gebhart/patrepeval huggingface dataset:
Estrogen Dendrimer Conjugates that Preferentially Activate Extranuclear, Nongenomic Versus Genomic Pathways of Estrogen Action (2005)

Estrogenic hormones are classically thought to exert their effects by binding to nuclear estrogen receptors and altering target gene transcription, but estrogens can also have nongenomic effects through rapid activation of membrane-initiated kinase cascades. The development of ligands that selectively activate only the nongenomic pathways would provide useful tools to investigate the significance of these pathways. We have prepared large, abiotic, nondegradable poly(amido)amine dendrimer macromolecules that are conjugated to multiple estrogen molecules through chemically robust linkages. Because of their charge and size, these estrogen-dendrimer conjugates (EDCs) remain outside the nucleus. They stimulate ERK, Shc, and Src phosphorylation in MCF-7 breast cancer cells at low concentrations, yet they are very ineffective in stimulating transcription of endogenous estrogen target genes, being approximately 10,000-fold less potent than estradiol in genomic actions. In contrast to estradiol, EDC was not effective in stimulating breast cancer cell proliferation. Because these EDC ligands activate nongenomic activity at concentrations at which they do not alter the transcription of estrogen target genes, they should be useful in studying extranuclear initiated pathways of estrogen action in a variety of target cells.
Characterization of group N streptococcus lipoteichoic acid (1975)

Lipoteichoic acid was extracted from the group N organism Streptococcus lactis ATCC 9936 with hot aqueous phenol and purified by gel chromatography followed by affinity chromatography using Ricinus communis lectin as the specific absorbent. The teichoic acid moiety of the lipoteichoic acid was calculated to contain 16 to 17 glycerol phosphate units, approximately half of which were substituted with alpha-D-galactosyl residues; the glycolipid moiety contained O-alpha-D-glucosyl-1 yields 2-O-alpha-D-glucosyl-1 yields 1-glycerol. The finding of 2-O-alpha-D-galactosyl glycerol in the lipid fraction of hydrofluoric acid hydrolysates suggests that fatty acids also occur as substituents on the main chain of the lipoteichoic acid. The reactivity of the lipoteichoic acid with R. communis lectin was studied by the quantitative precipitin method and compared with the reactivity of Lactobacillus fermenti lipoteichoic acid, which has a lower degree of alpha-D-galactosyl substitution. Group N antiserum reacted strongly with the S. lactis lipoteichoic acid and cross-reacted with L. fermenti lipoteichoic acid. From inhibition studies it is concluded that the antibodies are specific for alpha-D-galactosyl substituents. In addition to lipoteichoic acid, a fraction was obtained by gel chromatography which contained galactose and reacted with group N antiserum but could be distinguished from the lipoteichoic acid by immunoelectrophoresis.
Synthesis, microbicidal activity, and solution structure of the dodecapeptide from bovine neutrophils (2000)

The dodecapepetide sequence R-L-C-R-I-V-V-I-R-V-C-R with a disulfide bridge between the cysteine residues found in bovine neutrophils was synthesized by solid-phase procedures. Its antimicrobial activity against oral microorganisms such as Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Streptococcus mutans, and Streptococcus gordonii was examined, and its structural features were examined by CD and determined by two-dimensional (2D) nmr. The strains P. gingivalis (W50 and 381), A. actinomycetemcomitans (Y4 and 67), S. gordonii (DL1), and S. mutans (GS5) are found to be highly sensitive to this peptide at 2-2.5 microM concentrations, suggesting that the dodecapeptide is a potent antibiotic for oral pathogens. The weak negative n-sigma* band observed at approximately 265-270 nm in the CD spectra of this peptide provides evidence for the presence of a disulfide bridge. The negative n-pi* band at approximately 200 nm and the positive pi-pi* band at 185 nm suggest a folded structure for this peptide. The negative n-pi* shifts from 200 to 206 nm with an increase in intensity in dipalmitoylphosphotidylcholine vesicles, suggesting that the peptide might associate to form higher order aggregates in lipid medium. The assignment of backbone and side-chain proton resonances has been accomplished by the combined analysis of 2D total correlated and nuclear Overhauser effect spectroscopy. The temperature dependence of amide NH chemical shifts and (1)H-(2)H exchange effect on amide NH resonances indicate the involvement of amide NH groups of Cys3, Ile5, Ile8, Val10, and Arg12 in intramolecular hydrogen bonding. The coupling constant (J(NH-C(alpha)H)) values, the set of medium-, short-, and long-range nuclear Overhauser effects, and the results of restrained structure calculation using the distance geometry algorithm for nmr applications provide evidence for a folded, loop-like structure with a type I (III) beta-turn involving Ile5, Val6, Val7, and Ile8, and two antiparallel beta-strands involving the N-terminal Arg1, Leu2, Cys3, and Val4 and the C-terminal Arg9, Val10, Cys11, and Arg12 residues. The structure of the dodecapeptide mimics the amphiphilic structure of large 30-35 residue defensins and the peptide appears to exhibit similar antimicrobial potency.
The Use of Poly(ethylene glycol)-Enzymes in Nonaqueous Enzymology (1997)

Polyethylene glycolated enzymes are increasingly being used for a variety of applications in non-aqueous media including organic synthesis, redox chemistry, and mechanistic biochemistry. PEG-enzymes function well in relatively hydrophobic organic solvents, in harsh mixed solvent mixtures, and at elevated temperatures. PEG-enzymes retain the unique reactive characteristics of enzyme powders while affording those benefits unique to homogeneous catalysts.
Delivery and Specificity of CRISPR/Cas9 Genome Editing Technologies for Human Gene Therapy (2015)

Genome editing using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated 9 (Cas9) technology is revolutionizing the study of gene function and likely will give rise to an entire new class of therapeutics for a wide range of diseases. Achieving this goal requires not only characterization of the technology for efficacy and specificity but also optimization of its delivery to the target cells for each disease indication. In this review we survey the various methods by which the CRISPR-Cas9 components have been delivered to cells and highlight some of the more clinically relevant approaches. Additionally, we discuss the methods available for assessing the specificity of Cas9 editing; an important safety consideration for development of the technology.
Nevis Synchrocyclotron Conversion Program - RF System (1969)

The proposed three-fold symmetric and radially increasing magnetic field requires the arcelerating RF field to cover the frequency band from about 26.5 MHz to 18.5 MHz. The peak dee voltage will be between 30 and 50 kV, with the maximum near injection. The repetition rate will be ≥300 per second with the RF turned on for 4%/. of the time. The (single) dee-line structure will be 150 inches wide and between one-quarter and one-half a wavelength long. One of the three pairs of sectoriron shims will be incorporated in the dee and supported on BeO insulators. For the presently favored design, tuning will be accomplished by two rotating capacitors with axes directed towards the center of the magnet. Each rotor will have four layers of 12 blades each. Each set of stator blades will be coupled to four transmission lines which will run to the dee. The rotors will operate near RF ground potential. This design permits effective magnetic shielding of the rotor to minimize eddy current losses. Excitation of the dee will be provided by two grounded-grid, triode oscillators crosscoupled to quarter-wave stubs on the two sides of the dee.
AN INTRAOCULAR PRESSURE SENSOR BASED ON A GLASS REFLOW PROCESS (2010)

This paper presents an intraocular pressure sensor fabricated using a new process that reflows glass into DRIE-etched silicon cavities to form three-dimensional microstructures. The capacitive pressure sensor is formed using a 4!m thick boron etch-stopped silicon diaphragm having dimensions of 0.85mm x 1.65mm. The sensor operates in touch-mode with a linear response and sensitivity of 26fF/mmHg, resolving better than 1mmHg over a 650-850mmHg dynamic range. Vertical silicon feedthroughs in the glass provide electrical access to the sensor. This pressure sensor is part of an intraocular microsystem being developed for monitoring the eye pressure of patients diagnosed with glaucoma.
Extravasation of thrombus into the aortic root: A complication following use of an infusion catheter for intragraft thrombolysis (1996)

Overnight chronic urokinase infusion was used to successfully treat thrombotic occlusion of a saphenous vein graft. Following removal of the infusion catheter, a 3-cm linear thrombus was observed extending from the graft into the ascending aorta. This mobile thrombus was successfully treated with coumadinization for 9 wk. Potential preventive measures for this complication of indwelling catheters are discussed. © 1996 Wiley-Liss, Inc.
A human tumor xenograft model of therapy with a bispecific monoclonal antibody targeting c-erbB-2 and CD16. (1993)

New strategies are required to clinically exploit the ability of monoclonal antibodies to target tumor for lysis by cellular effector mechanisms. In this report we examine the therapeutic effects of 2B1, a bispecific monoclonal antibody with specificity for the extracellular domain of the c-erbB-2 oncogene product and the human Fc gamma receptor, Fc gamma RIII (CD16), describe the characteristics and limitations of this model, and examine the mechanisms underlying the observed responses. The model uses SK-OV-3 human ovarian carcinoma xenografts in scid mice. These cells are susceptible to 2B1-directed lysis by human peripheral blood lymphocytes or lymphokine-activated killer cells, and maintain c-erbB-2 expression in vivo. 125I-labeled 2B1 selectively accumulates in tumor, with a peak of 10.5% injected dose/g of tumor 24 h following its i.v. injection. However, the selectivity of this binding is lessened by 2B1 accumulation in the lungs and other normal organs and persistence in the blood. This is caused by antibody binding to murine lung, colon, stomach, and skin expressing the epitope recognized by the anti-c-erbB-2 component of 2B1 in tumor-bearing, but not normal mice. In treatment studies using various permutations of antibody, human peripheral blood lymphocytes or lymphokine-activated killer cells and interleukin 2, cellular therapy alone had minimal effects on SK-OV-3 xenograft growth, but significantly improved when 2B1 treatment was incorporated. Median survivals increased from 80 +/- 3.5 days with no therapy to 131 +/- 7.3 days following therapy with 100 micrograms 2B1, interleukin 2, and human peripheral blood lymphocytes, with 70% of animals exhibiting no evidence of tumor at day 150. These effects were preserved when the cells were administered in human serum. In contrast, human serum abolished the antitumor effects of 520C9, which is the parent anti-c-erbB-2 antibody of 2B1. Thus 2B1-based therapy has therapeutic effects, without obvious toxicity, despite the targeting of this antibody to normal murine tissues. Since combinations of 2B1 and interleukin 2 may have antitumor properties, mechanisms other than bispecific monoclonal antibody-promoted conjugation of c-erbB-2 antigen-expressing tumor to CD16-expressing effector cells may be involved.
The genome ofClostridium kluyveri, a strict anaerobe with unique metabolic features (2008)

Clostridium kluyveri is unique among the clostridia; it grows anaerobically on ethanol and acetate as sole energy sources. Fermentation products are butyrate, caproate, and H2. We report here the genome sequence of C. kluyveri, which revealed new insights into the metabolic capabilities of this well studied organism. A membrane-bound energy-converting NADH:ferredoxin oxidoreductase (RnfCDGEAB) and a cytoplasmic butyryl-CoA dehydrogenase complex (Bcd/EtfAB) coupling the reduction of crotonyl-CoA to butyryl-CoA with the reduction of ferredoxin represent a new energy-conserving module in anaerobes. The genes for NAD-dependent ethanol dehydrogenase and NAD(P)-dependent acetaldehyde dehydrogenase are located next to genes for microcompartment proteins, suggesting that the two enzymes, which are isolated together in a macromolecular complex, form a carboxysome-like structure. Unique for a strict anaerobe, C. kluyveri harbors three sets of genes predicted to encode for polyketide/nonribosomal peptide synthetase hybrides and one set for a nonribosomal peptide synthetase. The latter is predicted to catalyze the synthesis of a new siderophore, which is formed under iron-deficient growth conditions.
Circulation of the Plasma Membrane inDictyostelium (1999)

We have developed a fluorimetric assay with the use of the dye FM1-43 to determine the rate at which Dictyostelium amoebae endocytose their surface membrane. Our results show that they do so about once each 4-10 min. A clathrin null mutant takes its surface up only approximately 30% more slowly, showing that this membrane uptake cannot be caused by clathrin-coated vesicles. Surprisingly, Ax2 and its parent, NC4, which differ in their rates of fluid-phase internalization by approximately 60-fold, take up their surfaces at the same rates. These results show that, in axenic cells, the uptake of fluid and of surface area are separate processes. The large activity of this new endocytic cycle in both Ax2 and NC4 amoebae appears capable of delivering sufficient new surface area to advance the cells' fronts during migration.
Reconstitution of water channel function of an aquaporin overexpressed and purified from Pichia pastoris (2003)

The aquaporin PM28A is one of the major integral proteins in spinach leaf plasma membranes. Phosphorylation/dephosphorylation of Ser274 at the C-terminus and of Ser115 in the first cytoplasmic loop has been shown to regulate the water channel activity of PM28A when expressed in Xenopus oocytes. To understand the mechanisms of the phosphorylation-mediated gating of the channel the structure of PM28A is required. In a first step we have used the methylotrophic yeast Pichia pastoris for expression of the pm28a gene. The expressed protein has a molecular mass of 32462 Da as determined by matrix-assisted laser desorption ionization-mass spectrometry, forms tetramers as revealed by electron microscopy and is functionally active when reconstituted in proteoliposomes. PM28A was efficiently solubilized from urea- and alkali-stripped Pichia membranes by octyl-beta-D-thioglucopyranoside resulting in a final yield of 25 mg of purified protein per liter of cell culture.
Multifunctional Probe Array for Nano Patterning and Imaging (2005)

This letter reports the design, fabrication, and testing of a multifunctional scanning probe array for nanoscale imaging and patterning. The probe array consists of multiple cantilever probes, with each probe being able to perform a dedicated function such as scanning probe lithography (e.g., dip pen nanolithography and scanning probe contact printing) or scanning probe microscopy (e.g., atomic force microscopy and lateral force microscopy). The bending states of each probe can be controlled by using an integrated thermal electric actuator so that it is possible to engage any individual probe(s) independently for writing or imaging purposes. The multifunctional probe array is therefore capable of performing a rich variety of operations with minimal chemical crosstalk and high registration accuracy. It will eliminate the need for probe chip exchanges and increase the operational efficiency. The probe tips in a given array may be made of different materials. Further, the tip and cantilever may be made of different materials for a given probe. In this work, we focus on the development of a probe array consisting of dip pen nanolithography probes, scanning probe contact printing probes (of various tip sizes), and scanning probe microscopy probes.
Storyboard aided design to specify multimedia projects (2000)

This article describes a model for storyboard design that defines a multimedia application by means of nodes related among them as a Directed Graph. This Graph is used to obtain media reports and to estimate both an approximated developing time and the required storage space needed by the final product. © 2000 John Wiley & Sons, Inc. Comput Appl Eng Educ 8: 221–228, 2000
Mechanisms of B cell activation in patients with acquired immunodeficiency syndrome and related disorders. Contribution of antibody-producing B cells, of Epstein-Barr virus-infected B cells, and of immunoglobulin production induced by human T cell lymphotropic virus, type III/lymphadenopathy-associated virus. (1986)

Patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (ARC) have hyperimmunoglobulinemia and increased numbers of circulating immunoglobulin-secreting cells. In this paper, we studied the basis for this B cell hyperactivity. Limiting dilution studies of B cells from seven patients with ARC and four with AIDS revealed that some B cells spontaneously produced antibodies to human T cell lymphotropic virus, type III/lymphadenopathy-associated virus (HTLV-III/LAV) (39:10(6) and 7:10(6) B cells, respectively), suggesting that chronic antigenic stimulation by HTLV-III/LAV was one contributing factor. The patients also had an increased number of spontaneously outgrowing B cells than did normals (6:10(6) vs. less than 2:10(6) B cells), suggesting that they had an increased number of Epstein-Barr virus (EBV)-infected B cells. However, fewer B cells from patients were immortalized by exogenously added EBV than were B cells from normals. In additional studies, HTLV-III/LAV induced immunoglobulin secretion (mean 2,860 ng/ml) by peripheral blood mononuclear cells from normals; this HTLV-III/LAV-induced immunoglobulin secretion required the presence of both B and T cells. Thus, antigenic stimulation by HTLV-III/LAV, increased numbers of EBV-infected B cells, and HTLV-III/LAV-induced T cell-dependent B cell activation all contribute to the B cell hyperactivity in patients with HTLV-III/LAV disease.
Constitutively Activated Jak-STAT Pathway in T Cells Transformed with HTLV-I (1995)

Human T cell lymphotropic virus I (HTLV-I) is the etiological agent for adult T cell leukemia and tropical spastic paraparesis (also termed HTLV-I-associated myelopathy). HTLV-I-infected peripheral blood T cells exhibit an initial phase of interleukin-2 (IL-2)-dependent growth; over time, by an unknown mechanism, the cells become IL-2-independent. Whereas the Jak kinases Jak1 and Jak3 and the signal transducer and activator of transcription proteins Stat3 and Stat5 are activated in normal T cells in response to IL-2, this signaling pathway was constitutively activated in HTLV-I-transformed cells. In HTLV-I-infected cord blood lymphocytes, the transition from IL-2-dependent to IL-2-independent growth correlated with the acquisition of a constitutively activated Jak-STAT pathway, which suggests that this pathway participates in HTLV-I-mediated T cell transformation.
Matrix Protein 2 Vaccination and Protection against Influenza Viruses, Including Subtype H5N1 (2007)

Changes in influenza viruses require regular reformulation of strain-specific influenza vaccines. Vaccines based on conserved antigens provide broader protection. Influenza matrix protein 2 (M2) is highly conserved across influenza A subtypes. To evaluate its efficacy as a vaccine candidate, we vaccinated mice with M2 peptide of a widely shared consensus sequence. This vaccination induced antibodies that cross-reacted with divergent M2 peptide from an H5N1 subtype. A DNA vaccine expressing full-length consensus-sequence M2 (M2-DNA) induced M2-specific antibody responses and protected against challenge with lethal influenza. Mice primed with M2-DNA and then boosted with recombinant adenovirus expressing M2 (M2-Ad) had enhanced antibody responses that crossreacted with human and avian M2 sequences and produced T-cell responses. This M2 prime-boost vaccination conferred broad protection against challenge with lethal influenza A, including an H5N1 strain. Vaccination with M2, with key sequences represented, may provide broad protection against influenza A.
Chemokines (2010)

Chemokines (ie, chemoattractant cytokines) are a family of small secreted molecules that mediate leukocyte migration. It is becoming increasingly more evident that chemokines play an integral role in the initiation of a specific immune response. With respect to cancer, chemokines are being studied for both their role in tumor biology and as promising immunotherapy candidates. We review several areas of chemokine importance in tumor immunity and discuss the experimental evidence that is leading to the clinical use of this cytokine family in new treatment approaches for patients with cancer.
A complex signaling module governs the activity of MalT, the prototype of an emerging transactivator family (2001)

MalT, the specific activator of the maltose regulon, is the prototype of a family of high-molecular-mass ATP-binding bacterial transcription activators. On binding of its two positive effectors, the inducer maltotriose and ATP, MalT oligomerizes to an active state competent for promoter binding and transcription activation. In addition to its previously known DNA-binding domain, limited proteolysis showed that MalT contains three other domains, the boundaries of which were accurately delimited by N-terminal microsequencing. The N-terminal domain alone binds ATP. Maltotriose binding involves an extended region corresponding to domains 2 and 3, although weak binding to domain 3 alone was also observed. Moreover, maltotriose binding induces a conformational shift involving a movement of both domains 1 and 3 with respect to domain 2, leading to the active form of the protein. Sequence examination of the MalT homologues suggests that these three domains might constitute a signaling module.
Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9 (2018)

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.