gebhart/patrepeval huggingface dataset:
Expression of the eicosapentaenoic acid synthesis gene cluster from Shewanella sp. in a transgenic marine cyanobacterium, Synechococcus sp. (1997)

The eicosapentaenoic acid (EPA) synthesis gene cluster isolated from a marine bacterium, Shewanella putrefaciens strain SCRC-2738, was cloned and expressed in the marine cyanobacterium Synechococcus sp. A broad-host-range cosmid vector, pJRD215 (10.2 kb, Smr Kmr), was used to clone a 38 kb insert, pEPA, containing the EPA synthesis gene cluster, creating plasmid pJRDEPA (approx. 48 kb). This plasmid was transferred to the cyanobacterial host at a frequency of 2.2 x 10(-7). Cyanobacterial transconjugants grown at 29 degrees C produced 0.12 mg EPA (g dry weight)-1, whereas those grown at 23 degrees C produced 0.56 mg EPA (g dry weight)-1. The yield was further improved to 0.64 mg (g dry weight)-1 by incubation for 1 d at 17 degrees C. This is believed to be the first successful cloning and expression of such a large heterologous gene cluster in a marine cyanobacterium.
Analysis of Technical Lignins by Two- and Three-Dimensional NMR Spectroscopy (2003)

Modern multidimensional NMR spectroscopic methods were applied to investigate the effects of kraft pulping and oxygen delignification on lignin side-chain structures. In addition to the two-dimensional HSQC measurements, the three-dimensional HSQC-TOCSY technique was utilized to elucidate the (1)H-(1)H and (1)H-(13)C correlations of individual spin systems and thus indicate a certain lignin side-chain structure. Unlike earlier, nonlabeled samples were used for 3D measurements. According to 2D and 3D NMR spectra, most of the structures identified in milled wood lignin (MWL) are still present in technical lignins after kraft pulping and oxygen delignification. Although the main reaction during kraft pulping is the cleavage of beta-O-4 linkages, these structures are still left in spent liquor lignin as well as in residual lignin. The amount of coniferyl alcohol and dihydroconiferyl alcohol end groups, as well as some unidentified saturated end groups, is higher in technical lignins than in MWL. Contrary to our earlier observations, no diphenylmethane structures were observed in any technical lignins. Vinyl aryl ether structures could not be detected in technical lignins either.
Cloning of genes controlling alginate biosynthesis from a mucoid cystic fibrosis isolate of Pseudomonas aeruginosa (1984)

Mucoid strains of Pseudomonas aeruginosa isolated from the sputum of cystic fibrosis patients produce copious quantities of an exopolysaccharide known as alginic acid. Since clinical isolates of the mucoid variants are unstable with respect to alginate synthesis and revert spontaneously to the more typical nonmucoid phenotype, it has been difficult to isolate individual structural gene mutants defective in alginate synthesis. The cloning of the genes controlling alginate synthesis has been facilitated by the isolation of a stable alginate-producing strain, 8830. The stable mucoid strain was mutagenized with ethyl methanesulfonate to obtain various mutants defective in alginate biosynthesis. Several nonmucoid (Alg-) mutants were isolated. A mucoid P. aeruginosa gene library was then constructed, using a cosmid cloning vector. DNA isolated from the stable mucoid strain 8830 was partially digested with the restriction endonuclease HindIII and ligated to the HindIII site of the broad host range cosmid vector, pCP13. After packaging in lambda particles, the recombinant DNA was introduced via transfection into Escherichia coli AC80. The clone bank was mated (en masse) from E. coli into various P. aeruginosa 8830 nonmucoid mutants with the help of pRK2013, which provided donor functions in trans, and tetracycline-resistant exconjugants were screened for the ability to form mucoid colonies. Three recombinant plasmids, pAD1, pAD2, and pAD3, containing DNA inserts of 20, 9.5, and 6.2 kilobases, respectively, were isolated based on their ability to restore alginate synthesis in various strain 8830 nonmucoid (Alg-) mutants. Mutants have been assigned to at least four complementation groups, based on complementation by pAD1, pAD2, or pAD3 or by none of them. Introduction of pAD1 into the spontaneous nonmucoid strain 8822, as well as into other nonmucoid laboratory strains of P. aeruginosa such as PAO and SB1, was found to slowly induce alginate synthesis. This alginate-inducing ability was found to reside on a 7.5-kilobase EcoRI fragment that complemented the alg-22 mutation of strain 8852. The pAD1 chromosomal insert which complements the alg-22 mutation was subsequently mapped at ca. 19 min of the P. aeruginosa PAO chromosome.
Extracellular matrix 6: Role of matrix metalloproteinases in tumor invasion and metastasis (1993)

Tumor invasion and metastasis formation are major obstacles for successful cancer therapy. Metastasis is a complex multistep process that requires sequential interactions between the invasive cell and the extracellular matrix. A model system for tumor invasion of extracellular matrix barriers has been developed, and application of this model has facilitated our understanding of the molecular mechanisms of metastasis formation. This model consists of three steps: tumor cell adhesion, extracellular matrix proteolysis, and cell migration. The role of the matrix metalloprotease enzymes in tumor cell-mediated extracellular matrix proteolysis is well established. We review the functional domain structure of the matrix metalloprotease enzymes in general and specifically the interaction of metastasis-associated gelatinase A (72-kDa type IV collagenase) with the tissue inhibitor of metalloproteases-2 (TIMP-2). We also discuss the physiologic activation of the matrix metalloprotease enzymes and the specific cellular mechanism of action of gelatinase A.
Pivotal Role of Water in the Mechanism of P450BM-3 (2001)

Cytochrome P450s constitute a superfamily of enzymes that catalyze the oxidation of a vast number of structurally and chemically diverse hydrophobic substrates. Herein, we describe the crystal structure of a complex between the bacterial P450BM-3 and the novel substrate N-palmitoylglycine at a resolution of 1.65 A, which reveals previously unrecognizable features of active site reorganization upon substrate binding. N-palmitoylglycine binds with higher affinity than any other known substrate and reacts with a higher turnover number than palmitic acid but with unaltered regiospecificity along the fatty acid moiety. Substrate binding induces conformational changes in distinct regions of the enzyme including part of the I-helix adjacent to the active site. These changes cause the displacement by about 1 A of the pivotal water molecule that ligands the heme iron, resulting in the low-spin to high-spin conversion of the iron. The water molecule is trapped close to the heme group, which allows it to partition between the iron and the new binding site. This partitioning explains the existence of a high-spin-low-spin equilibrium after substrate binding. The close proximity of the water molecule to the heme iron indicates that it may also participate in the proton-transfer cascade that leads to heterolytic bond scission of oxygen in P450BM-3.
Immunoblot Assay Using Recombinant Antigens as a Supplemental Test To Confirm the Presence of Antibodies to Trypanosoma cruzi (2007)

The diagnosis of chronic Chagas' disease is generally made by detecting antibodies to Trypanosoma cruzi. Most conventional serological tests are based on lysates of whole parasites or semipurified antigen fractions from T. cruzi epimastigotes grown in culture. The occurrence of inconclusive and false-positive results has been a persistent problem with the conventional assays, and there is no universally accepted gold standard for confirmation of positive test results. We describe here an immunoblot assay for detecting antibodies to T. cruzi in which four chimeric recombinant antigens (rAgs), designated FP3, FP6, FP10, and TcF, are used as target antigens. Each of these rAgs is composed of several antigenically distinct regions and includes repetitive as well as nonrepetitive sequences. Each rAg is coated as a discrete line on a nitrocellulose strip. Assay sensitivity was assessed by testing 345 specimens known to be positive for antibodies to T. cruzi. All 345 of these samples showed two to four reactive test bands in addition to the three on-board control bands that are on each strip. Assay specificity was determined by testing 500 specimens from random U.S. blood donors, all of which gave negative results. Based on the results obtained in this study, we propose the following scheme for interpretation of test results: (i) no bands or a single test band = a negative result; (ii) two or more test bands with at least one band showing intensity of 1+ or higher = a positive result; and (iii) multiple faint test bands (+/-) = indeterminate result. Based on this scheme, the prototype immunoblot assay showed sensitivity of 100% (n = 345) and specificity of 100% (n = 500). Additionally, all 269 potentially cross-reacting and T. cruzi antibody-negative specimens tested negative in our immunoblot assay. The rAg-based immunoblot assay has potential as a supplemental test for confirming the presence of antibodies to T. cruzi in blood specimens and for identifying false-positive results obtained with other assays.
A solid-state video film dosimetry system (1983)

Describes a novel film dosimetry system which has been fabricated based on a solid-state television camera. The image receptor comprises a two dimensional array of individual photosensitive elements which covers a total active area of 0.34 cm2. This system offers maximum mechanical stability since there are no moving parts.
Role of the electrostatic attractive force in the adsorption of proteins by aluminum hydroxide adjuvant. (1997)

The fact that both aluminum hydroxide adjuvant and proteins have a pH dependent surface charge means that electrostatic forces play a role in the adsorption of proteins by aluminum hydroxide adjuvant during the preparation of vaccines. The objective of this study was to examine the contribution of the electrostatic attractive force in the adsorption of proteins by aluminum hydroxide adjuvant. Since the surface charge characteristics of aluminum hydroxide adjuvant can be modified by the adsorption of phosphate anion, a series of aluminum hydroxide adjuvants were prepared by treatment with various concentrations of phosphate anion. The isoelectric points (iep) of these adjuvants ranged from 11.0 to 4.6 and the electrophoretic mobilities at pH 7.4 ranged from 2.0 to -3.3 microns cm/V s. The line broadening of the (020) band of the X-ray diffraction pattern indicated that treatment with phosphate anion did not change the primary crystallite dimension. Adsorption at pH 7.4 of positively charged lysozyme (iep = 11.1) was directly related to the negative surface charge of the adjuvant. No adsorption occurred when the surface charge was positive. In contrast, negatively charged ovalbumin (iep = 4.6) was adsorbed by all of the adjuvants at pH 7.4, although the adsorptive capacity was the greatest when the surface charge was positive. The results indicate that adsorptive forces in addition to the electrostatic attractive force play an important role in the adsorption of some proteins by aluminum hydroxide adjuvant. It is believed the structurally flexible proteins, like ovalbumin, exhibit more complex adsorption behavior than structurally rigid proteins, like lysozyme, for which adsorptive behavior can be explained by electrostatic forces.
RETRACTED: Notch1 regulates the fate of cardiac progenitor cells (2008)

The Notch receptor mediates cell fate decision in multiple organs. In the current work we tested the hypothesis that Nkx2.5 is a target gene of Notch1 and raised the possibility that Notch1 regulates myocyte commitment in the adult heart. Cardiac progenitor cells (CPCs) in the niches express Notch1 receptor, and the supporting cells exhibit the Notch ligand Jagged1. The nuclear translocation of Notch1 intracellular domain (N1ICD) up-regulates Nkx2.5 in CPCs and promotes the formation of cycling myocytes in vitro. N1ICD and RBP-Jk form a protein complex, which in turn binds to the Nkx2.5 promoter initiating transcription and myocyte differentiation. In contrast, transcription factors of vascular cells are down-regulated by Jagged1 activation of the Notch1 pathway. Importantly, inhibition of Notch1 in infarcted mice impairs the commitment of resident CPCs to the myocyte lineage opposing cardiomyogenesis. These observations indicate that Notch1 favors the early specification of CPCs to the myocyte phenotype but maintains the newly formed cells in a highly proliferative state. Dividing Nkx2.5-positive myocytes correspond to transit amplifying cells, which condition the replicative capacity of the heart. In conclusion, Notch1 may have critical implications in the control of heart homeostasis and its adaptation to pathologic states.
IL-4 Preferentially Activates a Novel STAT6 Isoform in Mast Cells (1999)

IL-4 is a pleiotropic cytokine that signals through STAT6 to direct the transactivation of multiple gene targets. In this study, we demonstrate that mast cells express a distinct STAT6 isoform. This "mast cell STAT" is a product of the STAT6 gene, but is only 65 kDa in size and appears to lack the defined C-terminal transactivation domain. Despite the presence of the conventional 94-kDa STAT6 molecule, it is the smaller isoform that associates with a consensus STAT6 binding site in extracts from IL-4-treated mast cells. This is the first evidence that STAT6 isoforms can be preferentially activated and bind to DNA in a cell-specific manner. These results imply that an additional level of specificity in the IL-4R signaling mechanism exists and may partially explain the diverse effects that IL-4 exerts on different cell types.
Prolongation of adenoviral transgene expression in mouse liver by T lymphocyte subset depletion. (1996)

Although first generation recombinant adenoviruses are efficient vehicles for gene transfer, their immunogenicity precludes long-term persistence. We show that adenoviral transgene expression in the liver of normal mice is prolonged from a baseline of less than 2 weeks to 7 weeks by depleting CD4+ T lymphocytes with thymectomy and a 3-day course of anti-CD4 monoclonal antibody or by nonselectively depleting T cells with a single dose of anti-thymocyte serum (ATS). Transgene expression persisted despite the development of an antiviral humoral immune response by 3 weeks after virus administration. In vitro assays of T lymphocyte function revealed an initial diminished capacity to proliferate in the presence of adenoviral antigens in animals depleted of CD4+ T cells or given anti-thymocyte serum. Eventual loss of recombinant gene expression coincided with the development of adenovirus-specific cytotoxic T lymphocyte activity in vitro. Immunosuppression provides a useful experimental tool to elucidate the immunobiology of recombinant adenoviruses and may have clinical application to adenovirus-mediated gene therapy.
Primary and secondary immune response to human ige by rabbits immunized with synthetic ige peptides (1987)

Abstract Rabbits were immunized with eight chemically synthesized peptides representing sequences of the third and fourth constant domains (Fc fragment) of human IgE to obtain antibodies to predetermined sites on IgE. The peptides, varying in length from 15 to 28 amino acids, were coupled to either keyhole limpet hemocyanin (KLH) or tetanus toxoid and injected in complete Freund's adjuvant. The resulting antisera were tested for binding to the peptides and IgE by a polyvinyl plate radioimmunoassay. Immunization with all eight peptides produced high titers of antibodies to the corresponding peptide, and six also induced antibodies that cross‐reacted with native IgE or IgE Fc fragments but not with IgE F(ab′) 2 fragments or unrelated peptides and proteins. Conversely, goat, sheep, and rabbit antisera to native IgE or Fc IgE bound to the synthetic peptides that elicited cross‐reacting antibodies to IgE, indicative of a shared antigenic configuration between the peptides and IgE. However, the quantities of antipeptide antibodies cross‐reacting with IgE represented only a small fraction of the total antipeptide antibody titer, since absorption of the antisera with IgE reduced the titer of reactivity to the peptides only minimally and the yields of immunoadsorbent purified antibodies to IgE were low. Furthermore, the affinities of the antibodies cross‐reactive with IgE were low because the peptides inhibited binding to Fc IgE &gt; 100 times more efficiently than did IgE. Additionally, the binding to Fc IgE of monovalent Fab fragments of purified antibodies cross‐reactive with IgE could no longer be demonstrated. Because the synthetic peptides induced only low‐affinity cross‐reacting antibodies, the synthetic peptides were tested for the ability to prime rabbits for a secondary response to native IgE. Rabbits were injected with peptide‐KLH conjugates in complete Freund's adjuvant and challenged 6 months later with IgE in alum. None of the rabbits showed a secondary response to IgE; instead, they made a primary immune response identical to that of rabbits not given the synthetic peptides. Also, injection of IgE did not increase titers of antibody to the synthetic peptides still present 6 months after the primary injection, suggesting that the native IgE could not stimulate memory B cells induced by the peptide. Moreover, the nature of the secondary response to the synthetic peptide resembled that to a hapten in that it was elicited only by peptide conjugated to the carrier used for immunization but not to an unrelated carrier. The data demonstrate that, although immunization of rabbits with synthetic peptides of the human ϵ chain coupled to KLH elicits the formation of antibodies cross‐reactive with native IgE, these rabbits do not become primed for a secondary response to IgE. This indicates that, before a synthetic peptide coupled to a highly immunogenic carrier is considered for use in a vaccine, its ability to induce a secondary response to the native protein must be established.
CD70: A NEW TUMOR SPECIFIC BIOMARKER FOR RENAL CELL CARCINOMA (2005)

Our study identified CD70 as a new specific tumor marker for clear cell RCC. This new marker can be used for differential diagnosis in cases of uncertain histological classification. The function of this protein in tumorigenesis and its use as a diagnostic marker in serum and urine or as a therapeutic tool must be investigated in further studies.
Intervertebral Foraminal Widening Caused by the Tortuous Cervical Vertebral Artery (2013)

Tortuousity of the vertebral artery is clinically uncommon because it rarely causes symptoms. We described a patient with pain in the neck and both upper extremities in whom diagnosis of intervertebral foraminal widening and deformity of the vertebral artery were suggested by results of radiography and magnetic resonance. We confirmed the tortuous vertebral artery by results of computed tomography angiography. Correlation of the patient’s symptoms and abnormalities was not clear; conservative treatment was administered.
Incorporating prior knowledge with weighted margin support vector machines (2004)

Like many purely data-driven machine learning methods, Support Vector Machine (SVM) classifiers are learned exclusively from the evidence presented in the training dataset; thus a larger training dataset is required for better performance. In some applications, there might be human knowledge available that, in principle, could compensate for the lack of data. In this paper, we propose a simple generalization of SVM: Weighted Margin SVM (WMSVMs) that permits the incorporation of prior knowledge. We show that Sequential Minimal Optimization can be used in training WMSVM. We discuss the issues of incorporating prior knowledge using this rather general formulation. The experimental results show that the proposed methods of incorporating prior knowledge is effective.
Novel Taxol formulations: Taxol-containing liposomes. (1993)

Taxol is a complex diterpenoid natural product under investigation for therapy of colon, ovarian, lung, and breast cancer, as well as for melanoma and lymphoma. One problem associated with the administration of Taxol is its low solubility; the formulation used clinically contains polyethoxylated castor oil (Cremophor EL) and ethanol as excipients. Cremophor EL is implicated in hypersensitivity reactions observed on infusion of Taxol. To eliminate the Cremophor EL vehicle and possibly improve the antitumor efficacy of Taxol, a systematic approach was taken to formulate Taxol in phospholipid suspensions (liposomes). Prototype formulations were developed that have sufficient chemical and physical stability to test the hypothesis that liposomes can alter the pharmacology of Taxol, in addition to providing a biologically compatible carrier in which to administer the drug. In vitro. Taxol liposomes retain the growth-inhibitory activity of free Taxol against a variety of tumor cell lines. In vivo, preliminary results showed no effect of free Taxol (in Cremophor EL) on the growth of Colon-26, a Taxol-resistant murine tumor, when given at doses that included or exceeded the maximum tolerated dose (MTD). In contrast, Taxol liposomes delayed tumor progression at a dose that exceeded the MTD of free Taxol.
Myoblasts and macrophages are required for therapeutic morpholino antisense oligonucleotide delivery to dystrophic muscle (2017)

Abstract Exon skipping is a promising therapeutic strategy for Duchenne muscular dystrophy (DMD), employing morpholino antisense oligonucleotides (PMO-AO) to exclude disruptive exons from the mutant DMD transcript and elicit production of truncated dystrophin protein. Clinical trials for PMO show variable and sporadic dystrophin rescue. Here, we show that robust PMO uptake and efficient production of dystrophin following PMO administration coincide with areas of myofiber regeneration and inflammation. PMO localization is sustained in inflammatory foci where it enters macrophages, actively differentiating myoblasts and newly forming myotubes. We conclude that efficient PMO delivery into muscle requires two concomitant events: first, accumulation and retention of PMO within inflammatory foci associated with dystrophic lesions, and second, fusion of PMO-loaded myoblasts into repairing myofibers. Identification of these factors accounts for the variability in clinical trials and suggests strategies to improve this therapeutic approach to DMD.
In vitro immunization of naive human B cells yields high affinity immunoglobulin G antibodies as illustrated by phage display (1996)

In vitro antibody responses to a synthetic immunogen, consisting of both a B cell [V3 loop of gp120 from human immunodeficiency virus type 1 (HIV-1)] and a T-helper epitope (15 amino acids of tetanus toxoid) was studied. The in vitro activation was performed by primary and secondary in vitro immunizations, using lymphocytes obtained from uninfected, seronegative donors. Analysis of the in vitro immune response demonstrated an antigen-specific isotype switch, which was dependent on the presence of antigen-specific T-helper cells, CD40 ligation and antigen. Antibody libraries were constructed from cells derived directly from the naive donors, or from primary or secondary in vitro immunized B cells. Five libraries were displayed on filamentous phage and selected for anti-V3-specific Fab fragments, using a selection approach that linked recognition and phage replication. A panel of 19 recombinant antigen-specific Fab. representing different phases of the humoral in vitro immune response were sequenced, expressed and analysed using a biosensor. Recombinant Fab fragments derived from cultures on day 12 exhibited an increase in affinity of close to two orders of magnitude compared to those obtained from cells primary immunized for 7 days. This study provides the first evidence that an antigen-specific in vitro immune response can yield high-affinity immunoglobulinG antibodies.