gebhart/patrepeval huggingface dataset:
Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C (2008)

Derivatives of Escherichia coli C were previously described for succinate production by combining the deletion of genes that disrupt fermentation pathways for alternative products (ldhA::FRT, adhE::FRT, ackA::FRT, focA-pflB::FRT, mgsA, poxB) with growth-based selection for increased ATP production. The resulting strain, KJ073, produced 1.2 mol of succinate per mol glucose in mineral salts medium with acetate, malate, and pyruvate as significant co-products. KJ073 has been further improved by removing residual recombinase sites (FRT sites) from the chromosomal regions of gene deletion to create a strain devoid of foreign DNA, strain KJ091(DeltaldhA DeltaadhE DeltaackA DeltafocA-pflB DeltamgsA DeltapoxB). KJ091 was further engineered for improvements in succinate production. Deletion of the threonine decarboxylase (tdcD; acetate kinase homologue) and 2-ketobutyrate formate-lyase (tdcE; pyruvate formate-lyase homologue) reduced the acetate level by 50% and increased succinate yield (1.3 mol mol(-1) glucose) by almost 10% as compared to KJ091 and KJ073. Deletion of two genes involved in oxaloacetate metabolism, aspartate aminotransferase (aspC) and the NAD(+)-linked malic enzyme (sfcA) (KJ122) significantly increased succinate yield (1.5 mol mol(-1) glucose), succinate titer (700 mM), and average volumetric productivity (0.9 g L(-1) h(-1)). Residual pyruvate and acetate were substantially reduced by further deletion of pta encoding phosphotransacetylase to produce KJ134 (DeltaldhA DeltaadhE DeltafocA-pflB DeltamgsA DeltapoxB DeltatdcDE DeltacitF DeltaaspC DeltasfcA Deltapta-ackA). Strains KJ122 and KJ134 produced near theoretical yields of succinate during simple, anaerobic, batch fermentations using mineral salts medium. Both may be useful as biocatalysts for the commercial production of succinate.
Synaptic relationship between substance P and the substance P receptor: light and electron microscopic characterization of the mismatch between neuropeptides and their receptors. (1994)

Light microscopic studies have demonstrated significant mismatches in the location of neuropeptides and their respective binding sites in the central nervous system. In the present study we used an antiserum raised against a synthetic peptide corresponding to the carboxyl-terminal tail of the substance P (SP) receptor (SPR) to further explore the relationship between a neuropeptide and its receptor. Light microscopy revealed an excellent correlation between the patterns of SPR immunoreactivity and of 125I-labeled SPR-binding sites in the central nervous system. The SPR appeared to be exclusively expressed by neurons; in fact, the SPR decorates the somatic and dendritic surface of neurons, producing Golgi-like images. Electron microscopic analysis in cortex, striatum, and spinal cord revealed that approximately 70% of the surface membrane of immunoreactive neurons is SPR laden. Simultaneous electron microscopic labeling of SP and SPR demonstrated significant mismatch at the synaptic level. Although some SP terminals contacted SPR-immunoreactive membrane, no more than 15% of the SPR-laden membrane apposed synaptic terminals. These results suggest that in contrast to more "classical" central and peripheral nervous system synapses, wherein the receptor immediately apposes the site of neurotransmitter storage and release, much of the surface of SPR-expressing neurons can be targeted by SP that diffuses a considerable distance from its site of release.
Infection, Dissemination, Transmission, and Biological Attributes of Dengue-2 PDK53 Candidate Vaccine Virus after Oral Infection in Aedes aegypti (1994)

The capacity for oral infection, dissemination, and transmission of the dengue-2 candidate vaccine virus DEN-2 PDK53 and an isolate from a vaccinate individual, DEN-2 Ia8, were compared with the parent strain DEN-2 16681. Capacity for oral infection and dissemination to the brain and salivary gland tissues were significantly lower in the first two than in the parent strain (P < 0.001). Replication was more than 100 times higher for the parent strain when compared with the dengue-2 candidate vaccine virus. Transmission was not demonstrated in the mosquitoes orally infected with DEN-2 PDK53 and DEN-2 Ia8, whereas transmission was achieved in 57% (8 of 14) of mosquitoes infected with the parent virus strain. Using immunofluorescence, viral antigen was detected in the mosquitoes infected with DEN-2 PDK53 and DEN-2 Ia8. It was seen mainly in the form of specks scattered in some parts of the tissues, and was strikingly different from that seen in the parent strain, in which major parts of the tissues contained viral antigen in the form of rings and specks. The biological markers of DEN-2 PDK53 and DEN-2 Ia8 retained the biological characteristic of the vaccine after a mosquito passage and a human and mosquito passage, respectively.
Interleukin-17 in human inflammatory diseases (2014)

Human Th17 pro-inflammatory cells are currently defined as cells that produce IL-17A and F, tumor necrosis factor (TNF)-α, IL-6, IL-21, IL-22 and IL-23. Recently discovered related molecules are forming a family of cytokines, the IL-17 family, IL-17A, IL-17B, IL-17C, IL-17D, IL-17E and IL-17F. The associated receptors for the IL-17 family identified are IL-17R, IL-17RH1, IL-17RL (receptor like), IL-17RD and IL-17RE. This review introduces the roles of IL-17 and Th17 cells in human autoimmune diseases. Studies have shown that T cells with inflammatory effects on epithelial, endothelial and fibroblast cells express IL-17. Th17 cells are supposed to be involved in various autoimmune diseases, such as rheumatoid arthritis, psoriasis, multiple sclerosis, and inflammatory bowel diseases. Base on the biologic functions and regulation, IL-17 has regulatory roles in host defense and chronic inflammation which result in tissue damage and autoimmunity. So the IL-17 links links innate and adaptive immunity and has both beneficial and pathological effects on the immune system. This paper will focus on the possible roles of IL-17 in autoimmune diseases, a fundamental player in immune regulation.
Ion Exchange Resins: Catalyst Recovery and Recycle (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTIon Exchange Resins: Catalyst Recovery and RecyclePierluigi Barbaro* and Francesca LiguoriView Author Information Istituto di Chimica dei Composti Organo Metallici - Consiglio Nazionale delle Ricerche, Area di Ricerca di Firenze, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Firenze, Italy* To whom correspondence should be addressed. E-mail: [email protected]Cite this: Chem. Rev. 2009, 109, 2, 515–529Publication Date (Web):December 23, 2008Publication History Received9 June 2008Published online23 December 2008Published inissue 11 February 2009https://doi.org/10.1021/cr800404jCopyright © 2008 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views10641Altmetric-Citations253LEARN 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 InReddit Read OnlinePDF (559 KB) Get e-AlertsSUBJECTS:Anions,Catalysts,Metals,Organic polymers,Selectivity Get e-Alerts
Protection against Shiga Toxin 1 Challenge by Immunization of Mice with Purified Mutant Shiga Toxin 1 (2003)

Shiga toxin 1 (Stx1) of enterohemorrhagic Escherichia coli O157:H7 was cloned, and four mutant Stx1s were constructed by site-directed mutagenesis with PCR. The wild-type and mutant Stx1s with amino acid replacements at positions 167 and 170 of the A subunit were purified by one-step affinity chromatography with commercially available Globotriose Fractogel, and the mutant Stxs were used for the immunization of mice. The mutant toxins were nontoxic to Vero cells in vitro and to mice in vivo and induced the immunoglobulin G antibody against the wild-type Stx1, which neutralized the cytotoxicity of Stx1. The induced antibody titers depended on the mutation at position 170 of the A subunit. The mice immunized with the mutant Stx1s were protected against a challenge of approximately 100 times the 50% lethal dose of the wild-type Stx1, suggesting that the mutant toxins are good candidates for toxoid vaccines for infection by Stx1-producing E. coli.
Unlabeled uses of intravenous immune globulin (2008)

A literature review identified more than 150 unlabeled uses of IVIG. The evidence for these uses is being interpreted in different ways by various reviewing organizations.
Investigations of avidin and biotin for imaging applications. (1987)

The attractive properties of avidin (streptavidin) and biotin, in particular their strong affinities (Kd = 10(-15)M), may be used to advantage in imaging applications. These molecules have been used in this preliminary investigation to improve the targeting of 111In in animals. Antibodies have been conjugated with biotin and administered unlabeled while, at a later time, the radiolabel was administered attached to DTPA-coupled avidin or streptavidin. An alternative procedure was also considered whereby the antibodies were conjugated with avidin and administered before the administration of radiolabeled biotin. Using a model in which the target consisted of conjugated agarose beads deposited in the peritoneum of mice, it has been shown that the target/nontarget radioactivity ratios may be significantly improved with respect to the conventional procedures through the use of this approach.
Dendritic Cells Charged with Apoptotic Tumor Cells Induce Long-Lived Protective CD4+ and CD8+ T Cell Immunity against B16 Melanoma (2003)

Dendritic cells (DCs) are potent APCs and attractive vectors for cancer immunotherapy. Using the B16 melanoma, a poorly immunogenic experimental tumor that expresses low levels of MHC class I products, we investigated whether DCs loaded ex vivo with apoptotic tumor cells could elicit combined CD4(+) and CD8(+) T cell dependent, long term immunity following injection into mice. The bone marrow-derived DCs underwent maturation during overnight coculture with apoptotic melanoma cells. Following injection, DCs migrated to the draining lymph nodes comparably to control DCs at a level corresponding to approximately 0.5% of the injected inoculum. Mice vaccinated with tumor-loaded DCs were protected against an intracutaneous challenge with B16, with 80% of the mice remaining tumor-free 12 wk after challenge. CD4(+) and CD8(+) T cells were efficiently primed in vaccinated animals, as evidenced by IFN-gamma secretion after in vitro stimulation with DCs loaded with apoptotic B16 or DCs pulsed with the naturally expressed melanoma Ag, tyrosinase-related protein 2. In addition, B16 melanoma cells were recognized by immune CD8(+) T cells in vitro, and cytolytic activity against tyrosinase-related protein 2(180-188)-pulsed target cells was observed in vivo. When either CD4(+) or CD8(+) T cells were depleted at the time of challenge, the protection was completely abrogated. Mice receiving a tumor challenge 10 wk after vaccination were also protected, consistent with the induction of tumor-specific memory. Therefore, DCs loaded with cells undergoing apoptotic death can prime melanoma-specific helper and CTLs and provide long term protection against a poorly immunogenic tumor in mice.
A protein partially expressed on the surface of HepG2 cells that binds lipoproteins specifically is nucleolin (1990)

Nucleolin, a major nucleolar protein of rapidly growing eukaryotic cells, has been thought to be predominantly if not exclusively located in the nucleolus. Recent data however [Borer, R.A., Lehner, C.F., Eppenberger, H.M., & Nigg, N.A. (1989) Cell 56, 379-390] suggest that the protein shuttles constantly between the nucleus and cytoplasm. Ligand blotting studies of whole cell extracts of HepG2 cells identified, in addition to the LDL receptor, another LDL binding protein of Mr 109,000. The 109-kDa protein was partially purified by HPLC and, like the LDL receptor, bound apoB- and apoE-containing lipoproteins but not HDL. However, unlike the LDL receptor, the 109-kDa protein bound lipoproteins in the presence of EDTA and reducing agents, had a lower affinity for lipoproteins than the LDL receptor, and did not react with two antibodies raised against the LDL receptor. The protein sequences of three separate peptides derived from the partially purified 109-kDa species were determined and were identical except for one residue to three separate regions of the published sequence of nucleolin. On immunoblot analysis the 109-kDa protein reacted with a nucleolin-specific antibody, and purified nucleolin reacted both with anti-109-kDa antibody and with LDL. When intact HepG2 cells were treated with Pronase before harvest, there was a 46% decrease in 109-kDa protein while recovery of actin, an intracellular protein, was unaffected. When intact HepG2 cells were surface iodinated and the proteins subjected to HPLC fractionation, the 109-kDa protein was found to be iodinated.(ABSTRACT TRUNCATED AT 250 WORDS)
Skew and jitter removal using short optical pulses for optical interconnection (2000)

We demonstrate data resynchronization in a multichannel chip-to-chip free-space optical interconnect for complementary metal-oxide-semiconductor (CMOS) using short optical pulses. Operation of the system is shown at speeds of 82 Mb/s per channel, limited by the repetition rate of the mode-locked laser used. We show explicitly the ability to resynchronize parallel channels and eliminate timing fluctuations; we remove up to /spl plusmn/3/8 of a bit period of interchannel skew and single channel jitter from the transmitted signals in a complete interconnect link that includes optical transmission, reception, and retransmission of digital data.
Balancing performance, energy, and quality in pervasive computing (2003)

We describe Spectra, a remote execution system for battery-powered clients used in pervasive computing. Spectra enables applications to combine the mobility of small devices with the greater processing power of static compute servers. Spectra is self-tuning: it monitors both application resource usage and the availability of resources in the environment, and dynamically determines how and where to execute application components. In making this determination, Spectra balances the competing goals of performance, energy conservation, and application quality. We have validated Spectra's approach on the Compaq Itsy v2.2 and IBM ThinkPad 560X using a speech recognizer a document preparation system, and a natural language translator. Our results confirm that Spectra almost always selects the best execution plan, and that its few suboptimal choices are very close to optimal.
Ischemia-reperfusion in feline small intestine: a role for nitric oxide (1993)

The objective of this study was to assess whether nitric oxide synthesis inhibition affects intestinal barrier function after ischemia-reperfusion of the feline small bowel. Local intra-arterial infusion of the nitric oxide synthesis inhibitor NG-nitro-L-arginine methyl ester (L-NAME; 25 nmol.ml-1.min-1) was performed in autoperfused segments of cat ileum for 60 min after 90 min of ischemia and 60 min of reperfusion. Epithelial permeability was quantitated by measuring blood-to-lumen clearance of 51Cr-labeled EDTA, and microvascular dysfunction was assessed by measuring the clearance of protein from the vasculature into the interstitium. 125I-labeled albumin clearance from blood to lumen and histology were performed to further characterize the extent of intestinal dysfunction after reperfusion of the postischemic intestine in the presence and absence of L-NAME. Ischemia-reperfusion-induced mucosal and microvascular permeability increases were dramatically augmented by L-NAME infusion, and this effect was reversed by infusion of L-arginine (125 nmol.ml-1.min-1). Initiating L-arginine (but not D-arginine) infusion alone 10 min before reperfusion provided protection against ischemia-reperfusion-induced mucosal barrier dysfunction; however, this was not associated with a reduction in endogenous levels of L-arginine during ischemia-reperfusion. These data suggest that basal nitric oxide production is important in minimizing mucosal and microvascular barrier dysfunction associated with reperfusion of postischemic intestine.
An enzyme-linked immunosorbent assay for erythropoietin using monoclonal antibodies, tetrameric immune complexes, and substrate amplification (1989)

We recently reported the development of several monoclonal antibodies (MoAbs) to native human erythropoietin (Ep). In the present study we have used the two antibodies with highest affinity to develop a two- sided or sandwich enzyme-linked immunosorbent assay (ELISA) to measure Ep in human serum. In this assay Ep is incubated in microtiter wells precoated with the first (IgE) anti-Ep antibody. Assay wells are then incubated with the second (IgG1) anti-Ep antibody, which is labeled noncovalently with the enzyme alkaline phosphatase (AP) by means of bispecific tetrameric antibody complexes consisting of IgG1 anti-Ep cross-linked to IgG1 anti-AP using rat MoAbs specific for mouse IgG1. Application of this noncovalent labeling procedure, in combination with substrate amplification, results in a detection sensitivity of 0.5 to 1.0 mU/sample (5 to 10 mU/mL), which makes this assay suitable for measuring normal serum Ep levels. The validity of this ELISA for quantitating Ep in biological fluids was demonstrated by the parallelism obtained between pure recombinant Ep dose-response curves and those obtained with plasma and serum from healthy donors and patients with various hematologic disorders. Normal plasma Ep levels detected with this ELISA ranged from 9 to 101 mU/mL with a mean of 32 +/- 23 (SD) mU/mL. Ep levels in sera from patients with polycythemia vera were in the low to normal range, whereas Ep levels in sera from patients with secondary polycythemia and patients with aplastic anemia were moderately to strongly elevated. These results demonstrate that the Ep-ELISA is a sensitive, reliable, and nonradioactive immunologic method for quantitating Ep levels and should prove useful in a variety of clinical and laboratory settings.
Ontology guided access to document images (2005)

In this paper, we propose a scheme for accessing document images using ontology. We make use of an extension of OWL (ontology language for Web) to allow encoding of ontologies for document images. We experimentally demonstrate that reasoning with the concepts defined in ontology and their observation models provide a mechanism to support conceptual querying and automated hyperlinking of document images.
Antibody labeling with copper-67 using the bifunctional macrocycle 4-[(1,4,8,11-tetraazacyclotetradec-1-yl)methyl]benzoic acid (1991)

The high kinetic stability of the Cu2+ complex of the chelator 4-[(1,4,8,11-tetraazacyclotetradec-1-yl)-methyl]benzoic acid was demonstrated at physiological pH as well as under acidic conditions. The chelating agent was conjugated to AB35, a monoclonal antibody directed against CEA, without a significant loss of immunoreactivity. The conjugate could, under optimal labeling conditions, be labeled with 67Cu in acetate buffer with a full occupancy of ligands within 20 min. This radiolabeled conjugate showed no transfer of radiocopper to serum proteins in human serum over 7 days. The biodistribution in tumor-bearing mice was measured and compared to that of iodinated AB35. Tumor uptake was high with 15 +/- 3% ID (injected dose)/g after 24 h and 32 +/- 7% ID/g after 96 h for the 67Cu-labeled antibody and 13 +/- 4% ID/g after 24 h and 14 +/- 2% ID/g after 96 h for the 125I-labeled antibody. Whereas radioactivity in normal organs decreased with time after 24 h, increased residence time was shown up to 4 days with the 67Cu-labeled AB35.
Expression and significance of WISP3 in esophageal cancer tissue (2008)

Objective To investigate the WISP3 expression and the relations between WISP3 and the clinical and pathological features of esophagus cancer.Method The WISP3 in 186 cases of esophageal cancer tissues and matched normal esophagus tissues were quantified by real time RT-PCR and immunohistochemistry method.Results The WISP3 mRNA was 6.31±3.77(ΔCt) and WISP3 protein was 25.63%±7.81% in esophageal cancer tissues,8.93±3.83 and 7.50%±2.38% in normal esophagus tissues(P0.01).The WISP3 mRNA expression levels had association with esophagus carcinomas metastasis,infiltrating extent and tumor size and stage(P0.05).WISP3 protein expression levels had association with esophagus carcinomas metastasis,infiltrating extent,tumor stage(P0.05),WISP3 protein expression related to the survival of patients(CR was 2.287).Conclusion WISP3 expression is raised in esophageal cancer tissues,and it might serve as a valuable target to tumor stage,metastasis ability and prognosis for esophageal cancer.
Direct Analysis of Affinity-Bound Analytes by MALDI/TOF MS (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirect Analysis of Affinity-Bound Analytes by MALDI/TOF MSDamon I. Papac, John. Hoyes, and Kenneth B. TomerCite this: Anal. Chem. 1994, 66, 17, 2609–2613Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/ac00089a004https://doi.org/10.1021/ac00089a004research-articleACS PublicationsRequest reuse permissionsArticle Views387Altmetric-Citations68LEARN 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