gebhart/patrepeval huggingface dataset:
FORMATION OF C3a AND C5a ANAPHYLATOXINS IN WHOLE HUMAN SERUM AFTER INHIBITION OF THE ANAPHYLATOXIN INACTIVATOR (1973)

Two biologically and chemically distinct anaphylatoxins (ATs) could be generated in whole human serum after removal of the AT inactivator (AI) by immune-absorption or after inhibition of AI with 1 M epsilon-aminocaproic acid (EACA). Both human ATs could be generated by treatment of serum with antigen-antibody complexes, which activate the classical complement pathway, and with inulin or yeast, both of which trigger the alternate pathway. The ATs were isolated from serum in active form and characterized as C3a and C5a. Although human C3a had been characterized previously, C5a had not. The molecular weight of human C5a AT was 17,500; its electrophoretic mobility at pH 8.5 was -1.7 x 10(-5) cm(2) V(-1) s(-1). The minimal effective concentration in vitro was 7.5 x 10(-10) M. The minimal effective doses of human C5a in producing a wheal and erythema in the human skin was 1 x 10(-15) mol. The results strongly suggest a biological function for both ATs and indicate that the expression of their activity is controlled by the AI of normal blood plasma.
Dispersive regime of circuit QED: Photon-dependent qubit dephasing and relaxation rates (2009)

Superconducting electrical circuits can be used to study the physics of cavity quantum electrodynamics (QED) in new regimes, therefore realizing circuit QED. For quantum-information processing and quantum optics, an interesting regime of circuit QED is the dispersive regime, where the detuning between the qubit transition frequency and the resonator frequency is much larger than the interaction strength. In this paper, we investigate how nonlinear corrections to the dispersive regime affect the measurement process. We find that in the presence of pure qubit dephasing, photon population of the resonator used for the measurement of the qubit act as an effective heat bath, inducing incoherent relaxation and excitation of the qubit. Measurement thus induces both dephasing and mixing of the qubit, something that can reduce the quantum nondemolition aspect of the readout. Using quantum trajectory theory, we show that this heat bath can induce quantum jumps in the qubit state. Nonlinear effects can also reduce the achievable signal-to-noise ratio of a homodyne measurement of the voltage.
Sca-1+ Hematopoietic Cell–based Gene Therapy with a Modified FGF-2 Increased Endosteal/Trabecular Bone Formation in Mice (2007)

This study assessed the feasibility of using an ex vivo stem cell antigen-1-positive (Sca-1(+)) cell-based systemic fibroblast growth factor-2 (FGF-2) gene therapy to promote endosteal bone formation. Sca-1(+) cells were used because of their ability to home to, and engraft into, the bone marrow cavity. The human FGF-2 gene was modified to increase protein secretion and stability by adding the bone morphogenic protein (BMP)-2/4 hybrid signal sequence and by mutating two key cysteines. Retro-orbital injection of Sca-1(+) cells transduced with a Moloney leukemia virus (MLV)-based vector expressing the modified FGF-2 gene into sub-lethally irradiated W(41)/W(41) recipient mice resulted in long-term engraftment, more than 100-fold elevation in serum FGF-2 level, increased serum bone-formation markers, and massive endosteal bone formation. In recipient mice showing very high serum FGF-2 levels (>2,000 pg/ml), this enhanced endosteal bone formation was so robust that the marrow space was filled with bony tissues and insufficient calcium was available for the mineralization of all the newly formed bone, which led to secondary hyperparathyroidism and osteomalacia. These adverse effects appeared to be dose related. In conclusion, this study provided compelling test-of-principle evidence for the feasibility of using an Sca-1(+) cell-based ex vivo systemic FGF-2 gene therapy strategy to promote endosteal bone formation.
Identification of a Factor IX Binding Site on the Third Apple Domain of Activated Factor XI (1996)

Activated factor XI (factor XIa) participates in blood coagulation by activating factor IX. Previous work has demonstrated that a binding site for factor IX is present on the noncatalytic heavy chain of factor XIa (Sinha, D., Seaman, F. S., and Walsh, P. N. (1987) Biochemistry 26, 3768-3775). Recombinant factor XI proteins were expressed in which each of the four apple domains of the heavy chain (designated A1 through A4) were individually replaced with the corresponding domain from the homologous but functionally distinct protease prekallikrein (PK). To identify the site of factor IX binding, the chimeric proteins were activated with factor XIIa and tested for their capacity to activate factor IX in plasma coagulation and purified protein assays. The chimera with the substitution in the third apple domain (factor XI/PKA3) had <1% of the coagulant activity of wild type factor XIa in a plasma coagulation assay, whereas the chimeras with substitutions in A1, A2, and A4 demonstrated significant activity (68-140% of wild type activity). The Km for activation of factor IX by factor XIa/PKA3 (12. 7 microM) is more than 30-fold higher than the Km for activation by wild type factor XIa or the other factor XI/PK chimeras (0.11-0.37 microM). Two monoclonal antibodies (2A12 and 11AE) that recognize epitopes on the factor XI A3 domain were potent inhibitors of factor IX activation by factor XIa, whereas antibodies against the A2 (1A6) and A4 (3G4) domains were poor inhibitors. The data indicate that a binding site for factor IX is present on the third apple domain of factor XIa.
Expression on blood cells of sialophorin, the surface glycoprotein that is defective in Wiskott-Aldrich syndrome (1987)

Sialophorin, previously called gpL115, is the heavily sialylated surface protein that is defective in lymphocytes of Wiskott-Aldrich syndrome patients. Using the monoclonal antibody L10 as a probe, sialophorin expression was detected on isolated T lymphocytes and thymocytes, B cell lines, monocytes, neutrophils, and platelets, but not on erythrocytes, fibroblasts, and glioblastoma cells. This unusual distribution pattern suggests that sialophorin is expressed on all circulating cells except erythrocytes. Trace amounts of the sialophorin molecules on lymphocytes are incompletely sialylated, but significant amounts of the molecules on thymocytes are incompletely sialylated. The molecular form of sialophorin on T lymphocytes, thymocytes, and monocytes is the previously characterized species of apparent mol wt 115,000. A newly described sialophorin species of apparent mol wt 135,000 was found on neutrophils and platelets. The 115,000 lymphocyte/monocyte form and the 135,000 platelet/neutrophil form were shown to be substantially similar. The two forms have approximately the same content of sialylated O-linked carbohydrate units since both undergo the same atypical shift in electrophoretic mobility on desialylation. Both contain the epitope recognized by the monoclonal antibody L2 and the epitope recognized by L10 antibody. Moreover, evidence from another study indicates that the polypeptide portions are identical, cumulatively suggesting that 115,000 sialophorin and 135,000 sialophorin are identical except for the presence on the latter of additional neutral saccharide residues.
Two-stage association study and meta-analysis of mitochondrial DNA variants in Parkinson disease (2013)

In a 2-stage association study of mtDNA variants and PD, we confirm the reduced risk of PD with super-haplogroup JT and resolve this at the J1b level. Meta-analysis explains the previous inconsistent associations that likely arise through sampling effects. The reduced risk of PD with haplogroups J, K, and T is mirrored by an increased risk of PD in super-haplogroup HV, which increases survival after sepsis. Antagonistic pleiotropy between mtDNA haplogroups may thus be shaping the genetic landscape in humans, leading to an increased risk of PD in later life.
Kidney Fibrosis in Hypertensive Rats: Role of Oxidative Stress (2008)

Fibrosis of the glomerulus and the tubulointerstitium occurs in patients with hypertension. Studies have shown that renal oxidative stress appears in hypertensive kidney disease. The potential role of oxidative stress in renal fibrogenesis remains to be elucidated. Herein, we tested the hypothesis that oxidative stress contributes to the development of renal fibrosis during hypertension.Sprague-Dawley rats received angiotensin II (AngII; 9 microg/h s.c.) for 4 weeks with/without co-treatment of antioxidants, apocynin and tempol (120 mg/kg/day each, p.o.). Untreated rats served as controls. Appearance of renal oxidative stress and its effect on the expression of transforming growth factor (TGF)-beta(1), population of myofibroblasts, collagen synthesis/degradation and fibrosis in kidneys were examined. Chronic AngII infusion elevated systemic blood pressure (228 +/- 6 mm Hg), which was accompanied with extensive renal fibrosis and oxidative stress represented as upregulated NADPH oxidase and suppressed superoxide dismutase (SOD). Co-treatment with antioxidants led to: (1) markedly decreased renal NADPH oxidase; (2) significantly attenuated gene expression of TGF-beta(1), type I collagen, and tissue inhibitors of matrix metalloproteinase (TIMP)-I/-II in the kidney; (3) largely reduced population of myofibroblasts in both the cortex and medulla; (4) significantly reduced renal collagen volume, and (5) partially suppressed blood pressure (190 +/- 8 mm Hg). Thus, prolonged AngII administration promotes renal oxidative stress, which is associated with hypertensive renal disease. AngII induces renal oxidative stress by increasing NADPH oxidase and reducing SOD in the kidney, which, in turn, upregulates collagen synthesis, while suppressing collagen degradation, thereby promoting the development of fibrosis in kidneys of hypertensive rats.
Human Antibody Against C Domain of Tenascin-C Visualizes Murine Atherosclerotic Plaques Ex Vivo (2007)

The antibody G11, specific to the C domain of tenascin-C, visualizes murine atherosclerotic plaques ex vivo. In conjunction with the increased expression of the C domain of tenascin-C in macrophage-rich plaques, the colocalization of G11 uptake with activated macrophages, and the favorable target-to-blood ratio at 24 h, this antibody may be useful for molecular imaging of advanced atherosclerotic plaques in the intact organism.
New criteria for blind adaptive arrays (2002)

An alternative methodology for blind adaptive array processing is presented which generalizes the class of cost functions that are currently used. The methodology is based on the separation of independent, but not necessarily identically distributed, statistical components at the array output. Sufficient admissibility criteria are presented for blind adaptive array processing cost functions and examples based on the magnitude of complex, standardized cumulants as well as on order statistics are provided. In addition, a simple procedure for devising new candidate cost functions is discussed that can easily incorporate any available statistical information regarding the specific signal/interference environment of interest.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In‐vivo Tumor detection using diffusion reflection measurements of targeted gold nanorods – a quantitative study (2012)

The ability to quantitatively and non-invasively detect nanoparticles has important implications on their development as an in-vivo cancer diagnostic tool. The Diffusion Reflection (DR) method is a simple, non-invasive imaging technique which has been proven useful for the investigation of tissue's optical parameters. In this study, Monte Carlo (MC) simulations, tissue-like phantom experiments and in-vivo measurements of the reflected light intensity from tumor bearing mice are presented. Following intravenous injection of antibody conjugated poly (ethylene glycol)-coated (PEGylated) gold nanorods (GNR) to tumor-bearing mice, accumulation of GNR in the tumor was clearly detected by the DR profile of the tumor. The ability of DR measurements to quantitate in-vivo the concentration of the GNR in the tumor was demonstrated and validated with Flame Atomic Absorption spectroscopy results. With GNR as absorbing contrast agents, DR has important potential applications in the image guided therapy of superficial tumors such as head and neck cancer, breast cancer and melanoma.
Rearrangement and Expression of Immunoglobulin Light Chain Genes Can Precede Heavy Chain Expression during Normal B Cell Development in Mice (1999)

In mouse mutants incapable of expressing mu chains, VkappaJkappa joints are detected in the CD43(+) B cell progenitors. In agreement with these earlier results, we show by a molecular single cell analysis that 4-7% of CD43(+) B cell progenitors in wild-type mice rearrange immunoglobulin (Ig)kappa genes before the assembly of a productive VHDHJH joint. Thus, mu chain expression is not a prerequisite to Igkappa light chain gene rearrangements in normal development. Overall, approximately 15% of the total CD43(+) B cell progenitor population carry Igkappa gene rearrangements in wild-type mice. Together with the results obtained in the mouse mutants, these data fit a model in which CD43(+) progenitors rearrange IgH and Igkappa loci independently, with a seven times higher frequency in the former. In addition, we show that in B cell progenitors VkappaJkappa joining rapidly initiates kappa chain expression, irrespective of the presence of a mu chain.
Stability of RNA in developing Xenopus embryos and identification of a destabilizing sequence in TFIIIA messenger RNA (1988)

Synthetic capped RNA transcripts injected into fertilized eggs of Xenopus laevis have a half-life of 3-4 h. Addition of a long (approximately 200 nucleotide) poly(A) tail increases the half-life to 6-8 h which approaches the half-life of natural polyadenylated globin RNA injected into embryos. Since exonucleolytic action alone could account for the degradation of RNA, we tested whether circular RNA is stable after injection and find that circles are exceptionally stable (half-life greater than 40 h). After the midblastula transition, polyadenylated chloramphenicol transferase (CAT) mRNAs transcribed from injected plasmids have a half-life of 2.5 h. Insertion of a 1000 nucleotide 3' untranslated region from the Xhox-36 gene into the transcripts does not affect the half-life. In contrast to the finding that internal sequences do not affect stability, we find that sequences from the TFIIIA message reduce the half-life of CAT mRNA from 2.5 h to less than 30 min. We conclude that most RNAs are degraded exonucleolytically from the 3' end, but specialized internal sequences can greatly destabilize the RNA, possibly by acting as a site for an endonuclease.
Recognition by CD8 on cytotoxic T lymphocytes is ablated by several substitutions in the class I alpha 3 domain: CD8 and the T-cell receptor recognize the same class I molecule. (1990)

The CD8 molecule on class I-reactive cytotoxic T lymphocytes (CTLs) is believed to function as a coreceptor along with the alpha beta T-cell receptor. Whereas the alpha beta T-cell receptor recognizes polymorphic residues in the alpha 1/alpha 2 domains of the class I molecule, the CD8 molecule is believed to recognize monomorphic class I residues. Our previous experiments suggested that residue 227 in the alpha 3 domain of major histocompatibility complex class I molecules contributes to the determinant recognized by CD8. By using a panel of site-directed mutants of H-2Dd, this observation has been extended herein. Our findings indicate that for recognition by CD8-dependent CTLs, residue 227 must be either glutamic acid or aspartic acid and cannot be either basic or uncharged. However, the recognition by CD8-independent CTLs is unaffected by any of the substitutions at position 227 of H-2Dd. Similarly, alterations of other charged residues at positions 222, 223, and 229 have an analogous effect to substitution at residue 227, whereas substitutions at residues 192 and 232 do not affect the reactivity of CD8-dependent or CD8-independent CTLs. In addition, mutant H-2Dd molecules that are not recognized by CD8-dependent CTLs are unable to stimulate a primary CTL response, yet they can stimulate a secondary CD8-independent H-2Dd-specific CTL response. These findings suggest that CD8 recognition is obligatory for the priming of class I-dependent CTL responses. Since endogenous class I molecules were expressed by all of the transfected cell lines, these findings provide direct genetic evidence that CD8 and the alpha beta T-cell receptor must interact with the same class I molecule.
Silver Nanowire/Optical Adhesive Coatings as Transparent Electrodes for Flexible Electronics (2013)

We present new flexible, transparent, and conductive coatings composed of an annealed silver nanowire network embedded in a polyurethane optical adhesive. These coatings can be applied to rigid glass substrates as well as to flexible polyethylene terephthalate (PET) plastic and elastomeric polydimethylsiloxane (PDMS) substrates to produce highly flexible transparent conductive electrodes. The coatings are as conductive and transparent as indium tin oxide (ITO) films on glass, but they remain conductive at high bending strains and are more durable to marring and scratching than ITO. Coatings on PDMS withstand up to 76% tensile strain and 250 bending cycles of 15% strain with a negligible increase in electrical resistance. Since the silver nanowire network is embedded at the surface of the optical adhesive, these coatings also provide a smooth surface (root mean squared surface roughness<10 nm), making them suitable as transparent conducting electrodes in flexible light-emitting electrochemical cells. These devices continue to emit light even while being bent to radii as low as 1.5 mm and perform as well as unstrained devices after 20 bending cycles of 25% tensile strain.
The Dolastatins, A Family of Promising Antineoplastic Agents (1999)

The dolastatins and some related compounds are antineoplastic pseudopeptides isolated from the sea hare Dolabella auricularia by the groups of G. R. Pettit and K. Yamada. Several groups including ours have contributed to the development of synthetic routes to most of these compounds. We recently described the synthesis of dolatrienoic acid, the lipidic component of dolastatin 14. Among all these metabolites, dolastatin 10 and dolastatin 15 exhibit the most promising antiproliferative properties and are currently under evaluation in clinical trials. These antimitotic agents seem to exert their activity by interacting with tubulin and inducing apoptosis. Research in this domain could greatly benefit from the recent elucidation of the atomic structure of tubulin. However, other targets cannot be excluded. Elucidation of the structure-activity relationships is an important step in the development of therapeutic agents. Parallel to the studies developed by other groups, our approach to exploring structural requirements for the antineoplastic activity of these compounds involved the determination of their preferred conformations in solution. Our study showed that dolastatin 10 exists in two different conformations corresponding to a cis-trans isomerization of a central amide bond. Such a situation was not demonstrated in the case of dolastatin 15. In view of elucidating the biological relevance of these findings, we elaborated hybrid molecules constituted of parts of both compounds. We also synthesized a cyclic analogue of dolastatin 10 which locked this compound in its cis conformation. Our results as well as those of others could be interpreted in terms of an existing structural model.
Biochemical nomenclature and related documents : a compendium (1992)

The nomenclature of - stereochemistry natural products and related compounds isotopically modified compounds thermodynamic and related data bibliographic references amino acids and peptides synthetic polypeptides conformation of polypeptide chains peptide hormones glycoproteins, glycopeptides and peptidoglycans initiation, elongation and termination factors in eukaryotes multiple forms of enzymes enzyme kinetics multienzymes nucleic acids and polynucleotides conformation of polynucleotides conformation of polynucleotide chains incompletely specified bases in nucleic acid sequences carbohydrates cyclitols numbering of atoms in myo-inositol five-and six-membered forms of monosaccharides unsaturated monosaccharides branched-chain monosaccharides abbreviated terminology of oligosaccharide chains polysaccharides conformation of polysaccharides lipids steroids quinones with isoprenoid side chains carotenoids tocopherols vitamin D retinoids prenols phosphorus-containing compounds folic acids vitamins B-6 corrinoids tetrapyrroles excerpts from the newsletters of the nomenclature committees list of other documents of biochemical nomenclature and of interest to authors and editors.
Basal ganglia and thalamo-cortical hypermetabolism in patients with spasmodic torticollis (1996)

The results support the hypothesis that a dysfunction of a subcortical-cortical motor network may play a role in the pathogenesis of focal dystonia, in agreement with the experimental dystonia models.
Pluripotent cells (stem cells) and their determination and differentiation in early vertebrate embryogenesis† (2001)

Mammalian embryonic stem cells can be obtained from the inner cell mass of blastocysts or from primordial germ cells. These stem cells are pluripotent and can develop into all three germ cell layers of the embryo. Somatic mammalian stem cells, derived from adult or fetal tissues, are more restricted in their developmental potency. Amphibian ectodermal and endodermal cells lose their pluripotency at the early gastrula stage. The dorsal mesoderm of the marginal zone is determined before the mid-blastula transition by factors located after cortical rotation in the marginal zone, without induction by the endoderm. Secreted maternal factors (BMP, FGF and activins), maternal receptors and maternal nuclear factors (beta-catenin, Smad and Fast proteins), which form multiprotein transcriptional complexes, act together to initiate pattern formation. Following mid-blastula transition in Xenopus laevis (Daudin) embryos, secreted nodal-related (Xnr) factors become important for endoderm and mesoderm differentiation to maintain and enhance mesoderm induction. Endoderm can be induced by high concentrations of activin (vegetalizing factor) or nodal-related factors, especially Xnr5 and Xnr6, which depend on Wnt/beta-catenin signaling and on VegT, a vegetal maternal transcription factor. Together, these and other factors regulate the equilibrium between endoderm and mesoderm development. Many genes are activated and/or repressed by more than one signaling pathway and by regulatory loops to refine the tuning of gene expression. The nodal related factors, BMP, activins and Vg1 belong to the TGF-beta superfamily. The homeogenetic neural induction by the neural plate probably reinforces neural induction and differentiation. Medical and ethical problems of future stem cell therapy are briefly discussed.
Anti VLA-4 monoclonal antibody inhibits eosinophil infiltration in allergic conjunctivitis model of guinea pig (1999)

VLA-4 molecule was elucidated to play a critical roll in the eosinophil infiltration in experimentally-induced allergic conjunctivitis model of guinea pig.