gebhart/patrepeval huggingface dataset:
Fluid phase biopsy for detection and characterization of circulating endothelial cells in myocardial infarction (2014)

Elevated levels of circulating endothelial cells (CECs) occur in response to various pathological conditions including myocardial infarction (MI). Here, we adapted a fluid phase biopsy technology platform that successfully detects circulating tumor cells in the blood of cancer patients (HD-CTC assay), to create a high-definition circulating endothelial cell (HD-CEC) assay for the detection and characterization of CECs. Peripheral blood samples were collected from 79 MI patients, 25 healthy controls and six patients undergoing vascular surgery (VS). CECs were defined by positive staining for DAPI, CD146 and von Willebrand Factor and negative staining for CD45. In addition, CECs exhibited distinct morphological features that enable differentiation from surrounding white blood cells. CECs were found both as individual cells and as aggregates. CEC numbers were higher in MI patients compared with healthy controls. VS patients had lower CEC counts when compared with MI patients but were not different from healthy controls. Both HD-CEC and CellSearch® assays could discriminate MI patients from healthy controls with comparable accuracy but the HD-CEC assay exhibited higher specificity while maintaining high sensitivity. Our HD-CEC assay may be used as a robust diagnostic biomarker in MI patients.
Regulation of estrogen receptor concentration and activity by an erbB/HER ligand in breast carcinoma cell lines (1996)

Expression of the erbB-2 oncogene in breast cancer patients correlates with poor prognosis and failure of hormonal therapy. In this study, the effects of a putative erbB/HER ligand, gp30, on estrogen receptor (ER) concentration and activity was investigated in the estrogen receptor positive human breast cancer cells, BT474 and MCF-7, which express either high or low levels of erbB-2 and erbB-4, respectively. Treatment of cells with gp30 resulted in a decrease in the steady-state level of estrogen receptor protein by approximately 70-80%. The effect of gp30 on the concentration of ER was independent of serum in the media and was not inhibited by an epidermal growth factor receptor blocking antibody. In addition to the effect on ER protein, gp30 decreased the steady-state level of ER messenger RNA. Transcription run on experiments demonstrated that the decrease in ER expression was mediated by a decrease in ER gene transcription. The effect of gp30 on estrogen receptor activity was also investigated in this study. Treatment of cells with gp30 blocked estradiol induction of progesterone receptor. Inhibition was observed at the level of progesterone receptor protein, messenger RNA, and gene transcription. gp30 also blocked estradiol induction of pS2 gene transcription. In addition to its effects on progesterone receptor and pS2, gp30 blocked activation of an estrogen response element in a transient transfection assay and inhibited ER binding to its response element in a DNA mobility shift assay, suggesting a direct effect on the estrogen receptor. The effects of gp30 on estrogen receptor concentration and activity were independent of the level of erbB-2 and erbB-4 in the cell. These data show that gp30 regulates the concentration of ER and modulates ER activity.
Depletion of alveolar macrophages decreases neutrophil chemotaxis to Pseudomonas airspace infections (1996)

The mechanism for neutrophil (PMN) influx into infected airspaces of the lung is not known. To determine whether alveolar macrophage products are important in the initiation of chemotaxis, we depleted rats of alveolar macrophages by aerosolizing negatively charged oligolamellar liposomes complexed to clodronate disodium. Ninety-five percent of the alveolar macrophages were depleted, and lung injury and inflammation were minimized with this depletion technique. Rats depleted of alveolar macrophages were then anesthetized, and either 5 x 10(6) colony-forming units (CFU) or 5 x 10(7) CFU of Pseudomonas aeruginosa were instilled into the airspaces of these animals. When recombinant macrophage inflammatory protein MIP-2 was intratracheally instilled into rats depleted of alveolar macrophages, PMN were recruited to their airspaces. Nonetheless, PMN numbers were decreased in the lavage fluids when moderate or large inoculums of bacteria were instilled into depleted rats, although the PMN response appeared dose dependent. Levels of bioactive tumor necrosis factor-alpha and immunoreactive proteins CINC/gro (cytokine-induced PMN chemoattractant) in the lavage fluids obtained from infected rats depleted of alveolar macrophages were significantly decreased compared with the levels in the lavage fluids obtained from normal infected rats. MIP-2 mRNA expression, as detected by Northern analysis, was also decreased in the infected lungs of depleted rats, and the lavage fluid from these rats had significantly decreased chemotactic activity. Therefore these results suggest that alveolar macrophage products play a direct role in the initial recruitment of PMN into infected lungs.
Polar lipid and fatty acid distribution in carotenolipoprotein complexes extracted from sea buckthorn fruits (2001)

Sea buckthorn (Hippophae rhamnoides L., fam. Elaeagnaceae) fruits are rich in pigments and lipoproteins located in membranes and the fleshy mesocarp. In spite of many reports concerning the neutral lipids in the mesocarp, no data about the polar lipids and their fatty acid composition are available even though they play important structural and physiological roles in cell membranes and may offer interesting applications as emulsifiers and nutrients in cosmetic preparations. Carotenolipoprotein complexes are located particularly in fruit membranes where polar lipids may function as bridge compounds between the polar (protein) and non-polar (carotenoid) moieties. The fatty acid compositions of total and individual polar lipids separated from carotenolipoprotein complexes were determined by HPTLC and GC. The polar lipids included 61% phospholipids and 39% galactolipids, which contained mainly 16:0, 16:1 (9c), 18:1 (9c), 18:1 (11c) and 18:2 (9c, 12c) fatty acids. Almost all polar lipids showed high ratios of 16:0/16:1 (11c) and 18:1 (9c)/18:1 (11c), and higher quantities of 18 carbon unsaturated fatty acids than of the saturated analogue. Galactolipids proved to be richest in 18:1 (9c) and 18:3 (9c, 12c, 15c) fatty acids, while phospholipids contained higher concentrations of 16:0 and 18:1 (9c).
Established and emerging atmospheric pressure surface sampling/ionization techniques for mass spectrometry (2008)

The number and type of atmospheric pressure techniques suitable for sampling analytes from surfaces, forming ions from these analytes, and subsequently transporting these ions into vacuum for interrogation by MS have rapidly expanded over the last several years. Moreover, the literature in this area is complicated by an explosion in acronyms for these techniques, many of which provide no information relating to the chemical or physical processes involved. In this tutorial article, we sort this vast array of techniques into relatively few categories on the basis of the approaches used for surface sampling and ionization. For each technique, we explain, as best known, many of the underlying principles of operation, describe representative applications, and in some cases, discuss needed research or advancements and attempt to forecast their future analytical utility.
Anti-tick vaccines (2004)

There is now abundant evidence that vaccination with defined protein antigens is able to induce significant immunity to tick infestation. In a limited number of cases, this immunity has been duplicated by vaccination with recombinant antigens, a critical step on the pathway to commercial vaccine production. The existence of two commercial vaccines has allowed a number of field studies showing that the existing products can make an important contribution to an integrated approach to the control of ticks in the field. Under most circumstances however, the use of a tick vaccine as the single, stand alone control technology is likely to require more efficacious vaccines than those currently available. Increases in efficacy are most likely to come through the discovery of additional, effective vaccine antigens. The number of antigens with demonstrated effect is increasing, though only slowly, while the number of potential antigens that remain to be evaluated is increasing more quickly. There is limited, though convincing, evidence that some of these antigens will show effective cross-species protection, though in a poorly understood and unpredictable way. The groundwork has been laid; the potential of the field is still to be effectively exploited.
Acetylation of Poly(amidoamine) Dendrimers (2003)

The precise stoichiometry required for the acetylation of surface amines of a poly(amidoamine) (PAMAM) dendrimer generation 5 (G5) was verified by using potentiometric titration, gel permeation chromatography, and nuclear magnetic resonance spectroscopy. The average number of primary amine groups, absolute molecular weight, and molecular weight distribution of G5 PAMAM were determined by potentiometric titration and GPC. These fundamental parameters were used to design the stoichiometry of an acetylation reaction that yielded acetylation fractions from 0 to 100% of the primary amines on the macromolecule. GPC refractive index detector confirmed that the diameter of the dendrimer related inversely to the degree of acetylation. The acetylated dendrimers do not follow the elution behavior of the conventional polymer molecules most probably because of their spherical shape and polycationic nature. This study clarifies the nature of the acetylation reaction and provides a well-defined acylated macromolecule, which can serve as a scaffold for the development of complex dendrimeric structures.
Designing Herbicide Tolerance Based on Metabolic Alteration: the Challenges and the Future (2000)

The major basis for the tolerance of crops to most herbicides is differential rates and routes of herbicide metabolism. In spite of detailed knowledge on these routes of metabolism, it has been very difficult to synthesize new crop selective herbicides by deliberately altering the metabolism rate through rational design. The major problem is trying to predict the substrate affinities for the herbicide detoxifying enzymes that are known to exist in multiple isoforms and that vary greatly among plant species. Furthermore, changing a substituent in a molecule, even at a remote site from the actual site of metabolism, can often alter the pathway of degradation by similar enzymes from different plant species. Thus, a number of analogs with different substituents ("metabolic handles") must be synthesized in order to determine if any of these analogs will be detoxified. An alternative approach to generate herbicide tolerance is to introduce genes for metabolism from microbes into target crops. This approach has been successfully used in a number of crops.
Siderophore production by Vibrio vulnificus (1983)

Previous studies in our laboratory, as well as clinical evidence, have suggested that increased iron levels in the host may be important in infections caused by the halophilic pathogen Vibrio vulnificus. To study iron acquisition, we induced siderophore production by growth in a low-iron medium, and biochemical testing indicated the production of both hydroxamate- and phenolate-type siderophores. The siderophores were extracted from growth filtrates with ethyl acetate (for phenolates) and phenol-chloroform-ether (for hydroxamates). These extracts enhanced the growth of V. vulnificus when the bacterium was grown in iron-limited medium. The ability of these siderophores to stimulate the growth of Salmonella typhimurium LT-2 enb-7 (a mutant deficient in the biosynthesis of enterochelin) and Arthrobacter flavescens JG-9 (a hydroxamate auxotroph) supported the conclusion that V. vulnificus produces both hydroxamate- and phenolate-type siderophores.
Building hypertext from newspaper articles using lexical chaining (abstract) (1996)

No abstract available.
Molecular signature of a public clonotypic autoantibody in primary Sjögren's syndrome: A “forbidden” clone in systemic autoimmunity (2011)

The expression of a Ro 60-reactive public B cell clonotype in a subset of patients with primary SS as a long-lived, class-switched circulating autoantibody implies a common breach of B cell tolerance checkpoints in these patients. The unique heavy chain/light chain signature opens the possibility of tracking the development of a "forbidden" clone against a bona fide systemic autoantigen in human disease.
The interaction between Alzheimer amyloid β(1–40) peptide and ganglioside GM1‐containing membranes (1997)

The interaction between Alzheimer amyloid peptide A beta(1-40) and membrane lipids was studied by circular dichroism spectroscopy under the conditions of physiologically relevant ionic strength and neutral pH. The peptide binds to the membranes containing ganglioside GM1 and upon binding undergoes a conformational transition from random coil to an ordered structure rich in beta-sheet. This interaction appears to be ganglioside-specific as no changes in A beta(1-40) conformation were found in the presence of various phospholipids or sphingomyelin. The isolated oligosaccharide moiety of the ganglioside was ineffective in inducing alterations in the secondary structure of A beta(1-40). No interaction was observed between ganglioside GM1 and the N-terminal peptide fragment A beta(1-28). Binding to the ganglioside is likely to modulate the neurotoxic and/or amyloidogenic properties of A beta(1-40).
Optimizing 3D triangulations using discrete curvature analysis (2001)

Abstract. A tool for constructing a “good ” 3D triangulation of a given set of vertices in 3D is developed and studied. The constructed triangulation is “optimal ” in the sense that it locally minimizes a cost function which measures a certain discrete curvature over the resulting triangle mesh. The algorithm for obtaining the optimal triangulation is that of swapping edges sequentially, such that the cost function is reduced maximally by each swap. In this paper three easy-to-compute cost func-tions are derived using a simple model for defining discrete curvatures of triangle meshes. The results obtained by the different cost functions are compared. Operating on data sampled from simple 3D models, we com-pare the approximation error of the resulting optimal triangle meshes to the sampled model in various norms. The conclusion is that all three cost functions lead to similar results, and none of them can be said to be supe-rior to the others. The triangle meshes generated by our algorithm, when serving as initial triangle meshes for the butterfly subdivision scheme, are
Regulation of Flavin Synthesis by Escherichia coli (1962)

SUMMARY: An approach has been made to the problem of how the synthesis of coenzymes is regulated. Two aspects of the problem have been studied, especially as they concern the synthesis of flavins by bacteria: (1) How are coenzymes prevented from being synthesized as fast as amino acids or nucleic acid bases? (2) How is coenzyme synthesis adjusted to the often changing physiological needs of bacteria? Evidence is presented that flavins cannot inhibit the activity of enzymes in the flavin biosynthetic pathway of Escherichia coli, but the amount of these enzymes can be made to vary by a factor of at least two. Repression might, therefore, account for the low rate of flavin synthesis. The possibility that repression rather than feedback inhibition also accounts for the low rate of synthesis of other coenzymes is discussed. Flavin synthesis is not as precisely adjusted to the physiological needs of bacteria as are syntheses of major metabolites for the following reasons: (1) Flavins are greatly overproduced by bacteria during exponential growth; the ratio of flavins excreted to flavins retained in the cells is between 0.8 and 8 for all strains and cultural conditions tested. (2) Flavin synthesis is not tightly geared to growth; thus, flavin synthesis goes on uninterrupted for more than an hour when the growth rate of E. coli or Pseudormonas fluorescens is abruptly reduced from a rapid rate to zero; also growth goes on uninterrupted for over an hour when the flavin supply is abruptly cut off from rapidly growing lactic acid bacteria. Evidently the control mechanism in the flavin pathway is not very sensitive to physiological needs. This conclusion probably applies to other coenzymes as well. Some incidental findings of interest from other points of view were: (1) Although internal flavins can get out of E. coli, external flavins apparently cannot enter. This could account for the absence of flavinless mutants. (2) After brief treatment with penicillin, E. coli becomes permeable to external flavins while remaining both impermeable to inulin and capable of synthesizing flavins. (3) Less than 4 % of the intracellular flavins of E. coli are free, in a form that can be extracted with n-butanol (5 %, v/v), toluene (0.05 %, v/v), cetyl trimethylammonium bromide (0.001 %, w/v) or distilled water. The remaining flavins are bound, in a form that can be extracted with trichloracetic acid (5 %, w/v). The intracellular concentration of free flavins in E. coli is estimated to be less than 4 x 10−6M.
The epidemiology of biopsy-positive giant cell arteritis: special reference to cyclic fluctuations (1999)

The annual incidence of biopsy-positive GCA increased during the years 1976 through 1995. The significant seasonal variation, as well as considerable variation in annual incidence, might be due to the influence of exogenous triggering factors, such as infections. Further support for an exogenous aetiology, in terms of a statistically significant cyclic fluctuation of the annual incidence, was not found, however.
THE COVALENT STRUCTURE OF AN ENTIRE γG IMMUNOGLOBULIN MOLECULE (1969)

The complete amino acid sequence of a human gammaG1 immunoglobulin (Eu) has been determined and the arrangement of all of the disulfide bonds has been established. Comparison of the sequence with that of another myeloma protein (He) suggests that the variable regions of heavy and light chains are homologous and similar in length. The constant portion of the heavy chain contains three homology regions each of which is similar in size and homologous to the constant region of the light chain. Each variable region and each constant homology region contains one intrachain disulfide bond. The half-cystines participating in the interchain bonds are all clustered within a stretch of ten residues at the middle of the heavy chains.These data support the hypothesis that immunoglobulins evolved by gene duplication after early divergence of V genes, which specified antigen-binding functions, and C genes, which specified other functions of antibody molecules. Each polypeptide chain may therefore be specified by two genes, V and C, which are fused to form a single gene (translocation hypothesis). The internal homologies and symmetry of the molecule suggest that homology regions may have similar three-dimensional structures each consisting of a compact domain which contributes to at least one active site (domain hypothesis). Both hypotheses are in accord with the linear regional differential of function in antibody molecules.
Experimental and computational exploration of the dynamic behavior of (PNP)BF2, a boron compound supported by an amido/bis(phosphine) pincer ligand (2011)

The diarylamido/bis(phosphine) PNP pincer ligand (2-(i)Pr(2)P-4-MeC(6)H(3))(2)N has been evaluated as a scaffold for supporting a BF(2) fragment. Compound (PNP)BF(2) (6) was prepared by simple metathesis of (PNP)Li (5) with Me(2)SBF(3). NMR spectra of 6 in solution are of apparent C(2) symmetry, suggestive of a symmetric environment about boron. However, a combination of X-ray structural studies, low-temperature NMR investigations, and DFT calculations consistently establish that the ground state of this molecule contains a classical four-coordinate boron with a PNBF(2) coordination environment, with one phosphine donor in PNP remaining "free". Fortuitous formation of a single crystal of (PNP)BF(2)·HBF(4) (7), in which the "free" phosphine is protonated, furnished another structure containing the same PNBF(2) environment about boron for comparison and the two PNBF(2) environments in 6 and 7 are virtually identical. DFT studies on several other diarylamido/bis(phosphine) pincer (PNP)BF(2) systems were carried out and all displayed a similar four coordinate PNBF(2) environment in the ground state structures. The symmetric appearance of the room-temperature NMR spectra is explained by the rapid interconversion between two degenerate four-coordinate, C(1)-symmetric ground-state forms. Lineshape analysis of the (1)H and (19)F NMR spectra over a temperature range of 180-243 K yielded the activation parameters ΔH(‡) = 8.1(3) kcal mol(-1) and ΔS(‡) = -6.0(15) eu, which are broadly consistent with the calculated values. Calculations indicate that the exchange of phosphine donors at the boron center proceeds by an intrinsically dissociative mechanism.
Independent Contributions of Hypothermia and Acidosis to Coagulopathy in Swine (2005)

Acidosis and hypothermia cause a clinical coagulopathy with different thrombin generation kinetics. These results confirm the need to prevent or correct hypothermia and acidosis and indicate the need for improved techniques to monitor coagulopathy in the trauma population.
Rat Thy‐1 antigen has a hydrophobic segment at the carboxyl terminus (1984)

We have isolated a cDNA clone coding for rat Thy-1 antigen from a rat thymocyte cDNA library. The 549 base pairs insert includes the complete coding region of a mature Thy-1 polypeptide of 142 amino acids, 31 amino acids longer than the previously reported glycoprotein sequence. These 31 amino acids contain an extremely hydrophobic region of 26 uncharged amino acids which apparently represent the transmembrane segment that allows for integration within the membrane. The presence of this additional protein segment will solve most of the enigmas regarding the properties of the C-terminal region of Thy-1 antigen.
Human monoclonal antibodies against a plethora of viral pathogens from single combinatorial libraries. (1993)

Conventional antibody generation usually requires active immunization with antigen immediately prior to the preparation procedure. Combinatorial antibody library technology offers the possibility of cloning a range of antibody specificities at a single point in time and then accessing these specificities at will. Here we show that human monoclonal antibody Fab fragments against a plethora of infectious agents can be readily derived from a single library. Further examination of a number of libraries shows that whenever antibody against a pathogen can be detected in the serum of the donor, then specific antibodies can be derived from the corresponding library. We describe the generation of human Fab fragments against herpes simplex virus types 1 and 2, human cytomegalovirus, varicella zoster virus, rubella, human immunodeficiency virus type 1, and respiratory syncytial virus. The antibodies are shown to be highly specific and a number are effective in neutralizing virus in vitro.