gebhart/patrepeval huggingface dataset:
Mouse monoclonal antibodies against human cancer cell lines with specificities for blood group and related antigens. Characterization by antibody binding to glycosphingolipids in a chromatogram binding assay. (1983)

Solid phase radioimmunoassay and a chromatogram binding assay were used to characterize the binding specificities of five monoclonal antibodies generated from mice immunized with human tumor cell lines when tested against various glycolipids. Four antibodies derived from mice immunized with pancreatic carcinoma cells detected specifically the human blood group B determinant, Gal alpha 1 leads to 3Gal (2 comes from 1 alpha Fuc). These antibodies preferred type 2 (Gal beta 1 leads to 4GlcNAc) glycolipids. No reactivity was detected with a rat B determinant based on GalNAc. An antibody derived following immunization with a rectal carcinoma cell line was shown to have binding properties identical with those of an antibody that reacts specifically with the stage-specific embryonic mouse antigen (SSEA-1), bearing the determinant Gal beta 1 leads to 4GlcNAc (3 comes from 1 alpha Fuc) (Gooi, H. C., Feizi, T., Kapadia, A., Knowles, B. B., Solter, D., and Evans, M. J. (1981) Nature 292, 156-158). Thin layer chromatography was used to detect the binding of a monoclonal anti-tumor antibody recently shown to react with a sialylated Lea glycolipid (Magnani, J. L., Nilsson, B., Brockhaus, M., Zopf, D., Steplewski, Z., Koprowski, H., and Ginsburg, V. (1982) Fed. Proc 41, 898) and an anti-Leb antibody (Brockhaus, M., Magnani, J. L., Blaszczyk, M., Steplewski, Z., Koprowski, H., Karlsson, K.-A., Larson, G., and Ginsburg, V. (1981) J. Biol. Chem. 256, 13223-13225) to mixtures of glycolipids from normal and tumor tissues.
Reactions of 4-Amino-4,5-Dihydro-1H-1,2,4-Triazol-5-ones and 4-Amino-4H-1,2,4-Triazoles with Some Carboxylic Acid Anhydrides (1998)

3-Alkyl(Aryl)-4-tetrachlorophthalimido-4,5-dihydro-1H-1,2,4-triazol-5-ones (2) and 3-alkyl(aryl)-4-(1,8-naphthalimido)-4,5-dihydro-1H-1,2,4-triazol-5-ones (3) were synthesized from the reactions of 3-alkyl(aryl)-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-ones (1) with tetrachlorophthalic anhydride and 1,8-naphthalic anhydride, respectively. In addition, the reactions of 4-amino-4H-1,2,4-triazoles (4) with succinic anhydride and phthalic anhydride were studied.
Contribution of monosaccharide residues in heparin binding to antithrombin III (1985)

The importance of 3-O- and 6-O-sulfated glucosamine residues within the heparin octasaccharide iduronic acid(1)----N-acetylglucosamine 6-O-sulfate(2)----glucuronic acid(3)----N-sulfated glucosamine 3,6-di-O-sulfate(4)----iduronic acid 2-O-sulfate(5)----N-sulfated glucosamine 6-O-sulfate(6)----iduronic acid 2-O-sulfate(7)----anhydromannitol 6-O-sulfate(8) was determined by comparing with synthetic tetra- and penta-saccharides its ability to bind human antithrombin. The octasaccharide had an affinity for antithrombin of 1 X 10(-8) M (10.2 kcal/mol) measured by intrinsic fluorescence enhancement at 6 degrees C. The synthetic pentasaccharide, consisting of residues 2-6, had an affinity of 3 X 10(-8) M (9.6 kcal/mol). The same pentasaccharide, except lacking the 3-O-sulfate on residue 4, had an affinity of 5 X 10(-4) M (4.5 kcal/mol) measured by equilibrium dialysis. The tetrasaccharide, consisting of residues 2-5, bound antithrombin with an affinity of 5 X 10(-6) M (6.8 kcal/mol). The tetrasaccharide, consisting of residues 3-6, had an affinity of 5 X 10(-5) M (5.5 kcal/mol). Since the loss of either the 6-O-sulfated residue 2 or the 3-O-sulfate of residue 4 results in a 4-5 kcal/mol or a 40-50% loss in binding energy of the pentasaccharide, these two residues must be the major contributors to the binding and must be linked to the biologic activity of the octasaccharide.
An Arabidopsis Mutant Defective in the General Phenylpropanoid Pathway (1992)

Clint C. S. Chapple, Thomas Vogt, Brian E. Ellis, Chris R. Somerville, An Arabidopsis Mutant Defective in the General Phenylpropanoid Pathway, The Plant Cell, Vol. 4, No. 11 (Nov., 1992), pp. 1413-1424
Influence of Amplitude and Starting Point on Accommodative Dynamics in Humans (2005)

The dynamics of accommodation and disaccommodation are strongly influenced by the starting point, but less so by amplitude.
Cultivation of mammalian cells as aggregates in bioreactors: Effect of calcium concentration of spatial distribution of viability (1993)

Recombinant human kidney epithelial 293 cells were cultivated as aggregates in suspension. The concentration calcium ion, in the range of 100 muM to 1mM, affected the rate of aggregate formation. During the course of cultivation the size distribution of aggregates shifted and the fraction of larger aggregates increased. This effect was more profound in cultures with a high calcium concentration. Scanning and transmission microscopic examination of the aggregates revealed that cell packing was greater in the high calcium cultures and that ultrastructural integrity was retained in aggregates from both low and high calcium cultures. Confocal microscopy was applied to examine the viability of cells in the interior of the aggregates. High viability was observed in the aggregates obtained from exponentially growing cultures. Aggregates from the high calcium culture in the stationary phase exhibited lower viability in the interior. With its ease of retention in a perfusion bioreactor, aggregate cultures offer an alternative choice for large-scale operation.
Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization (2003)

Myosin V is a dimeric molecular motor that moves processively on actin, with the center of mass moving approximately 37 nanometers for each adenosine triphosphate hydrolyzed. We have labeled myosin V with a single fluorophore at different positions in the light-chain domain and measured the step size with a standard deviation of <1.5 nanometers, with 0.5-second temporal resolution, and observation times of minutes. The step size alternates between 37 + 2x nm and 37 - 2x, where x is the distance along the direction of motion between the dye and the midpoint between the two heads. These results strongly support a hand-over-hand model of motility, not an inchworm model.
Identification, Characterization and Application of a G-Quadruplex Structured DNA Aptamer against Cancer Biomarker Protein Anterior Gradient Homolog 2 (2012)

In this work, we have developed new aptamer probes for specific recognition of the AGR2. Structural study have identified that the binding motif of aptamer is an intramolecular parallel G-quadruplex structure and its structure and binding affinity are strongly dependent on the nature of the monovalent ion. Furthermore, with our design of AGR2-aMB, AGR2 could be sensitively and selectively detected. This aptamer probe has great potential to serve as a useful tool for early diagnosis and prognosis of cancer and for fundamental research to elucidate the biochemical functions of AGR2.
HUMAN IMMUNITY TO THE MENINGOCOCCUS (1969)

High molecular weight group A and group C meningococcal polysaccharides had no significant toxicity for mice or guinea pigs. Furthermore, these polysaccharide preparations contained negligible amounts of biologically active endotoxin. The high molecular weight group A and group C meningococcal polysaccharides were excellent immunogens in six human volunteers. Antibodies belonging to the immunoglobulin classes IgG, IgM, and IgA were produced. These antibodies were highly meningococcocidal in the presence of complement.
A soluble form of the receptor for advanced glycation endproducts (RAGE) is produced by proteolytic cleavage of the membrane‐bound form by the sheddase a disintegrin and metalloprotease 10 (ADAM10) (2008)

The receptor for advanced glycation endproducts (RAGE) mediates responses to cell danger and stress. When bound by its many ligands (which include advanced glycation endproducts, certain members of the S100/calgranulin family, extracellular high-mobility group box 1, the integrin Mac-1, amyloid beta-peptide and fibrils), RAGE activates programs responsible for acute and chronic inflammation. RAGE is therefore also involved in cancer progression, diabetes, atherosclerosis, and Alzheimer's disease. RAGE has several isoforms deriving from alternative splicing, including a soluble form called endogenous secretory RAGE (esRAGE). We show here that most soluble RAGE, either produced by cell lines or present in human blood, is not recognized by an anti-esRAGE antibody. Cells transfected with the cDNA for full-length RAGE, and thus not expressing esRAGE, produce a form of soluble RAGE, cleaved RAGE (cRAGE) that derives from proteolytic cleavage of the membrane-bound molecules and acts as a decoy receptor. By screening chemical inhibitors and genetically modified mouse embryonic fibroblasts (MEFs), we identify the sheddase ADAM10 as a membrane protease responsible for RAGE cleavage. Binding of its ligand HMGB1 promotes RAGE shedding. Our data do not disprove the interpretation that high levels of soluble forms of RAGE protect against chronic inflammation, but rather suggest that they correlate with high levels of ongoing inflammation.
Comparison between 1-deoxynojirimycin and N-methyl-1-deoxynojirimycin as inhibitors of oligosaccharide processing in intestinal epithelial cells (1985)

The alpha-glucosidase inhibitor N-methyl-1-deoxynojirimycin (MDJN) inhibits the synthesis of N-linked complex oligosaccharides in rat intestinal epithelial cells to the same extent as reported previously for 1-deoxynojirimycin (DJN) [Saunier, Kilker, Tkacz, Quaroni & Herscovics (1982) J. Biol. Chem. 257, 14155-14161]. Analysis of each of the endo-beta-N-acetylglucosaminidase H (endo H)-sensitive oligosaccharides separated by h.p.l.c. with yeast glucosidase I, which specifically removes the terminal glucose residue from oligosaccharides containing three glucose residues, and with jack-bean (Canavalia ensiformis) alpha-mannosidase, indicates that both inhibitors cause the accumulation of a mixture of glucosylated oligosaccharides containing one to three glucose residues and seven to nine, and even possibly six, mannose residues. About 70% of the endo H-sensitive oligosaccharides formed in the presence of MDJN contain three glucose residues, compared with only about 20% of the corresponding oligosaccharides of the DJN treated cells. It is concluded that both compounds inhibit the formation of N-linked complex oligosaccharides by interfering with the processing glucosidases. These compounds are valuable in the study of the role of oligosaccharides in glycoproteins.
Neutrophil Elastase Activity Is Associated with Exacerbations and Lung Function Decline in Bronchiectasis (2017)

Sputum neutrophil elastase activity is a biomarker of disease severity and future risk in adults with bronchiectasis.
Misfit Dislocation Nucleation Study in p/p[sup +] Silicon (2001)

Different edge treatments were used during the processing of 150 mm diameter highly boron-doped silicon substrate wafers to create a variation of crystallographic damage around the wafer edges. We studied the wafer edge as misfit dislocation generation sites in epitaxial silicon wafers. These strain-relaxing defects nucleate heterogeneously at the lattice-mismatched interface. We examined the effect of a variation of wafer edge treatments on misfit dislocation formation in silicon test wafers. We determined that a lower microroughness of the wafer edge results in a decrease in the misfit dislocation density and length. We were able to show that a careful combination of edge treatments including damage removal steps helps significantly reduce misfit dislocations in strained layer epitaxy. © 2001 The Electrochemical Society. All rights reserved.
Four dark corners of requirements engineering (1997)

Research in requirements engineering has produced an extensive body of knowledge, but there are four areas in which the foundation of the discipline seems weak or obscure. This article shines some light in the “four dark corners,” exposing problems and proposing solutions. We show that all descriptions involved in requirements engineering should be descriptions of the environment. We show that certain control information is necessary for sound requirements engineering, and we explain the close association between domain knowledge and refinement of requirements. Together these conclusions explain the precise nature of requirements, specifications, and domain knowledge, as well as the precise nature of the relationships among them. They establish minimum standards for what information should be represented in a requirements language. They also make it possible to determine exactly what it means for requirements and engineering to be successfully completed.
The ICL1 gene of Pichia pastoris, transcriptional regulation and use of its promoter (2003)

We cloned and characterized a gene encoding isocitrate lyase from the methylotrophic yeast Pichia pastoris. This gene was isolated from a P. pastoris genomic library using a homologous PCR hybridization probe, amplified with two sets of degenerate primers designed from conserved regions in yeast isocitrate lyases. The cloned gene was sequenced and consists of an open reading frame of 1563 bp encoding a protein of 551 amino acids. The molecular mass of the protein is calculated to be 60.6 kDa with high sequence similarity to isocitrate lyase from other organisms. There is a 64% identity between amino acid sequences of P. pastoris Icl and Saccharomyces cerevisiae Icl. Northern blot analyses showed that, as in S. cerevisiae, the steady-state ICL1 mRNA levels depend on the carbon source used for cell growth. Expression in P. pastoris of the dextranase gene (dexA) from Penicillium minioluteum under control of the ICL1 promoter proved that P(ICL1) is a good alternative for the expression of heterologous proteins in this methylotrophic yeast. The sequence presented here has been deposited in the EMBL data library under Accession No. AJ272040.
On the Spreading of Liquids on Solid Surfaces: Static and Dynamic Contact Lines (1979)

The field of fluid mechanics is rapidly advancing, driven by unprecedented volumes of data from experiments, field measurements, and large-scale simulations at multiple spatiotemporal scales. Machine learning (ML) offers a wealth of techniques to extract ...Read More
Information retrieval on the World Wide Web (1997)

Effective search and retrieval are enabling technologies for realizing the full potential of the Web. The authors examine relevant issues, including methods for representing document content. They also compare available search tools and suggest methods for improving retrieval effectiveness.
Music Database Retrieval Based on Spectral Similarity (2001)

We present an efficient algorithm to retrieve similar music pieces from an audio database. The algorithm tries to capture the intuitive notion of similarity perceived by human: two pieces are similar if they are fully or partially based on the same score, even if they are performed by different people or at different speed. Each audio file is preprocessed to identify local peaks in signal power. A spectral vector is extracted near each peak, and a list of such spectral vectors forms our intermediate representation of a music piece. A database of such intermediate representations is constructed, and two pieces are matched against each other based on a specially-defined distance function. Matching results are then filtered according to some linearity criteria to select the best result to a user query. 1
Human erythrocytes as nanoparticle carriers for magnetic particle imaging (2010)

The potential of red blood cells (RBCs) loaded with iron oxide nanoparticles as a tracer material for magnetic particle imaging (MPI) has been investigated. MPI is an emerging, quantitative medical imaging modality which holds promise in terms of sensitivity in combination with spatial and temporal resolution. Steady-state and dynamic magnetization measurements, supported by semi-empirical modeling, were employed to analyze the MPI signal generation using RBCs as novel biomimetic constructs. Since the superparamagnetic iron oxide (SPIO) bulk material that is used in this study contains nanoparticles with different sizes, it is suggested that during the RBC loading procedure, a preferential entrapment of nanoparticles with hydrodynamic diameter ≤60 nm occurs by size-selection through the erythrocyte membrane pores. This affects the MPI signal of an erythrocyte-based tracer, compared to bulk. The reduced signal is counterbalanced by a higher in vivo stability of the SPIO-loaded RBCs constructs for MPI applications.
NMR Study on the Aggregation Behavior of the Therapeutic Peptide Carbetocin (2018)

Carbetocin is an uncharged cyclic therapeutic peptide with a tendency to aggregate in solution. Aggregation is undesirable since it, for example, can lead to loss of pharmaceutical effects. To gain a better understanding of peptide aggregation, along with a potential to develop better drug formulations, aggregation of carbetocin was studied. In focus were soluble aggregates in contrast to phase-separated aggregates. The behavior of these soluble aggregates was studied with NMR spectroscopy. NMR diffusometry and 1 H NMR spectroscopy were used as the main analytic methods. Aqueous solutions of carbetocin at different concentrations alone, and with added sodium dodecyl sulfate (SDS) and pentaethylene glycol monododecyl ether (C12E5) were analyzed using these methods. The peptide has an increased self-aggregation in solution at higher peptide concentrations, with a distinct increase in aggregation at around 15-20 mM carbetocin. Hydrophobic interactions and hydrogen bonding are suggested to be the major attractive forces in the aggregation mechanism based on that the chemical shifts of hydrophobic and hydrogen-bonding sites in carbetocin show significant changes at higher peptide concentrations. Surfactants significantly affect the aggregation behavior of carbetocin and co-aggregates are formed. To fully understand the aggregation behavior of carbetocin and other peptides, more research has to be conducted.
Vancomycin-Resistant Enterococcus faecium Bacteremia: Risk Factors for Infection (1995)

We describe an outbreak of vancomycin-resistant Enterococcus faecium (vanA phenotype) bacteremia on the oncology ward of a tertiary care community hospital. In 10 of the 11 cases the patients had leukemia and were neutropenic (median duration of neutropenia, 21 days) at the time of bacteremia. On average, patients received six antibiotic agents for a total of 61 agent-days prior to development of vancomycin-resistant E. faecium bacteremia. The mortality rate was 73%. Molecular typing of 22 isolates revealed that the majority (83%) represented a common strain, indicating nosocomial spread. When the 11 cases were compared to 22 matched control patients, gastrointestinal colonization with vancomycin-resistant E. faecium (odds ratio [denominator, 0] infinity, P = .005) and the use of antimicrobial agents with significant activity against anaerobes (metronidazole, clindamycin, and imipenem; odds ratio infinity, P = .02) were found to be risk factors for the development of vancomycin-resistant E. faecium bacteremia. Since no proven therapy for such infection exists, there is an urgent need to identify effective measures to prevent and control the development of vancomycin-resistant E. faecium bacteremia.
The Automation of Small Television Stations (1971)

The introduction of automation into television station operations offers advantages in staff utilization and data handling that have become more apparent as equipment has become more sophisticated. To take maximum advantage requires that station design and operation be adapted to the requirements of automation. The problems that arise in an average existing station where this ideal situation does not exist are outlined, together with an estimate of the probable future development of automation systems.
Factors affecting the antigen-antibody reaction. (2007)

The antigen-antibody reaction is widely used in laboratory diagnostics, including immunohaematology. It is a reversible chemical reaction:


antigen+antibody⇄antigen-antibody complex

(1)


The forces joining the antigen-antibody complex are not strong covalent bonds but weaker bonds, appropriately named “weak interactions”1.
Requirement of SH2-containing Protein Tyrosine Phosphatases SHP-1 and SHP-2 for Paired Immunoglobulin-like Receptor B (PIR-B)–mediated Inhibitory Signal (1998)

Paired immunoglobulin-like receptor B (PIR-B) (p91) molecule has been proposed to function as an inhibitory receptor in B cells and myeloid lineage cells. We demonstrate here that the cytoplasmic region of PIR-B is capable of inhibiting B cell activation. Mutational analysis of five cytoplasmic tyrosines indicate that tyrosine 771 in the motif VxYxxL plays the most crucial role in mediating the inhibitory signal. PIR-B-mediated inhibition was markedly reduced in the SH2-containing protein tyrosine phosphatases SHP-1 and SHP-2 double-deficient DT40 B cells, whereas this inhibition was unaffected in the inositol polyphosphate 5'-phosphatase SHIP-deficient cells. These data demonstrate that PIR-B can negatively regulate B cell receptor activation and that this PIR-B-mediated inhibition requires redundant functions of SHP-1 and SHP-2.
Activated microglia in the human glaucomatous optic nerve head (2001)

To investigate the distribution and potential participation of microglia, the resident defense cells of the central nervous system, in the optic nerve head (ONH) in glaucoma, histological paraffin sections of optic nerves from normal and glaucoma patients with mild to advanced nerve damage were studied using double labeling immunohistofluorescence. A monoclonal antibody for HLA-DR, indicating activated microglia, was colocalized with antibodies for functional proteins. In normal ONHs, microglia do not contain TGF-beta2, COX-2, or TNF-alpha and are not positive for PCNA; however, in glaucomatous ONHs, microglia contain abundant TGF-beta2, TNF-alpha, and PCNA. In glaucomatous eyes, a few microglia are usually positive for COX-2. In normal ONHs, there are rarely microglia containing TGF-beta1, NOS-2, TSP, TIMP-2, and CD68, but, in glaucomatous tissue, a few microglia are positive from the prelaminar to the postlaminar regions. MMP-1, MMP-2, MMP-3, and MMP-14 are constitutively present in the perivascular microglia in normal ONHs and appear to be more abundant in glaucomatous tissue. COX-1, TNF-R1, TIMP-1, and c-fms are constitutively present in normal tissues and appear to be increased in microglia in the glaucomatous ONHs. HSP27 is not present in microglia. In glaucomatous ONHs, microglia become activated and phagocytic and produce cytokines, mediators, and enzymes that can alter the extracellular matrix. Our findings suggest that activated microglia may participate in stabilizing the tissue early in the disease process, but, as the severity of the glaucomatous damage increases, the activities of microglia may have detrimental consequences for the pathological course of glaucomatous optic neuropathy.