gebhart/patrepeval huggingface dataset:
Interleukin‐1β expression is induced by adherence and is enhanced by Fc‐receptor binding to immune complex in THP‐1 cells (1996)

Adherence of monocytes to endothelial cells and subsequently to basement membrane represents the initial steps in monocyte migration from the vasculature to the interstitium. We investigated the role of adhesion to endothelial cells and basement membrane in the induction of the cytokine IL-1beta. We demonstrated that mRNA for IL-1beta is induced in adherent THP-1 cells, but not in a matrix-specific manner. Adherence to fibrinogen, however, causes an increase in mRNA for IL-1beta. A background level of IL-1beta mRNA induction was observed in cells adherent to all matrices, including the non-specific human serum albumin substrate, as compared to non-adherent cells cultured in teflon troughs. In addition, antibodies to CD11a, CD11b, beta1 integrin, VLA4, (alpha)v(beta)3 (VNR), and ICAM-1 did not induce significant IL-1beta mRNA when THP-1 cells were adherent to those immunoglobulins. THP-1 cells adherent to immune complexes of anti-CD11a, anti-CD11b, anti-VLA4, anti-VNR, and anti-ICAM-1 showed greater mRNA induction than cells adherent to primary antibodies alone. THP-1 cells adherent to non-specific immune complexes gave the highest level of mRNA induction. Secretion of IL-1beta protein, measured by ELISA at 24 h, was greatest when cells were adherent to immobilized immune complexes or to fibrinogen. Our results demonstrate that a general adherence-induced increase in IL-1beta gene expression is greatly enhanced by the presence of immune complex.
Interaction of Warfarin With Drugs, Natural Substances, and Foods (2005)

Variability in the anticoagulant response to warfarin is an ongoing clinical dilemma. Fluctuations in dietary vitamin K are an important source of variance, and the need for constancy in vitamin K intake is routinely emphasized for warfarin-treated patients. Anticoagulant response is also influenced by a number of drugs that induce or inhibit warfarin metabolism, as well as by genetic polymorphisms that may modulate expression or activity of CYP2C9, the isoform mediating clearance of S-warfarin. The possible role of dietary factors other than vitamin K, as well as of herbal medicines or supplements as contributors to the instability of anticoagulation in warfarin-treated patients, has received recent attention. St. John's wort and possibly some ginseng formulations may have the potential to diminish warfarin anticoagulation, apparently by inducing CYP2C9 activity. Otherwise, there is no reliable evidence to indicate that any dietary component (other than vitamin K) or any herbal product has an effect on the anticoagulant response to warfarin. Scientific conclusions on this important therapeutic issue should be based on valid scientific data rather than unvalidated case reports.
Comparison of machine learning and traditional classifiers in glaucoma diagnosis (2002)

Glaucoma is a progressive optic neuropathy with characteristic structural changes in the optic nerve head reflected in the visual field. The visual-field sensitivity test is commonly used in a clinical setting to evaluate glaucoma. Standard automated perimetry (SAP) is a common computerized visual-field test whose output is amenable to machine learning. We compared the performance of a number of machine learning algorithms with STATPAC indexes mean deviation, pattern standard deviation, and corrected pattern standard deviation. The machine learning algorithms studied included multilayer perceptron (MLP), support vector machine (SVM), and linear (LDA) and quadratic discriminant analysis (QDA), Parzen window, mixture of Gaussian (MOG), and mixture of generalized Gaussian (MGG). MLP and SVM are classifiers that work directly on the decision boundary and fall under the discriminative paradigm. Generative classifiers, which first model the data probability density and then perform classification via Bayes' rule, usually give deeper insight into the structure of the data space. We have applied MOG, MGG, LDA, QDA, and Parzen window to the classification of glaucoma from SAP. Performance of the various classifiers was compared by the areas under their receiver operating characteristic curves and by sensitivities (true-positive rates) at chosen specificities (true-negative rates). The machine-learning-type classifiers showed improved performance over the best indexes from STATPAC. Forward-selection and backward-elimination methodology further improved the classification rate and also has the potential to reduce testing time by diminishing the number of visual-field location measurements.
A Ca2+ concentration of 1.5 mM, as present in IMDM but not in RPMI, is critical for maximal response of Th cells to PMA/ionomycin (2014)

Restimulation of memory–effector T helper lymphocytes with PMA/ionomycin is an established technique to determine their imprinting for the expression of cytokine genes, that is their functional potential. Here, we show that for the maximal reexpression of cytokine genes, the Ca 2+ concentration of the medium has to be greater than 1.5 mM. For RPMI (Roswell Park Memorial Institute 1640), the most commonly used medium, the Ca 2+ concentration has to be increased from the regular 0.42 to 1.5 mM.
Enzyme immunoassay to determine exposure to Chlamydia pneumoniae (strain TWAR) (1989)

Recent studies suggest that a group of Chlamydia strains known as TWAR, which are now proposed to be a new species called Chlamydia pneumoniae, may be a frequent cause of respiratory disease in the United States and many other countries. Current serotesting methods do not allow rapid screening of large numbers of samples to distinguish C. trachomatis exposure from C. pneumoniae exposure. We developed an enzyme immunoassay to decrease cross-reactivity between immunoglobulin G antibodies reactive with C. trachomatis and C. pneumoniae. Elementary bodies of C. trachomatis or C. pneumoniae were treated with a detergent-chelating solution to decrease the reactivity of the common lipopolysaccharide antigens. Sera from four groups of patients, totaling 143 persons, were tested by this assay. The prevalences of titers of greater than or equal to 128 to C. trachomatis and C. pneumoniae, respectively, were as follows: (i) for 23 women seropositive for C. trachomatis by the microimmunofluorescence test, 21 (91%) and 18 (78%); (ii) for 50 adult blood donors, 13 (26%) and 39 (78%); (iii) for 40 sexually transmitted disease clinic patients, 20 (50%) and 32 (80%); (iv) for 30 healthy children 5 to 7 years old, 0 (0%) and 8 (27%). Western blots (immunoblots) of each antigen corroborated the differential reactivity of C. trachomatis-positive, C. pneumoniae-negative and C. trachomatis-negative, C. pneumoniae-positive serum samples. Western blots of serum samples from rabbits immunized with either C. trachomatis or C. pneumoniae elementary bodies revealed at least two protein bands (30 and 80 kilodaltons) which appeared to represent unique C. pneumoniae antigens.
An ATP-activated channel is involved in mitogenic stimulation of human T lymphocytes (1996)

We investigated the effect of pharmacologic modulation of the ATP receptor on intracellular ion changes and proliferative response of human peripheral blood lymphocytes (PBLs) and purified T lymphocytes. Extracellular ATP (ATPe) triggered in these cells an increase in the cytoplasmic Ca2+ concentration ([Ca2+]i) and plasma membrane depolarization. Whereas both Ca2+ release from intracellular stores and influx across the plasma membrane were detected in the whole PBL population, only Ca2+ influx was observed in T cells. In the presence of near physiologic extracellular Na+ concentrations (125 mmol/L), Ca2+ permeability through the ATPe-gated channel was very low, suggesting a higher selectivity for monovalent over divalent cations. The selective P2Z agonist benzoylbenzoic ATP (BzATP) increased [Ca2+]i in the presence but not the absence of extracellular Ca2+ and also caused plasma membrane depolarization. The covalent blocker oxidized ATP (oATP), an inhibitor of P2X and P2Z receptors, prevented Ca2+ influx and plasma membrane depolarization, but had no effect on Ca2+ release from stores. Stimulation with ATPe alone had no significant effects on PBL 3H-thymidine incorporation. On the contrary, ATPe or BzATP had a synergistic effect on DNA synthesis stimulated by selective T-cell mitogens such as phytohemagglutinin, anti-CD3 monoclonal antibody, or allogenic PBLs (mixed lymphocyte cultures). Treatment with oATP inhibited mitogenic stimulation by these receptor-directed agents but not by the combined application of the Ca2+ ionophore ionomycin and phorbol myristate acetate. Interleukin-2 partially relieved inhibition by oATP. These results suggest that human T lymphocytes express a plasma membrane channel gated by ATPe that is involved in mitogenic stimulation.
Oil degradation during oil shale retorting (1976)

Powdered oil shale samples of 22 gal/ton were heated at 12/sup 0/C/min to a temperature in the 150 to 450/sup 0/C range, held isothermally for 8, 80, 800 hours, and then heated again at 12/sup 0/C/min to 500/sup 0/C. The oil yields relative to assay passed through a minimum of 80 to 92% if the holding temperature was in the 350 to 450/sup 0/C range. The loss was directly related to the amount of oil produced in the isothermal period and to its residence time in the retort, i.e., the loss was smaller in nitrogen and decreased with increasing nitrogen flow rate. The loss was thus caused by decomposition of produced oil to char and gas. A kinetic equation for the first order degradation of the oil produced in a first order reaction was developed. The activation energy of degradation was 49.4 kcal/mole. 11 references.
Immune Reconstitution in HIV‐Infected Patients (2004)

The prognosis of patients infected with human immunodeficiency virus (HIV) type 1 has dramatically improved since the advent of potent antiretroviral therapies (ARTs), which have enabled sustained suppression of HIV replication and recovery of CD4 T cell counts. Knowledge of the function of CD4 T cells in immune reconstitution was derived from large clinical studies demonstrating that primary and secondary prophylaxis against infectious agents, such as Pneumocystis jirovecii (Pneumocystis carinii), Mycobacterium avium complex, cytomegalovirus, and other pathogens, can be discontinued safely once CD4 T cell counts have increased beyond pathogen-specific threshold levels (usually >200 CD4 T cells/mm3) for 3-6 months. The downside of immune reconstitution is an inflammatory syndrome occurring days to months after the start of ART, with outcomes ranging from minimal morbidity to fatal progression. This syndrome can be elicited by infectious and noninfectious antigens. Microbiologically, the possible pathogenic pathways involve recognition of antigens associated with ongoing infection or recognition of persisting antigens associated with past (nonreplicating) infection. Specific antimicrobial therapy, nonsteroidal anti-inflammatory drugs, and/or steroids for managing immune reconstitution syndrome should be considered.
Convergent tree-reweighted message passing for energy minimization. (2005)

Abstract—Algorithms for discrete energy minimization are of fundamental importance in computer vision. In this paper, we focus on the recent technique proposed by Wainwright et al. [33]—tree-reweighted max-product message passing (TRW). It was inspired by the problem of maximizing a lower bound on the energy. However, the algorithm is not guaranteed to increase this bound—it may actually go down. In addition, TRW does not always converge. We develop a modification of this algorithm which we call sequential tree-reweighted message passing. Its main property is that the bound is guaranteed not to decrease. We also give a weak tree agreement condition which characterizes local maxima of the bound with respect to TRW algorithms. We prove that our algorithm has a limit point that achieves weak tree agreement. Finally, we show that, our algorithm requires half as much memory as traditional message passing approaches. Experimental results demonstrate that on certain synthetic and real problems, our algorithm outperforms both the ordinary belief propagation and tree-reweighted algorithm in [33]. In addition, on stereo problems with Potts interactions, we obtain a lower energy than graph cuts. Index Terms—Energy minimization, graph algorithms, message passing, belief propagation, early vision, Markov random fields, stereo. Ç 1
Constitutively Oxidized CXXC Motifs within the CD3 Heterodimeric Ectodomains of the T Cell Receptor Complex Enforce the Conformation of Juxtaposed Segments (2014)

The CD3ϵγ and CD3ϵδ heterodimers along with the CD3ζζ homodimer are the signaling components of the T cell receptor (TCR). These invariant dimers are non-covalently associated on the T cell plasma membrane with a clone-specific (i.e. clonotypic) αβ heterodimer that binds its cognate ligand, a complex between a particular antigenic peptide, and an MHC molecule (pMHC). These four TCR dimers exist in a 1:1:1:1 stoichiometry. At the junction between the extracellular and transmembrane domains of each mammalian CD3ϵ, CD3γ, and CD3δ subunit is a highly conserved CXXC motif previously found to be important for thymocyte and T cell activation. The redox state of each CXXC motif is presently unknown. Here we show using LC-MS and a biotin switch assay that these CXXC segments are constitutively oxidized on resting and activated T cells, consistent with their measured reduction potential. NMR chemical shift perturbation experiments comparing a native oxidized CD3δ CXXC-containing segment with that of a mutant SXXS-containing CD3δ segment in LPPG (1-palmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)) micelles show extensive chemical shift differences in residues within the membrane-proximal motif as well as throughout the transmembrane and cytoplasmic domains as a result of the elimination of the native disulfide. Likewise, direct comparison of the native CD3δ segment in oxidizing and reducing conditions reveals numerous spectral differences. The oxidized CXXC maintains the structure within the membrane-proximal stalk region as well as that of its contiguous transmembrane and cytoplasmic domain, inclusive of the ITAM (immunoreceptor tyrosine-based activation motif) involved in signaling. These results suggest that preservation of the CD3 CXXC oxidized state may be essential for TCR mechanotransduction.
Single-Chain Insulins as Receptor Agonists (2009)

Single-chain insulins (SCIs) are single polypeptide chains in which the insulin B-chain links contiguously with the insulin A-chain via an uncleaved connecting peptide. Although direct linkage of insulin B- and A-chains produces SCIs with little insulin receptor binding, biologists have been interested in bioengineering linker peptides that form a flexible reverse turn, allowing SCIs to activate insulin receptors. In this report, we have investigated a series of cDNAs intended to explore the significance of linker length, cleavability, and the impact of certain site-dependent residues for the bioactivity of recombinant SCIs on insulin receptors. SCI concentration is readily measured by RIA with a (proinsulin plus insulin)-specific polyclonal antibody. Although dibasic flanking residues may result in potential endoproteolytic susceptibility, a linker with -Gln-Arg- flanking sequences resisted cleavage even in secretory granules, ensuring single-chain behavior. Effective SCIs exhibit favorable and specific binding with insulin receptors. SCIs with linkers bearing an Arg residue immediately preceding the A-chain were most bioactive, although efficient receptor interaction was inhibited as SCI linker length increased, approaching that observed for proinsulin. SCIs activate downstream metabolic signaling, stimulating glucose uptake into adipocytes and suppressing gluconeogenic enzyme biosynthesis in hepatocytes, with only limited cross-reactivity on IGF-I receptors. SCIs might theoretically have utility either in immunotherapy or gene therapy in insulin-deficient diabetes.
An Azido-Biotin Reagent for Use in the Isolation of Protein Adducts of Lipid-derived Electrophiles by Streptavidin Catch and Photorelease (2009)

HNE (4-hydroxynonenal), a byproduct of lipid peroxidation, reacts with nucleophilic centers on proteins. A terminal alkynyl analog of HNE (alkynyl HNE, aHNE) serves as a surrogate for HNE itself, both compounds reacting with protein amine and thiol functional groups by similar chemistry. Proteins modified with aHNE undergo reaction with a click reagent that bears azido and biotin groups separated by a photocleavable linker. Peptides and proteins modified in this way are affinity purified on streptavidin beads. Photolysis of the beads with a low intensity UV light releases bound biotinylated proteins or peptides, i.e. proteins or peptides modified by aHNE. Two strategies, (a) protein catch and photorelease and (b) peptide catch and photorelease, are employed to enrich adducted proteins or peptide mixtures highly enriched in adducts. Proteomics analysis of the streptavidin-purified peptides by LC-MS/MS permits identification of the adduction site. Identification of 30 separate peptides from human serum albumin by peptide catch and photorelease reveals 18 different aHNE adduction sites on the protein. Protein catch and photorelease shows that both HSA and ApoA1 in human plasma undergo significant modification by aHNE.
The lifting scheme: A construction of second generation wavelets (1995)

. We present the lifting scheme, a simple construction of second generation wavelets, wavelets that are not necessarily translates and dilates of one fixed function. Such wavelets can be adapted to intervals, domains, surfaces, weights, and irregular samples. We show how the lifting scheme leads to a faster, in-place calculation of the wavelet transform. Several examples are included. Key words. wavelet, multiresolution, second generation wavelet, lifting scheme AMS subject classifications. 42C15 1. Introduction. Wavelets form a versatile tool for representing general functions or data sets. Essentially we can think of them as data building blocks. Their fundamental property is that they allow for representations which are efficient and which can be computed fast. In other words, wavelets are capable of quickly capturing the essence of a data set with only a small set of coefficients. This is based on the fact that most data sets have correlation both in time (or space) and frequenc...
Comparison of immunoglobulin A (IgA), IgG, and IgM enzyme-linked immunosorbent assays, plaque reduction neutralization assay, and complement fixation in detecting seroresponses to rotavirus vaccine candidates (1989)

In a phase 1 study to evaluate human-rhesus rotavirus reassortant vaccines, 116 infants 1 to 5 months of age received one of the following five preparations: the serotype 1 reassortant, the serotype 2 reassortant, rhesus rotavirus (serotype 3), a bivalent preparation (serotypes 1 and 3), or a placebo. Seroresponses to the different vaccines were measured by plaque reduction neutralization assay (PRNA); rotavirus-specific immunoglobulin A (IgA), IgG, and IgM enzyme-linked immunosorbent assays (ELISAs); and complement fixation (CF). The seroresponse rate, calculated by using a fourfold or greater antibody rise by any assay, was similar in the four vaccine groups (83 to 96%). When the data from all the vaccinees were pooled, IgA ELISA, IgG ELISA, and PRNA were comparable in detecting seroresponses (67, 62, and 70%, respectively) and more efficient than IgM ELISA (53%) and CF (44%). When the vaccinees were analyzed by age, the overall seroresponse rates were the same for infants 1 to 2 and 3 to 5 months old (90%). The IgA ELISA and PRNA were the most efficient for detecting antibody rises in both age groups. IgG ELISA was among the least efficient methods for detecting antibody rises in the younger age group but among the most efficient in the older age group (44 versus 78%). CF was among the least efficient methods in both age groups but was significantly better in the older age group than in the younger age group (54 versus 21%). Our findings show that ELISA, in particular rotavirus-specific IgA ELISA, is a sensitive indicator of vaccine takes in 1- to 5 month-old infants, the target population for vaccination. ELISA should also be very useful in demonstrating natural rotavirus infections in field studies in which a stool specimen from a diarrheal episode is not always available. The ELISA has the advantages of being easier and quicker and requiring less serum than PRNA, but it does not give serotype-specific information about the immune response.
Activation and injury of endothelial cells by cytokines. (1998)

Vascular endothelial cells (EC) are primary cellular targets for the actions of pro-inflammatory cytokines such as tumor necrosis factor (TNF). We have studied the signaling pathways used by TNF that lead to new gene expression (endothelial cell activation) or apoptosis (endothelial cell injury). Both responses are initiated by ligand binding to TNFR-I (the p55 receptor). TNF initiates transcription of the E-selectin gene by activation of the transcription factors NF-kappa B and c-Jun/ATF-2. NF-kappa B is activated following degradation of I kappa B alpha and I kappa B-beta. Activation of c-Jun/ATF-2 involves new c-Jun synthesis, and more importantly, phosphorylation of the amino terminus of c-Jun by Jun N-terminal kinase (JNK). Studies in transiently transfected human umbilical vein endothelial cells have revealed that NF-kappa B activation is initiated through the adaptor protein TRAF-2. The activation of JNK also depends upon TRAF-2 and probably involves a kinase cascade initiated by the small G proteins Rac-1 and/or cdc-42. Normally, TNF does not injure human EC. However, TNF can cause apoptosis of EC when cells are co-treated with either the protein synthesis inhibitor cycloheximide (CHX) or the lipid mediator ceramide (cer). The pathways leading to apoptosis following treatment with TNF + CHX and TNF + cer are different since only TNF + CHX is blocked by the caspase inhibitors crmA protein or the peptide zVAD.fmk while only TNF + cer is blocked by the anti apoptotic proteins Bcl-2, Bcl-XL or Al. Both pathways may be inhibited by the anti-apoptotic protein A-20. TNF does not cause the liberation of cer in EC, perhaps because of limited expression of neutral sphingomyelinase-activating adaptor protein FAN. These observations suggest that TNF normally acts as an activator of EC but may change from an activator to a killer of EC when combined with agents that release ceramide, such as u.v. irradiation or cytotoxic drugs, or with ceramide mimetics such as lipopolysaccharide. The activation and injury of endothelial cells induced by TNF and other proinflammatory cytokines may underlie the local effects of these mediators in vivo.
Natural products of the medicinal fungus Ganoderma lucidum: Occurrence, biological activities, and pharmacological functions (2003)

Ganoderma lucidum, a fungus used in traditional Chinese medicine, produces polysaccharides and oxygenated triterpenoids with a very broad spectrum of biological activities and pharmacological functions. Among the Ganoderma triterpenoids, many pairs of C-3 alpha/beta stereoisomers and C-3/C-15 positional isomers have been identified. Biosynthetic study has indicated that the C-3alpha series of oxygenated triterpenoids is derived from the C-3beta series via an oxidation-reduction pathway. The interaction of Ganoderma triterpenoids with human platelets in the induction of aggregation and inhibition of agonist-induced aggregation and signal transduction has been elucidated. Reduction of cellular mevalonate content to a stage in which cholesterol synthesis is strongly inhibited and cell growth is marginally arrested sensitizes hepatoma cells to the oxygenated triterpenoids. A combination treatment of lovastatin and Ganoderma triterpenoids in animal studies has exhibited a potential anticancer effect.