gebhart/patrepeval huggingface dataset:
Ordered multisite protein phosphorylation. Analysis of glycogen synthase kinase 3 action using model peptide substrates. (1990)

Recognition of substrates by the protein kinase glycogen synthase kinase 3 (GSK-3) usually requires prior phosphorylation of the substrate. Using a peptide based on the glycogen synthase sequence PRPAS(3a)VPPS (3b)PSLS(3c)RHSS(4)PHQS(5)EDEEEP (where the numbers in parentheses denote sites of phosphorylation), we showed previously that phosphorylation of site 5 by casein kinase II was necessary for GSK-3 to phosphorylate the peptide at sites 3a, 3b, 3c, and 4 (Fiol, C. J., Mahrenholz, A. M., Wang, Y., Roeske, R. W., and Roach, P. J. (1987) J. Biol. Chem. 262, 14042-14048). In the present study, variant peptides were synthesized in which sites 3a, 3b, 3c, and 4 were individually replaced by Ala residues (denoted Ala-3c, etc.). All of the variant peptides were substrates for casein kinase II. The peptide Ala-4,Ser(P)-5 was not a substrate for GSK-3 confirming the minimal recognition sequence for the protein kinase as -SXXXS(P)-. The peptides Ala-3c,Ser(P)-5, Ala-3b,Ser(P)-5, and Ala-3a,Ser(P)-5, however, were all good substrates for GSK-3 with apparent Km values in the range 3-6 microns, comparable with that of the parent peptide. GSK-3 could introduce 1, 2, and 3 phosphates, respectively, into these substrates, always COOH-terminal to the substituted Ala residue. Ala-4,Ser(P)-5 and Ala-3c,Ser(P)-4,Ser(P)-5 were competitive inhibitors for phosphorylation of the parent peptide, with Ki values of 2 and 5 microns, respectively. The data suggest (i) that GSK-3 recognizes serines in the motif -SXXXS(P)-, and (ii) that multiple phosphorylation of the peptide substrate has an obligate order, with the sequential formation of new recognition sequences.
Mechanism of bacitracin resistance in gram-negative bacteria that synthesize exopolysaccharides (1994)

Four representative species from three genera of gram-negative bacteria that secrete exopolysaccharides acquired resistance to the antibiotic bacitracin by stopping synthesis of the exopolysaccharide. Xanthomonas campestris, Sphingomonas strains S-88 and NW11, and Escherichia coli K-12 secrete xanthan gum, sphingans S-88 and NW11, and colanic acid, respectively. The gumD gene in X. campestris is required to attach glucose-P to C55-isoprenyl phosphate, the first step in the assembly of xanthan. A recombinant plasmid carrying the gumD gene of X. campestris restored polysaccharide synthesis to bacitracin-resistant exopolysaccharide-negative mutants of X. campestris and Sphingomonas strains. Similarly, a newly cloned gene (spsB) from strain S-88 restored xanthan synthesis to the same X. campestris mutants. However, the intergeneric complementation did not extend to mutants of E. coli that were both resistant to bacitracin and nonproducers of colanic acid. The genetic results also suggest mechanisms for assembling the sphingans which have commercial potential as gelling and viscosifying agents.
Development of a Sensory Neuronal Cell Model for the Estimation of Mild Eye Irritation (2004)

In an attempt to improve the in vitro test strategy for the estimation of eye irritation, a neuronal cell model has been developed, with cells expressing vanilloid receptor type 1 (VR1) nociceptors. The currently accepted method for measuring eye irritancy is the ethically and scientifically criticised Draize rabbit eye test, despite the fact that alternative in vitro methods are available which have proved to be reliable and reproducible for predicting severe ocular toxicity. However, no alternative tests for measuring neuronal stimulation have yet been developed, and the prediction of eye irritation in the mild range is therefore insufficient. VR1 is a nociceptor localised in C-fibre neurons innervating the cornea and the surrounding tissue, and it responds to potentially damaging stimuli by releasing Ca2+ into the cytoplasm. As a sensory endpoint, [Ca2+]i was measured in VR1 transfected cells, as well as in control cells. Short-term cell cytotoxicity studies (cell membrane rupture and morphological divergence) were used to determine the non-corrosive concentrations of the test chemicals. Preliminary results indicated that hygiene products used daily may induce eye irritation via VR1 nociceptors. The lowest toxic concentration (0.025%) of liquid hand soap, as determined by morphologic divergences of cells, generated an 80% increase in [Ca2+]i over the basal [Ca2+]i in VR1 transfected cells, whereas the non-specific [Ca2+]i increased by 33%. Furthermore, all the endpoints studied indicated that shampoo for children was less active than shampoo for adults. If this method is successfully validated with standardised reference chemicals, the model could complete the test battery of in vitro alternatives, resulting in the saving of thousands of laboratory animals.
Fatty Acid Composition of Three Cultured Algal Species (Isochvysis galbana, Chaetoceros gracilis and Chaetoceros calcitrans) Used as Food for Bivalve Larvae (1990)

Abstract Fatty acids of three cultured unicellular algae wldely used in aquaculture ( Isochrysis galbana , clone T‐iso, Chaetoceros calcitrans , and Chaetoceros gracilis ) were analyzed in detail by gas‐liquid chromatography and mass spectrometry. Fatty acid compositions of the individual species, harvested at monthly intervals during a four month period, showed a very consistent pattern. Shorter chain (C16) fatty acids accounted for more than 70% of total fatty acids in the diatoms but less than 20% in I. galbana . Medium chain (C18) and the long chain 22:6w3 unsaturated fatty acids represented more than 50% of the total fatty acids in I. galbana but less than 10% of the total In the Chaetoceros spp. However, in the latter, 20:5w3 replaced 22:6w3 at an equivalent level. Fatty acid profiles of c. calcitrans and c. gracilis were similar, except that the latter contained lower levels of 16:2w4, 16:3w4 and 16:4w1, and higher levels of 18:2w6 and 18:3w6. In particular C. gracilis contained a higher proportion of the biochemically important fatty acid 20:4w6 (arachldonic acid). One of the salient features of I. galbana lipids was the presence of the fatty acid 18:5w3. This fatty acid is not generally reported in algae or invertebrate lipid analyses, but is a typical component of I. galbana and of other marine photosynthetic flagellates. Its potential for utilization by aquatic organisms is unknown.
Layer-by-Layer Growth of CdSe-Based Nanocrystal Light-Emitting Diodes (2001)

The partial exchange of surface-passivating trioctylphosphine oxide (TOPO) on CdSe and ZnS-clad CdSe (CdSe/ZnS) nanocrystals with primary amines was utilized to grow ultra-thin films of these nanocrystals under nonaqueous conditions. This growth was achieved using 1,12-diaminododecane in a layer-by-layer assembly format, where one of the amino groups binds with the nanocrystal surface and the other regenerates the interface for further binding of nanocrystals. The nature of the growth is dependent on the relative surface affinity between the TOPO and the primary amine toward the zinc or cadmium sites on the nanocrystals. Using this technique, high-quality luminescent films of these nanocrystals can be built with well-defined thicknesses. Electroluminescent devices have been fabricated using this methodology.
Intravenous immunoglobulins – understanding properties and mechanisms (2009)

High-dose intravenous immunoglobulin (IVIg) preparations are used currently for the treatment of autoimmune or inflammatory diseases. Despite numerous studies demonstrating efficacy, the precise mode of action of IVIg remains unclear. Paradoxically, IgG can exert both pro- and anti-inflammatory activities, depending on its concentration. The proinflammatory activity of low-dose IVIg requires complement activation or binding of the Fc fragment of IgG to IgG-specific receptors (FcgammaR) on innate immune effector cells. In contrast, when administered in high concentrations, IVIg has anti-inflammatory properties. How this anti-inflammatory effect is mediated has not yet been elucidated fully, and several mutually non-exclusive mechanisms have been proposed. This paper represents the proceedings of a session entitled 'IVIg--Understanding properties and mechanisms' at the 6th International Immunoglobulin Symposium that was held in Interlaken on 26-28 March 2009. The presentations addressed how IgG may affect the cellular compartment, evidence for IVIg-mediated scavenging of complement fragments, the role of the dimeric fraction of IVIg, the anti-inflammatory properties of the minor fraction of sialylated IgG molecules, and the genetic organization and variation in FcgammaRs. These findings demonstrate the considerable progress that has been made in understanding the mechanisms of action of IVIgs, and may influence future perspectives in the field of Ig therapy.
Insulin-like growth factor (IGF)-binding protein-5-(201—218) region regulates hydroxyapatite and IGF-I binding (1997)

Insulin-like growth factor-binding protein-5 (IGFBP-5), the major bone IGFBP, modifies the biological activity of IGFs within the osteoblastic pericellular environment. Because glycosaminoglycans modulate IGFBP-5 binding to osteoblast organic extracellular matrix (ECM), we assessed whether the heparin binding domain of IGFBP-5, IGFBP-5-(102-218), modifies the interaction of IGFBP-5 with the inorganic bone ECM hydroxyapatite (HA). Synthetic IGFBP-5-(201-218) peptide increased the binding of IGFBP-5 to HA as well as the binding of IGF-I to HA-bound IGFBP-5. This action was specific for the heparin-binding domain, because IGFBP-5-(130-138), IGFBP-5-(138-152), and IGFBP-5-(1-169) were without effect. IGFBP-5-(201-218) was found to bind directly to IGFBP-5 and cause a threefold enhancement of the IGF-I binding affinity for IGFBP-5, whether IGFBP-5 was bound to HA or was in a matrix-free fluid phase. Heparin inhibited the binding of IGFBP-5 to HA and blocked the interaction of IGFBP-5 with IGFBP-5-(201-218) in the fluid phase, suggesting that the primary heparin-binding domain of IGFBP-5 specifically enhances the binding of IGFBP-5 to HA and increases IGF-I binding to IGFBP-5.
Role of Surfactant in the Stability of Liquid Crystal-Based Nanocolloids (2009)

We examine the dependence of liquid crystalline nanocolloid formation and stability on surfactant. Nanocolloids composed of polymerizable liquid crystal mesogens and cross-linking agents and capped with either ionic or nonionic surfactants are prepared via the miniemulsion technique. Colloids synthesized with anionic surfactant were stable and displayed 2D hexagonal packing when deposited via slow vertical pulling of the silicon substrate from an aqueous suspension. Liquid crystal nanocolloids stabilized with the nonionic, polar polymer polyvinyl alcohol (PVA) were stable in aqueous environments but coalesced upon drying to form relatively large, well-defined crystal-like structures with uniform birefringence. SEM images reveal that the coalesced structures have mesalike features. Polarized light, atomic force, and polarized Raman microscopy of these structures indicate that the liquid crystal molecules are arranged with their long molecular axis slightly tilted with respect to the surface normal. A mechanism is proposed to explain the formation of the mesalike structures from the nanocolloids. These studies provide fundamental insight into the incorporation and stabilization of polymerizable liquid crystal molecules into nanovolumes and open up opportunities for the incorporation of functionality and anisotropy into isotropically shaped nanocolloids.
The lymphatic tissue microenvironments in chronic lymphocytic leukemia: in vitro models and the significance of CD40-CD154 interactions (2009)

To the editor:

Despite major improvements of treatments, chronic lymphocytic leukemia (CLL) remains an incurable disease. One of the reasons for the inability to completely eliminate the leukemic clone is survival signals from the microenvironment. Coculture models demonstrated that various stromal
Vertical Seismic Profiling--Processing and Analysis Case Study: ABSTRACT (1981)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Immunofluorescence localization of Z-DNA in chromosomes: quantitation by scanning microphotometry and computer-assisted image analysis. (1985)

Anti-Z-DNA polyclonal and monoclonal immunoglobulins raised against left-handed polynucleotides show various degrees of specificity for base sequence and substitution. Class 1 IgGs recognize all Z-DNA with equal affinity; class 2 IgGs show a preference for d(G-C)n sequences and class 3 IgGs for d(G-C)n sequences with substitutions at the C5 position of the pyrimidine. These antibodies served as probes for the localization of Z-DNA in polytene and metaphase chromosomes and in interphase chromatin by indirect immunofluorescence. A quantitative assessment of the binding of anti-Z-DNA IgGs to polytene chromosomes of Chironomus and Drosophila was made by scanning microphotometry and by computer-assisted image analysis of double immunofluorescence and DNA-specific dye fluorescence images. The three classes of antibodies bind to most of the bands in acid fixed polytene chromosomes of C. thummi; however, preferential binding of one class of antibody over another can be observed in certain regions. These differences can be quantitated by arithmetic division or subtraction of the normalized digital images. If a class 2 antibody is first bound at saturating concentrations the binding of class 1 antibody is reduced throughout most bands by 40-50%. However, the telomeres of the three large chromosomes bind greater than 10 times as much class 1 antibody as class 2 antibody, indicating that the Z-DNA tracts in these regions are comprised largely of alternating sequences containing the A X T basepair, e.g., A-C. High-resolution image analysis of class 1 and class 2 immunofluorescence patterns and the total DNA distribution from polytene chromosomes of D. melanogaster show that the two antibody distributions are very similar in a large majority of the bands, but they often deviate from the mean DNA distribution profile. Z-DNA sequences of both G-C and A-C type are detectable at all levels of ploidy from 2n to 2(13)n and in species as diverse as insects and man. We conclude that the vast majority of polytene chromosome bands (genes) contain one or a few DNA sequences with potential for undergoing the B----Z transition and contain both alternating purine-pyrimidine G-C and A-C tracts or mixed sequences. Highly heterochromatic bands and telomeres have more Z potential sequences than do other bands.
Bayesian Exploration for Intelligent Identification of Textures (2012)

In order to endow robots with human-like abilities to characterize and identify objects, they must be provided with tactile sensors and intelligent algorithms to select, control, and interpret data from useful exploratory movements. Humans make informed decisions on the sequence of exploratory movements that would yield the most information for the task, depending on what the object may be and prior knowledge of what to expect from possible exploratory movements. This study is focused on texture discrimination, a subset of a much larger group of exploratory movements and percepts that humans use to discriminate, characterize, and identify objects. Using a testbed equipped with a biologically inspired tactile sensor (the BioTac), we produced sliding movements similar to those that humans make when exploring textures. Measurement of tactile vibrations and reaction forces when exploring textures were used to extract measures of textural properties inspired from psychophysical literature (traction, roughness, and fineness). Different combinations of normal force and velocity were identified to be useful for each of these three properties. A total of 117 textures were explored with these three movements to create a database of prior experience to use for identifying these same textures in future encounters. When exploring a texture, the discrimination algorithm adaptively selects the optimal movement to make and property to measure based on previous experience to differentiate the texture from a set of plausible candidates, a process we call Bayesian exploration. Performance of 99.6% in correctly discriminating pairs of similar textures was found to exceed human capabilities. Absolute classification from the entire set of 117 textures generally required a small number of well-chosen exploratory movements (median = 5) and yielded a 95.4% success rate. The method of Bayesian exploration developed and tested in this paper may generalize well to other cognitive problems.
Interaction of Fatty Acid Monolayers with Cobalt Nanoparticles (2004)

Stable colloidal suspension of magnetic nanoparticles is challenging owing to both van der Waals forces and magnetic dipolar interactions. Thus, it is essential to coat magnetic nanoparticles with a surfactant during chemical synthesis in order to prepare well-dispersed nanoparticle colloid. In the present study, cobalt nanoparticles (∼15 nm in size) were synthesized with the fatty acid (oleic acid) as a surfactant. The chemical interaction of the surfactant with the Co nanoparticles was studied by using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). The results indicated that oleic acid gets chemisorbed as a carboxylate on the Co nanoparticle surfaces, and the two oxygen atoms in the carboxylate are coordinated symmetrically to the Co atoms, leading to the formation of the covalent Co−O bond. This result has implications for the strong interaction between the surfactant and Co nanoparticle, which enhances the stability of Co colloid.
Industrial Purification of Pharmaceutical Antibodies: Development, Operation, and Validation of Chromatography Processes (2001)

(2001). Industrial Purification of Pharmaceutical Antibodies: Development, Operation, and Validation of Chromatography Processes. Biotechnology and Genetic Engineering Reviews: Vol. 18, No. 1, pp. 301-327.
Deferoxamine for Advanced Hepatocellular Carcinoma (2011)

The iron chelator deferoxamine has shown some potential as an antitumor agent in a small number of patients with hepatocellular carcinoma who did not have a response to other agents.
Trends in Androgen Prescribing in the United States, 2001 to 2011 (2013)

Although commercial sales of androgen replacement therapy (ART) have increased substantially in recent years,1,2 to our knowledge, no national population-based studies of this treatment have been reported. In view of the conflicting evidence on the risks and benefits of ART,3-7 understanding androgen prescribing patterns in the United States is important from both a clinical and a public health perspective. We used data from Clinformatics DataMart (CDM), one of the nation's largest commercial health insurance populations, to examine androgen prescribing patterns in the United States over the past decade.
Material parameters for electrostriction (1996)

Electrostriction is often described by a phenomenological tensor relating a material’s deformation to an applied electric field. However, this tensor is not a material parameter; for deformable, weakly compressible materials (e.g., elastomers), the field-induced deformations depend strongly upon boundary conditions. A different approach that relates the deformation to material properties as well as boundary conditions is required. In this article, we describe a linear theory which introduces five material parameters governing electrostriction: the relative dielectric constant, ε0, two derivatives of the dielectric constant tensor, a1 and a2, Young’s modulus, Ey and Poisson’s ratio, ν. Knowledge of these parameters and appropriate boundary conditions allow one to predict field-induced deformations for arbitrary configurations. We demonstrate an experimental procedure for measuring deformations and permittivity changes, from which the parameters a1 and a2 may be extracted (ε0, ν, and Ey can be measured by a variety of established methods). The linear theory reproduces experimental results for two polyurethane films at small to moderate electric field strengths. We find that the electrostatic force associated with the parameters a1 and a2 is at least ten times larger than the Coulombic attractive force between the electrodes.
Occurrence of Sulfatide as a Major Glycosphingolipid in WHHL Rabbit Serum Lipoproteins1 (1987)

Glycosphingolipids in serum and lipoproteins from Watanabe hereditable hyperlipidemic rabbit (WHHL rabbit), which is an animal model for human familial hypercholesterolemia (FH), were analyzed for the first time in this study. Chylomicrons and very low density, low density, and high density lipoproteins contained sulfatide as a major glycosphingolipid (12 nmol/mumol total phospholipids (PL) in chylomicrons, 19 nmol/mumol PL in VLDL, 18 nmol/mumol PL in LDL, and 14 nmol/mumol PL in HDL) with other minor glycosphingolipids such as glucosylceramide, galactosylceramide, GM3 ganglioside, lactosylceramide, and globotriaosylceramide. The concentration of sulfatide as a major glycosphingolipid in WHHL rabbit serum (121 nmol/ml) was much higher than that in normal rabbit serum (3 nmol/ml). Fatty acids of the sulfatides comprised mainly nonhydroxy fatty acids (C22, 23, and 24) and significant amounts of hydroxy fatty acids (about 10%) whereas long chain bases of the sulfatides comprised mostly (4E)-sphingenine with a significant amount of 4D-hydroxysphinganine (about 10%). Furthermore, sulfatides in the liver and small intestine from normal and WHHL rabbits (where serum lipoproteins are produced) were determined to amount to 260 nmol/g liver in WHHL rabbit, 104 nmol/g liver in control rabbit, 99.6 nmol/g small intestine in WHHL rabbit, and 31.2 nmol/g small intestine in control rabbit. Ceramide portions of the sulfatides in the liver were mainly composed of (4E)-sphingenine and nonhydroxy fatty acids, while those in the small intestine were mainly composed of 4D-hydroxysphinganine and hydroxy fatty acids. These results indicated that the sulfatides of serum lipoproteins were mostly derived from the liver (90% of the total), and that the remaining sulfatides (10% of the total) might be derived from the small intestine. These two sulfatides, which have different ceramide portions, could be useful markers for metabolic and biosynthetic studies of various lipoproteins in WHHL rabbit, and thus would be helpful to further elucidate the relationship between hypercholesterolemia and atherosclerosis in the rabbit.
Über die Reduktionsprodukte des Thebains (1920)

Ober die Reduktionsprodukte des Thebains.(nach Versuchen von ]:
Evidence of epoxide hydrase activity in human intestinal microflora. (1978)

Cholesterol-5 alpha, 6 alpha-epoxide has been implicated as an etiologic agent in human colon cancer. The epoxide is metabolized by human intestinal microflora to a product which was characterized by thin-layer and gas-liquid chromatography as well as combined gas-liquid chromatography-mass spectrometry. Chromatographic properties are identical with authentic cholestan-3 beta, 5 alpha, 6 beta-triol, and these results suggest that microbial epoxide hydrase activity is present in the human colon.
Adiabatic Quantum Computing in systems with constant inter-qubit couplings (2005)

We propose an approach suitable for solving NP-complete problems via adiabatic quantum computation with an architecture based on a lattice of interacting spins (qubits) driven by locally adjustable effective magnetic fields. Interactions between qubits are assumed constant and instance-independent, programming is done only by changing local magnetic fields. Implementations using qubits coupled by magnetic-, electric-dipole and exchange interactions are discussed.