr) near 1 atm and 300 K, including accurate determinations of pH2 around the lower explosive limit of 4% in air. The addition of Ni suppresses the α to β phase transition found in pure Pd under these conditions. The measurement of resistivity changes in the thin films along with flatband shifts of metal-oxide-semiconductor capacitors on the same Si wafer gives accurate values of pH2 over more than six decades.
Molecular Mechanisms of Ligand Interaction with the Gonadotropin-Releasing Hormone Receptor (1997)

I. Introduction II. Amino Acid Sequences of GnRH Receptors A. GnRH receptor cDNAs B. General structural features C. Covalent modifications D. Gene structure III. Structure-Activity Relations of GnRH Peptides A. Overview B. Comparative structures and activities of vertebrate GnRHs C. Roles of individual amino acids in GnRH activity at the mammalian receptor D. Conclusions from peptide structure-activity data IV. Structure and Conformation of GnRH and Its Analogs A. Early studies of GnRH conformation B. Integrated computational and experimental studies C. Exploration of the entire conformation space of GnRH analogs V. Functional Structure of the Receptor and Ligand-Receptor Complex A. Extracellular domains B. Helix domains C. Intracellular loop domains D. Computational modeling of three-dimensional receptor structure VI. Conclusions
Capillary Electrophoresis Separation in the Presence of an Immiscible Boundary for Droplet Analysis (2006)

This paper demonstrates the ability to use capillary electrophoresis (CE) separation coupled with laser-induced fluorescence for analyzing the contents of single femtoliter-volume aqueous droplets. A single droplet was formed using a T-channel (3 microm wide by 3 microm tall) connected to microinjectors, and then the droplet was fluidically moved to an immiscible boundary that isolates the CE channel (50 microm wide by 50 microm tall) from the droplet generation region. Fusion of the aqueous droplet with the immiscible boundary effectively injects the droplet content into the separation channel. In addition to injecting the contents of droplets, we found aqueous samples can be introduced directly into the separation channel by reversibly penetrating and resealing the immiscible partition. Because droplet generation in channels requires hydrophobic surfaces, we have also investigated the advantages to using all hydrophobic channels versus channel systems with patterned hydrophobic and hydrophilic regions. To fabricate devices with patterned surface chemistry, we have developed a simple strategy based on differential wetting to deposit selectively a hydrophilic polymer (poly(styrenesulfonate)) onto desired regions of the microfluidic chip. Finally, we applied our device to the separation of a simple mixture of fluorescein-labeled amino acids contained within a approximately 10-fL droplet.