gebhart/patrepeval huggingface dataset:
The antigen-binding domain of a human IgG-anti-F(ab′)2 autoantibody (1997)

Recent studies revealed an immunoregulatory role of natural IgG-anti-F(ab')2 antibodies in both healthy individuals and patients with certain diseases. The implication of anti-F(ab')2 antibodies in the pathogenesis of diseases prompted us to study the gene segment structure of their antigen-binding domains and their binding characteristics. cDNA was prepared from the lymphocytes of a patient with a high IgG-anti-F(ab')2 serum titer. Variable heavy and light gene segments were amplified by PCR and inserted into a phagemid surface expression vector. Single-chain antibodies displayed on the phage surface were screened for binding to F(ab')2 fragments. The subsequent analysis of 95 single clones demonstrated that they all bound specifically to F(ab')2. Sequence analyses of 12 clones showed that 11 were identical and 1 contained a silent point mutation in the heavy chain and three amino acid exchanges in the light chain. The heavy chains belonged to the V(H)3 and the light chains to the V(kappa)2 gene family. The 11 identical light-chain genes were completely homologous to a germ-line sequence (DPK-15). Binding assays showed that the single-chain antibodies bind to F(ab')2, but not to Fab, Fc, or intact IgG. This binding pattern was confirmed by surface plasmon resonance studies, which revealed a relatively high affinity (Ka = 2.8 x 10(7) M(-1)). The strong binding capacity was further demonstrated by competitive inhibition of the serum anti-IgG antibody's interaction with antigen. The present study defines for the first time to our knowledge the gene segment structure of the antigen-binding domain of two human IgG-anti-F(ab')2 autoantibody clones and describes the binding kinetics of the purified monomeric fragments.
IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics (2008)

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION', 'NUMEROTATION', 'LOCALIZATION', 'ORIENTATION' and 'OBTENTION', that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. These axioms have been essential for the conceptualization of the molecular immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGY represents a paradigm for the elaboration of ontologies in system biology.
Protein Analysis by Hydrogen Exchange Mass Spectrometry (2003)

Mass spectrometry has provided a powerful method for monitoring hydrogen exchange of protein backbone amides with deuterium from solvent. In comparison to popular NMR approaches, mass spectrometry has the advantages of higher sensitivity, wider coverage of sequence, and the ability to analyze larger proteins. Proteolytic fragmentation of proteins following the exchange reaction provides moderate structural resolution, in some cases enabling measurements from single amides. The technique has provided new insight into protein-protein and protein-ligand interfaces, as well as conformational changes during protein folding or denaturation. In addition, recent studies illustrate the utility of hydrogen exchange mass spectrometry toward detecting protein motions relevant to allostery, covalent modifications, and enzyme function.
Quantitative pulsed CEST‐MRI using Ω‐plots (2015)

Chemical exchange saturation transfer (CEST) allows the indirect detection of dilute metabolites in living tissue via MRI of the tissue water signal. Selective radio frequency (RF) with amplitude B1 is used to saturate the magnetization of protons of exchanging groups, which transfer the saturation to the abundant water pool. In a clinical setup, the saturation scheme is limited to a series of short pulses to follow regulation of the specific absorption rate (SAR). Pulsed saturation is difficult to describe theoretically, thus rendering quantitative CEST a challenging task. In this study, we propose a new analytical treatment of pulsed CEST by extending a former interleaved saturation-relaxation approach. Analytical integration of the continuous wave (cw) eigenvalue as a function of the RF pulse shape leads to a formula for pulsed CEST that has the same structure as that for cw CEST, but incorporates two form factors that are determined by the pulse shape. This enables analytical Z-spectrum calculations and permits deeper insight into pulsed CEST. Furthermore, it extends Dixon's Ω-plot method to the case of pulsed saturation, yielding separately, and independently, the exchange rate and the relative proton concentration. Consequently, knowledge of the form factors allows a direct comparison of the effect of the strength and B1 dispersion of pulsed CEST experiments with the ideal case of cw saturation. The extended pulsed CEST quantification approach was verified using creatine phantoms measured on a 7 T whole-body MR tomograph, and its range of validity was assessed by simulations.
Electrophysiological basis for antiarrhythmic drug action. (1985)

Arrhythmias result from abnormalities of impulse initiation or impulse conduction or a combination of both. Abnormal impulse initiation results from either automaticity or triggered activity. Automaticity can further be subdivided into (1) automaticity caused by the normal automatic mechanism (a normal property of cardiac cells in the sinus node, in some parts of the atria, in the atrioventricular junctional region, and in the His-Purkinje system) and (2) automaticity caused by an abnormal mechanism (resulting from a decrease in membrane potential of cardiac fibers, which normally have a high level of membrane potential). Triggered activity is caused by afterdepolarizations, which are second depolarizations that occur either during repolarization (referred to as early afterdepolarizations) or after repolarization is complete or nearly complete (referred to as delayed afterdepolarizations). Abnormal impulse conduction results in reentrant excitation. Usually a combination of slowed conduction and unidirectional conduction block provides the conditions necessary for reentry to occur.
Improved hemostasis with superactive analogs of factor VIIa in a mouse model of hemophilia A (2003)

It is currently debated whether the mechanism of action of therapeutic doses of recombinant factor VIIa (rFVIIa, Novo-Seven) relies on the tissue factor (TF)-independent activity of the enzyme. The present study was conducted to investigate the in vivo hemostatic effects of rFVIIa and 3 analogs thereof with superior intrinsic activity (FVIIaIIa, K337A-FVIIaIia, and M298Q-FVIIa) in mice with antibody-induced hemophilia A. A highly significant dose response was observed for the bleeding time and blood loss for each of the rFVIIa variants. The bleeding time and blood loss were normalized after administration of 10 mg/kg rFVIIa, 3 mg/kg K337A-FVIIaIia, and 3 mg/kg M298Q-FVIIa, indicating a potency of these FVIIa analogs 3-4 times above that of rFVIIa in FVIII-depleted mice. The different in vivo potencies of the various forms of FVIIa could not be explained by the pharmacokinetics. Histopathological evaluation of kidneys revealed no signs of treatment-related pathological changes even after treatment with the superactive variants. The fact that FVIIa analogs with enhanced intrinsic activity are more efficacious in the murine hemophilia A model strongly suggests that the TF-independent procoagulant activity of FVIIa contributes to its clinical hemostatic effect.
BBN PLUM (1992)

Our mid-term to long-term goals in data extraction from text for the next one to three years are to achieve much greater portability to new languages and new domains, greater robustness, and greater scalability. The novel aspect to our approach is the use of learning algorithms and probabilistic models to learn the domain-specific and language-specific knowledge necessary for a new domain and new language. Learning algorithms should contribute to scalability by making it feasible to deal with domains where it would be infeasible to invest sufficient human effort to bring a system up. Probabilistic models can contribute to robustness by allowing for words, constructions, and forms not anticipated ahead of time and by looking for the most likely interpretation in context.
Guidelines for the diagnosis and monitoring of paroxysmal nocturnal hemoglobinuria and related disorders by flow cytometry (2010)

This document should both enable laboratories interested in beginning PNH testing to establish a valid procedure and allow experienced laboratories to improve their techniques.
Methylation-silencing RCC1 expression is associated with tumorigenesis and depth of invasion in gastric cancer. (2015)

Our data indicate that RCC1 expression is frequently lost in poorly differentiated gastric cell lines and gastric carcinoma tissues. Loss of RCC1 expression is correlated with tumor differentiation and depth of invasion. These findings suggest that RCC1 may play a tumor suppressor role in gastric carcinoma.
Effect of Bucindolol on Heart Failure Outcomes and Heart Rate Response in Patients with Reduced Ejection Fraction Heart Failure and Atrial Fibrillation (2012)

In HFREF patients with AF, bucindolol was associated with reductions in composite HF endpoints in those who achieved a resting heart rate ≤ 80 b.p.m. and nominally in those with the β(1)389-Arg homozygous genotype.
Purification and Sequence Analysis of Bioactive Atrial Peptides (Atriopeptins) (1984)

Mammalian cardiac atria have several biologically active peptides that exert profound effects on sodium excretion, urine volume, and smooth muscle tone. In the present study two such peptides of low molecular weight were purified and separated from each other on the basis of differences in charge, hydrophobicity, and biological profile. The first peptide, designated atriopeptin I, exhibits natriuretic and diuretic activity and selectivity relaxes intestinal smooth muscle but not vascular smooth muscle strips. The second peptide, atriopeptin II, is a potent natriuretic and diuretic that relaxes both intestinal and vascular strips. Sequence analysis of atriopeptin I indicates that it is composed of 21 amino acids, of which serine and glycine residues predominate. The amino terminal sequence of atriopeptin II up to residue 21 is the same as that of atriopeptin I, with the addition of the Phe-Arg extension at the carboxyl terminus. Both peptides appear to be derived from a common high molecular weight precursor (designated atriopeptigen); their biological selectivity and potency may be determined by the site of carboxyl terminal cleavage.
Comparison of pathogen‐induced expression and efficacy of two amphibian antimicrobial peptides, MsrA2 and temporin A, for engineering wide‐spectrum disease resistance in tobacco (2007)

The rapid accumulation of defensive transgene products in plants only on pathogen invasion has clear advantages over their constitutive synthesis. In this study, two antimicrobial peptides from the skin secretions of frogs, MsrA2 (N-methionine-dermaseptin B1) and temporin A, were evaluated for engineering pathogen-induced disease resistance in plants. Both peptides inhibited plant-specific pathogens in vitro at micromolar concentrations that were not toxic to plant protoplasts. The plant-optimized nucleotide sequences encoding MsrA2 and temporin A were transcriptionally fused to the inducible win3.12T poplar promoter, which had strong systemic activity in response to fungal infection, and introduced into tobacco (Nicotiana tabacum L. cv. Xanthi). Transgene expression was very low in the leaves of unstressed plants; however, it was strongly increased after pathogen challenge or wounding. The pathogen responsiveness of the win3.12T promoter was found to be universal rather than species specific, with high activity in response to all pathogens tested. On induction, the amount of MsrA2 was up to 6-7 microg per gram of fresh leaf tissue. Most importantly, the induced accumulation of MsrA2 and temporin A in transgenic tobacco was sufficient to confer resistance to a variety of phytopathogenic fungi, such as Fusarium solani, F. oxysporum, Alternaria alternata, Botrytis cinerea, Sclerotinia sclerotiorum, the oomycete Pythium aphanidermatum and the bacterium Pectobacterium carotovorum. The accumulation of these peptides in transgenic plants did not alter the normal phenotype of tobacco. Thus, the expression of MsrA2 and temporin A in a pathogen-inducible manner enables the development of tobacco, and possibly other plant species, with wide-spectrum disease resistance, which can reduce the use of pesticides and the associated environmental risks.
Lysyl hydroxylase 3 (LH3) modifies proteins in the extracellular space, a novel mechanism for matrix remodeling (2006)

Lysyl hydroxylase 3 (LH3), the multifunctional enzyme associated with collagen biosynthesis that possesses lysyl hydroxylase and collagen glycosyltransferase activities, has been characterized in the extracellular space in this study. Lysine modifications are known to occur in the endoplasmic reticulum (ER) prior to collagen triple-helix formation, but in this study we show that LH3 is also present and active in the extracellular space. Studies with in vitro cultured cells indicate that LH3, in addition to being an ER resident, is secreted from the cells and is found both in the medium and on the cell surface associated with collagens or other proteins with collagenous sequences. Furthermore, in vivo, LH3 is present in serum. LH3 protein levels correlate with the galactosylhydroxylysine glucosyltransferase (GGT) activity of mouse tissues. This, together with other data, indicates that LH3 is responsible for GGT activity in the tissues and that GGT activity assays can be used to quantify LH3 in tissues. LH3 in vivo is located in two compartments, in the ER and in the extracellular space, and the partitioning varies with tissue type. In mouse kidney the enzyme is located mainly intracellularly, whereas in mouse liver it is located solely in the extracellular space. The extracellular localization and the ability of LH3 to modify lysyl residues of extracellular proteins in their native, nondenaturated conformation reveals a new dynamic in extracellular matrix remodeling, suggesting a novel mechanism for adjusting the amount of hydroxylysine and hydroxylysine-linked carbohydrates in collagenous proteins.
p21 Cip1 Levels Differentially Regulate Turnover of Mature Endothelial Cells, Endothelial Progenitor Cells, and In Vivo Neovascularization (2004)

p21(Cip1) (p21) controls cell cycle progression and apoptosis in mature endothelial cells (ECs) and regulates size and cycling of the hematopoietic progenitor cell pool. Because circulating endothelial progenitor cells (EPCs) contribute to postnatal neovascularization in addition to mature ECs, we investigated the regulation of ECs and EPCs in p21-deficient mice. Mature aortic EC proliferation was increased in homozygous p21(-/-) and heterozygous p21(+/-) mice, in which p21 protein levels are reduced to one third of wild-type (WT). In contrast, apoptosis sensitivity was increased by 3.5-fold only in p21(-/-), but not in p21(+/-) mice. Consistently, in vivo apoptosis of ECs within areas of neovascularization was elevated in p21(-/-) but not in p21(+/-) mice. EPC numbers were elevated 2-fold in p21(-/-) mice compared with WT (P<0.001), and clonal expansion capacity of EPCs was increased from 25+/-4 (WT) to 57+/-8 colony-forming units in p21(-/-) mice (P<0.005). EPC numbers and expansion were likewise increased in p21(+/-) mice. As the integrative endpoint, in vivo neovascularization reflecting all p21-affected parameters was increased over WT only in p21(+/-) (P<0.001), but not in p21(-/-) mice. In conclusion, reduced p21 protein levels of mice lacking one p21 allele are associated with increased proliferation of ECs and EPCs, whereas survival of ECs to apoptotic stimuli in vitro and in vivo is not impaired. Under these conditions, neovascularization was increased. In contrast, complete p21 deficiency did not result in an increased neovascularization despite increased mature EC and EPC proliferation. This may be due to the sensitization of ECs against apoptosis.
GaInN light-emitting diode with conductive omnidirectional reflector having a low-refractive-index indium-tin oxide layer (2005)

Enhancement of light extraction in a GaInN light-emitting diode (LED) employing a conductive omnidirectional reflector (ODR) consisting of GaN, an indium-tin oxide (ITO) nanorod low-refractive-index layer, and an Ag layer is presented. An array of ITO nanorods is deposited on p-type GaN by oblique-angle electron-beam deposition. The refractive index of the nanorod ITO layer is 1.34 at 461nm, significantly lower than that of dense ITO layer, which is n=2.06. The GaInN LEDs with GaN∕low-n ITO/Ag ODR show a lower forward voltage and a 31.6% higher light-extraction efficiency than LEDs with Ag reflector. This is attributed to enhanced reflectivity of the ODR that employs the low-n ITO layer.
Nanocrystal Diffusion in a Liquid Thin Film Observed by in Situ Transmission Electron Microscopy (2009)

We have directly observed motion of inorganic nanoparticles during fluid evaporation using a transmission electron microscope. Tracking real-time diffusion of both spherical (5-15 nm) and rod-shaped (5 x 10 nm) gold nanocrystals in a thin film of water-15% glycerol reveals complex movements, such as rolling motions coupled to large-step movements and macroscopic violations of the Stokes-Einstein relation for diffusion. As drying patches form during the final stages of evaporation, particle motion is dominated by the nearby retracting liquid front.
Esterification and Alkylation Reactions Employing Isoureas (1979)

The synthetic applications of isoureas as alkylating agents are evaluated and reviewed. Esterifications employing isoureas were reported many years ago, but extended applications were inhibited by lack of isourea availability. A high-yield, mild synthesis of a major group of isoureas first appeared in 1955. This spurred numerous exploratory efforts which have extended alkylation reactions to a variety of carbon- and heteroatom-containing groups. These procedures are discussed in detail with respect to generality and selectivity. A discussion of the probable mechanism helps explain the observed selectivity and indicates potential developments of isoureas as general alkylating agents. A brief survey of the large number of available isoureas supports predictions as to their importance as reagents for analysis and organic synthesis. 1 . Introduction 2. Carboxylic Ester Formation 3. Phosphate Ester and Phenyl Ether Synthesis 4. Sulfur Alkylation 5. Nitrogen Alkylations 6. Active Carbon Alkylations 7. Isourea Rearrangements/Internal Alkylation 8.1 Mechanism of Alkylation 8.2 Heteroatom Selectivity in Alkylations 9. lsourea Availability
Nonclassical Behavior in the Capacitance of a Nanojunction (2001)

The capacitance of a nanojunction formed by a scanning tunneling microscope (STM) tip and a two-dimensional gold cluster was measured through the single electron tunneling spectroscopy of a double-barrier tunnel junction. By decreasing the STM tip-cluster separation, it was observed that the capacitance first increases and then decreases at short separation. This characteristic clearly deviates from the classical behavior and provides evidence for potential quantum effects on the capacitance.
Absence of the T‐bet Gene Coding for the Th1‐Related Transcription Factor Does Not Affect Diabetes‐Associated Phenotypes in Balb/c Mice (2003)

The T-box expressed in T cells gene (T-bet) is a member of the T-box family of transcription factors. T-bet-deficient mice show normal lymphoid development, but exhibit profound defects in their Th1-mediated immune responses. As the balance between Th1- and Th2-mediated immune responses plays a role in autoimmune-prone diseases, we have investigated the diabetes-related insulin autoantibody (IAA) and cellular immune responses (insulitis), in the absence of Th1 lineage commitment, in T-bet KO Balb/c mice, after immunization with the B9-23 insulin peptide. We have therefore investigated whether absence of the T-bet gene influences diabetes-related phenotypes in Balb/c T-bet KO mice.
Chiral-Selective Growth of Single-Walled Carbon Nanotubes on Lattice-Mismatched Epitaxial Cobalt Nanoparticles (2013)

Controlling chirality in growth of single-walled carbon nanotubes (SWNTs) is important for exploiting their practical applications. For long it has been conceptually conceived that the structural control of SWNTs is potentially achievable by fabricating nanoparticle catalysts with proper structures on crystalline substrates via epitaxial growth techniques. Here, we have accomplished epitaxial formation of monometallic Co nanoparticles with well-defined crystal structure, and its use as a catalyst in the selective growth of SWNTs. Dynamics of Co nanoparticles formation and SWNT growth inside an atomic-resolution environmental transmission electron microscope at a low CO pressure was recorded. We achieved highly preferential growth of semiconducting SWNTs (~90%) with an exceptionally large population of (6, 5) tubes (53%) in an ambient CO atmosphere. Particularly, we also demonstrated high enrichment in (7, 6) and (9, 4) at a low growth temperature. These findings open new perspectives both for structural control of SWNTs and for elucidating the growth mechanisms.
Spermine stabilization of folded ribonuclease T1. (1990)

The interaction of ribonuclease T1 with tetraprotonated spermine (SPM4+), Mg2+, phosphate and other ionic ligands at pH 6.0 was investigated in binding experiments at 25 degrees C and/or by their effects on the midpoint temperature for thermal unfolding of the enzyme. SPM4+ binding with the native protein at 25 degrees C was characterized by an association constant of approximately 2 x 10(4) M-1. This ligand also binds to the unfolded protein but with a approximately 35-fold lower affinity. Phosphate binds at the active site whereas Mg2+ and SPM4+ cations compete for binding at a polyanionic locus that probably involves residues Glu-28, Asp-29, and Glu-31 at the C-terminal end of the alpha-helix. Steady-state kinetic studies using minimal RNA substrates demonstrated that SPM4+ binding with the enzyme does not affect its catalytic activity. SPM4+ also preferentially binds with the folded form of the disulfide-reduced enzyme which has the same or slightly enhanced catalytic properties compared with native ribonuclease T1. The unfolding rate for the native protein in 8 M urea was approximately 8-fold lower in the presence of 0.05 M SPM4+. SPM4+ appears to increase the amplitude of an unobserved fast phase(s) for refolding of the native enzyme. A single kinetic phase characterized refolding of the reduced enzyme which was slightly faster than the slowest refolding phase for the native form.