gebhart/patrepeval huggingface dataset:
Ethyl-substituted erythromycin derivatives produced by directed metabolic engineering (1998)

A previously unknown chemical structure, 6-desmethyl-6-ethylerythromycin A (6-ethylErA), was produced through directed genetic manipulation of the erythromycin (Er)-producing organism Saccharopolyspora erythraea. In an attempt to replace the methyl side chain at the C-6 position of the Er polyketide backbone with an ethyl moiety, the methylmalonate-specific acyltransferase (AT) domain of the Er polyketide synthase was replaced with an ethylmalonate-specific AT domain from the polyketide synthase involved in the synthesis of the 16-member macrolide niddamycin. The genetically altered strain was found to produce ErA, however, and not the ethyl-substituted derivative. When the strain was provided with precursors of ethylmalonate, a small quantity of a macrolide with the mass of 6-ethylErA was produced in addition to ErA. Because substrate for the heterologous AT seemed to be limiting, crotonyl-CoA reductase, a primary metabolic enzyme involved in butyryl-CoA production in streptomycetes, was expressed in the strain. The primary macrolide produced by the reengineered strain was 6-ethylErA.
Tetracycline-Regulated overexpression of glycosyltransferases in Chinese hamster ovary cells (1999)

The glycosylation patterns of recombinant therapeutic glycoproteins can be engineered by overexpression of glycosyltransferases in the host cells used for glycoprotein production. Most prior glycosylation engineering experiments have involved constitutive expression of cloned glycosyltransferases. Here we use tetracycline-regulated expression of two glycosyltransferases, N-acetylglucosaminlytransferases III and V (GnTIII and GnTV) to manipulate glycoform biosynthesis in Chinese hamster ovary (CHO) cells and to study the effect of glycosyltransferase overexpression on this host. The amount of GnTIII and GnTV in these cells, and the glycosylation patterns of several cellular glycoproteins, could be controlled simply by manipulating the concentration of tetracycline in the culture medium. Using this system, it was found that overexpression of either GnTIII or GnTV to high levels led to growth inhibition and was toxic to the cells, indicating that this may be a general feature of glycosyltransferase overexpression. This phenomenon has not been reported previously, probably due to the widespread use of constitutive promoters, and should be taken into account when designing vectors for glycosylation engineering. The growth inhibition effect sets an upper limit to the level of glycosyltransferase overexpression, and may thereby also limit the maximum extent of in vivo modification of poorly accessible glycosylation sites. Also, such inhibition implies a bound on constitutive glycosyltransferase expression which can be cloned.
Respiratory syncytial virus specific serum antibodies in infants under six months of age: Limited serological response upon infection (1997)

The decline of maternal respiratory syncytial virus (RSV) specific serum antibodies was studied in 45 children during the first 6 months of life, using a virus neutralization assay and competition ELISAs measuring fusion protein and glycoprotein specific antibodies. In all children RSV neutralizing antibodies were demonstrated at birth, with titers ranging from 33 to 1382. The calculated mean half life of these antibodies was 26 days. Furthermore, in a group of 38 children with suspected RSV infection, all younger than 6 months of age on admission, the diagnostic value of serological assays was evaluated. In 32 children RSV infection was confirmed by virus isolation, direct immune fluorescence and RT-PCR. In 7 patients of this group a significant titer rise in virus neutralization assay was demonstrated. Six additional RSV infected children could be identified by showing the presence of RSV-specific IgM or IgA serum antibodies or by showing an increase in fusion protein or glycoprotein specific antibodies. All serological tests together identified 13 (41%) of the 32 RSV infected patients. It is concluded that in children of this age group, which represent the majority of patients hospitalized with RSV infections, serological assays not only have a limited diagnostic value but are of limited value for sero-epidemiological studies.
F4/80, a monoclonal antibody directed specifically against the mouse macrophage (1981)

A hybridoma clone which secretes a macrophage (M phi)-specific monoclonal antibody, F4/80, was produced by fusing spleen cells from a rat hyperimmunized with cultured thioglycollate-induced mouse peritoneal M phi with a mouse myeloma, NS1. Binding of antibody to primary cells and cell lines was detected by radioimmune indirect binding assay, autoradiography or fluorescence-activated cell sorter analysis. F4/80 binds to mouse M phi from the peritoneal cavity or other sources, blood monocytes, M phi derived from bone marrow precursors in culture and M phi-like cell lines, but not to other cells, including polymorphonuclear leukocytes, lymphocytes or fibroblasts. F4/80 does not bind to M phi via Fc receptors, is not cytotoxic and is of the rat IgG2b subclass. Since F4/80 binds to all M phi defined by adherence, morphology and immune phagocytosis, it provides a new marker to define the M phi in the mouse. Large differences in expression of antigen F4/80 were found, depending on intraperitoneal stimulation, time in culture and stage of maturation. Immunoprecipitation experiments demonstrated that the antigen F4/80 is part of a component of Mr 160000 which is synthesized by the M phi and, at least in part, exposed on the cell surface.
The Emerging Role of the Insulin-Like Growth Factor Pathway as a Therapeutic Target in Cancer (2008)

The insulin-like growth factor signaling pathway is important in many human cancers based on data from experimental models as well as epidemiological studies. Important therapies targeted at this pathway have been or are being developed, including monoclonal antibodies to the insulin-like growth factor-I receptor and small molecule inhibitors of the tyrosine kinase function of this receptor. These investigational therapies are now being studied in clinical trials. Emerging data from phase I trials are encouraging regarding the safety of the monoclonal antibodies. In this manuscript, the rationale for targeting the insulin-like growth factor system is reviewed in addition to a summary of the available clinical trial data.
Identification of major proteins associated with Dictyostelium discoideum endocytic vesicles (1995)

Magnetic isolation of endocytic vesicles from Dictyostelium discoideum was accomplished after feeding the amoebae with iron oxide particles. Proteins associated with the endocytic vesicles were resolved by SDS-PAGE and digested 'in-gel' with endoproteinase Lys-C or Asp-N to generate peptides for amino acid sequencing. This strategy allowed the identification of the major protein constituents of the vesicles: namely, the A, B, D, E and 110 kDa subunits of a vacuolar type H(+)-ATPase, actin, a Rab 7-like GTPase, a p34 protein corresponding to a new cysteine proteinase and the 25 kDa product of a recently sequenced D. discoideum open reading frame.
Aspirin in the Prevention of Thrombosis (1991)

More than a decade has passed since the introduction of the concept that inhibition of platelet function may be helpful in preventing the initiation of thrombus formation. Aspirin has been recognized as inhibiting normal platelet function and the mechanism has been clearly delineated. Legions of patients have been studied to answer the question of whether aspirin is efficacious in the primary prevention of acute myocardial infarction. At the present time, however, a solid, clear answer is not available and firm recommendations cannot be made. A large number of studies evaluating aspirin and other antiplatelet agents in the prevention or delay of recurrent myocardial infarction (secondary prevention) have been completed and those studies reporting a favorable beneficial effect are in the minority. In these secondary prevention studies reporting success, the doses of aspirin employed were large enough to inhibit both the cyclo-oxygenase system and thromboxane A2 production as well as the synthesis of prostacyclin. Thus, in these studies if aspirin is effective in reducing adverse cardiovascular events, its efficacy is being mediated by an unknown mechanism. If the reader of the few studies that report positive results is convinced of the benefit of aspirin, it must be emphasized that thoughtful, cautious patient selection based upon the individual's cardiovascular risk profile must be exercised. Individual variation may exist with respect to aspirin's beneficial effect. It must be absolutely recognized that aspirin or any antiplatelet agent does not in any way substitute for the removal or treatment of coexisting risk factors such as tobacco, obesity, hypercholesterolemia, hyperlipidemia, hypertension, and metabolic disease. In contrast to aspirin, control of the above risk factors has been established as beneficial. Aspirin is not free of undesirable side-effects; fatalities secondary to hemorrhage have been reported, and these must be known in detail and understood by both physician and patient before this agent is prescribed in the prophylactic treatment of cardiovascular disease.
Synthesis and central nervous system properties of 2-[(alkoxycarbonyl)amino]-4(5)-phenyl-2-imidazolines (1984)

A series of 2-[( alkoxycarbonyl )amino]-4(5)-phenyl-2-imidazolines was prepared and evaluated for central nervous system (CNS) effects (antidepressant, anticonvulsant, muscle relaxant, and depressant) in animal models. Some separation of those CNS activities was achieved through substitutions on the phenyl and imidazoline moieties. Halo-substituted phenyl compounds were among the most potent antidepressants in this series, while imidazole N-alkylation produced compounds with increased depressant effects (loss of righting reflex, mouse behavior). Comparison of in vitro and in vivo data for pairs of 2-[(methoxycarbonyl)amino]-4(5)-phenyl-2-imidazolines and their parent, 2-amino-4(5)-phenyl-2-imidazolines, suggests that the title compounds were prodrugs for the 2-amino-4(5)-phenyl-2-imidazolines in inhibition of norepinephrine reuptake.
Synthetic NGF peptide derivatives prevent neuronal death via a p75 receptor-dependent mechanism (1997)

Cyclized peptides corresponding to beta-loop regions of NGF were purified by HPLC and assayed for neurotrophic activity using DRG neurons. Peptides with the highest activity corresponded to loop region 29-35, a domain likely to interact with the p75 receptor. Unexpectedly, activity was confined to late-eluting HPLC fractions containing peptide multimers and primarily promoted neuronal survival without neurite outgrowth. Directed synthesis of dimer and monomer cyclized peptides demonstrated that dimers acted as partial NGF agonists in that they had both survival-promoting and NGF-inhibiting activity while monomer and linear peptides were inactive. Dimer activity was not affected by the Trk inhibitor K252a but was blocked by p75 receptor antibody and absent using p75 null mutant neurons. These studies suggest that region 29-35 peptide derivatives inhibit neuronal death via a structure- and p75-dependent mechanism.
A global sampling method for alpha matting (2011)

Alpha matting refers to the problem of softly extracting the foreground from an image. Given a trimap (specifying known foreground/background and unknown pixels), a straightforward way to compute the alpha value is to sample some known foreground and background colors for each unknown pixel. Existing sampling-based matting methods often collect samples near the unknown pixels only. They fail if good samples cannot be found nearby. In this paper, we propose a global sampling method that uses all samples available in the image. Our global sample set avoids missing good samples. A simple but effective cost function is defined to tackle the ambiguity in the sample selection process. To handle the computational complexity introduced by the large number of samples, we pose the sampling task as a correspondence problem. The correspondence search is efficiently achieved by generalizing a randomized algorithm previously designed for patch matching[3]. A variety of experiments show that our global sampling method produces both visually and quantitatively high-quality matting results.
Electrospray‐assisted laser desorption/ionization mass spectrometry for direct ambient analysis of solids (2005)

A new method of electrospray-assisted laser desorption/ionization (ELDI) mass spectrometry, which combines laser desorption with post-ionization by electrospray, was applied to rapid analysis of solid materials under ambient conditions. Analytes were desorbed from solid metallic and insulating substrata using a pulsed nitrogen laser. Post-ionization produced high-quality mass spectra characteristic of electrospray, including protein multiple charging. For the first time, mass spectra of intact proteins were obtained using laser desorption without adding a matrix. Bovine cytochrome c and an illicit drug containing methaqualone were chosen in this study to demonstrate the applicability of ELDI to the analysis of proteins and synthetic organic compounds.
Factors influencing immune response after in vivo retrovirus‐mediated gene transfer to the liver (2004)

Our present results suggest that both supernatant contamination and viral spreading contribute to immune response after retrovirus-mediated gene delivery to the liver.
Homology Between Type-C Viruses of Various Species as Determined by Molecular Hybridization (1973)

Two strains of feline leukemia virus, two endogenous feline type-C viruses (RD/CCC group), several endogenous and laboratory strains of murine "leukemia" virus, two rat viruses, two primate viruses (woolly monkey and gibbon ape), as well as hamster, pig, and avian type-C viruses were examined for their relatedness to one another by molecular hybridization. The extent of nucleic-acid homology was determined by hybridization of the various viral RNAs to a [(3)H]DNA product synthesized from each virus. Among the murine type-C viruses (Rauscher, Kirsten, AT-124, and endogenous BALB/c virus) a high degree of homology is observed, although the viruses are not identical. The two primate viruses are also closely related to one another. The feline, rat, hamster, and pig endogenous viruses can be readily distinguished from one another and from the murine and primate viruses since their DNA products share very little or no nucleic-acid homology. However, the murine and primate type-C virus groups possess a surprising degree of relatedness. Feline type-C viruses fall into two distinct groups, the feline leukemia virus group and the RD-114/CCC group, with little detectable nucleic-acid homology between them. Infection of feline or rat cells with type-C virus results in production of the endogenous type-C virus of the species along with the infecting virus.
A tagging-via-substrate technology for detection and proteomics of farnesylated proteins (2004)

A recently developed proteomics strategy, designated tagging-via-substrate (TAS) approach, is described for the detection and proteomic analysis of farnesylated proteins. TAS technology involves metabolic incorporation of a synthetic azido-farnesyl analog and chemoselective derivatization of azido-farnesyl-modified proteins by an elegant version of Staudinger reaction, pioneered by the Bertozzi group, using a biotinylated phosphine capture reagent. The resulting protein conjugates can be specifically detected and/or affinity-purified by streptavidin-linked horseradish peroxidase or agarose beads, respectively. Thus, the technology enables global profiling of farnesylated proteins by enriching farnesylated proteins and reducing the complexity of farnesylation subproteome. Azido-farnesylated proteins maintain the properties of protein farnesylation, including promoting membrane association, Ras-dependent mitogen-activated protein kinase kinase activation, and inhibition of lovastatin-induced apoptosis. A proteomic analysis of farnesylated proteins by TAS technology revealed 18 farnesylated proteins, including those with potentially novel farnesylation motifs, suggesting that future use of this method is likely to yield novel insight into protein farnesylation. TAS technology can be extended to other posttranslational modifications, such as geranylgeranylation and myristoylation, thus providing powerful tools for detection, quantification, and proteomic analysis of posttranslationally modified proteins.
Novel Formaldehyde-Activating Enzyme in Methylobacterium extorquens AM1 Required for Growth on Methanol (2000)

Formaldehyde is toxic for all organisms from bacteria to humans due to its reactivity with biological macromolecules. Organisms that grow aerobically on single-carbon compounds such as methanol and methane face a special challenge in this regard because formaldehyde is a central metabolic intermediate during methylotrophic growth. In the alpha-proteobacterium Methylobacterium extorquens AM1, we found a previously unknown enzyme that efficiently catalyzes the removal of formaldehyde: it catalyzes the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin, a reaction which also proceeds spontaneously, but at a lower rate than that of the enzyme-catalyzed reaction. Formaldehyde-activating enzyme (Fae) was purified from M. extorquens AM1 and found to be one of the major proteins in the cytoplasm. The encoding gene is located within a cluster of genes for enzymes involved in the further oxidation of methylene tetrahydromethanopterin to CO(2). Mutants of M. extorquens AM1 defective in Fae were able to grow on succinate but not on methanol and were much more sensitive toward methanol and formaldehyde. Uncharacterized orthologs to this enzyme are predicted to be encoded by uncharacterized genes from archaea, indicating that this type of enzyme occurs outside the methylotrophic bacteria.
Oligosaccharide Synthesis on a Fluorous Support (2003)

The fluorous support Hfb (see picture) enabled high-yielding oligosaccharide syntheses in which the synthetic intermediates could be purified by simple fluorous–organic solvent extraction, and the reactions could be monitored spectroscopically and by TLC. Hfb was readily attached to the anomeric hydroxy group of a carbohydrate. The fluorous support could be removed in high yield, and was recyclable.
Cellular Attachment to Ultraviolet Ozone Modified Polystyrene Surfaces (2000)

The surfaces of standard untreated polystyrene cell culture dishes have been oxidatively modified for up to 8 min exposure time using an ultraviolet ozone treater in order to promote cell adhesion. Surface oxygen chemisorption and topographical modification has been characterized using monochromatic X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), respectively. The oxidation process is shown to proceed at low exposure times (<60 s) via the formation of COR groups, although some R2CO and RO−CO groups are also formed. At longer treatments, RO−CO groups become the dominant species, although the other groups are also present. The maximum level of oxygen reached is 36 atomic %. Some of the oxygen present at surfaces treated at times of >60 s is in the form of loosely bound low molecular weight oxidized material (LMWOM) which is produced by oxidative scission of the PS backbone. Water washing leads to a reduction in surface oxygen content mainly by the removal of ROCO and R2CO functional groups. The residual stable oxygen levels, which can be introduced, are approximately 20−25 atomic %. Surface chemistry changes are accompanied by the formation of surface spikes which are about 30 nm high and 300−400 nm wide. A correlation between treatment time/oxygen level and overall roughness is observed. The effect of washing upon the topography is to slightly increase the surface roughness, although not to a significant degree. The attachment kinetics of adhesion for Chinese hamster ovary cells show that adhesion occurs much more rapidly for oxidized surfaces than for untreated control materials. A direct correlation between the levels of oxidation and the rate of cell adhesion is demonstrated.
MerMade: An Oligodeoxyribonucleotide Synthesizer for High Throughput Oligonucleotide Production in Dual 96-Well Plates (1998)

We have designed and constructed a machine that synthesizes two standard 96-well plates of oligonucleotides in a single run using standard phosphoramidite chemistry. The machine is capable of making a combination of standard, degenerate, or modified oligos in a single plate. The run time is typically 17 hr for two plates of 20-mers and a reaction scale of 40 nM. The reaction vessel is a standard polypropylene 96-well plate with a hole drilled in the bottom of each well. The two plates are placed in separate vacuum chucks and mounted on an xy table. Each well in turn is positioned under the appropriate reagent injection line and the reagent is injected by switching a dedicated valve. All aspects of machine operation are controlled by a Macintosh computer, which also guides the user through the startup and shutdown procedures, provides a continuous update on the status of the run, and facilitates a number of service procedures that need to be carried out periodically. Over 25,000 oligos have been synthesized for use in dye terminator sequencing reactions, polymerase chain reactions (PCRs), hybridization, and RT-PCR. Oligos up to 100 bases in length have been made with a coupling efficiency in excess of 99%. These machines, working in conjunction with our oligo prediction code are particularly well suited to application in automated high throughput genomic sequencing.
Polychemotherapy for early breast cancer: an overview of the randomised trials. Early Breast Cancer Trialists' Collaborative Group. (1998)

Some months of adjuvant polychemotherapy (eg, with CMF or an anthracycline-containing regimen) typically produces an absolute improvement of about 7-11% in 10-year survival for women aged under 50 at presentation with early breast cancer, and of about 2-3% for those aged 50-69 (unless their prognosis is likely to be extremely good even without such treatment). Treatment decisions involve consideration not only of improvements in cancer recurrence and survival but also of adverse side-effects of treatment, and this report makes no recommendations as to who should or should not be treated.
Theory of the grafted polymer brush (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory of the grafted polymer brushS. T. Milner, T. A. Witten, and M. E. CatesCite this: Macromolecules 1988, 21, 8, 2610–2619Publication Date (Print):August 1, 1988Publication History Published online1 May 2002Published inissue 1 August 1988https://pubs.acs.org/doi/10.1021/ma00186a051https://doi.org/10.1021/ma00186a051research-articleACS PublicationsRequest reuse permissionsArticle Views8421Altmetric-Citations1328LEARN 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