gebhart/patrepeval huggingface dataset:
A physicochemical study of protein G, a molecule with unique immunoglobulin G-binding properties. (1986)

Protein G, an IgG-binding molecule, was prepared from the cell walls of a group G streptococcal strain, G-148. The protein could be extracted from the cells by papain digestion and purified by the sequential use of ion-exchange chromatography on DEAE-Sephadex, affinity chromatography on Sepharose-coupled human IgG, and gel chromatography on Sephadex G-200. Two protein bands with similar molecular weight, 34,000 and 36,000, were obtained when analyzing the pure protein G on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The yield using this purification scheme was 27% of the protein G solubilized from the cells or 70 micrograms/ml packed bacteria. The Stokes radius and frictional ratio of protein G were determined to 3.53 nm and 1.64, respectively, suggesting an elongated fibrous molecule. The protein did not contain any intrachain disulfide bonds. The amino acid composition of protein G was determined and was found to be different from that of protein A, the well known staphylococcal IgG-binding protein. The equilibrium constants of the reactions between protein G and human, rabbit, mouse, and goat polyclonal IgG, determined by Scatchard plots, ranged between 1 X 10(10) and 7 X 10(10), for rat polyclonal IgG 1.4 X 10(9), and human monoclonal IgG1, IgG2, IgG3, and IgG4 between 2 X 10(9) and 6 X 10(9). These affinity constants were always greater than the corresponding values for protein A. The binding between protein G and various polyclonal and monoclonal IgG was pH dependent between 2.8 and 10, strongest at pH 4 and 5, and weakest at pH 10.
The development of articular cartilage: II. The spatial and temporal patterns of glycosaminoglycans and small leucine-rich proteoglycans. (1996)

Articular cartilage is both morphologically and biochemically heterogeneous. Its susceptibility to degenerative diseases such as arthritis and its limited repair capacity has made cartilage the focus of intense study; surprisingly, little is known of its development. Using a panel of specific antibodies, we have documented the temporal and spatial patterns of the small leucine-rich proteoglycans fibomodulin, decorin and biglycan in the developing knee cartilage of the marsupial South American opposum (Monodelphis domestica) from parturition to adulthood. The major proteoglycan of cartilage, aggrecan, can be substituted with a variety of isomers of chondroitin sulphate (CS) and keratan sulphate (KS) glycosaminoglycans. Consequently, we have used monoclonal antibodies to determine the distribution of the chondroitinase generated epitopes of CS isomers (delta di-6S and delta di-4S oligosaccharide 'stubs'). Other monoclonal antibodies (3B3[-], 7D4) were used to investigate temporal changes in the expression of specific sulphation patterns within native chondroitin sulphate chains in addition to keratan sulphate chains (5D4). We found the distributions of the small proteoglycans (PGs) to be highly dynamic during development. Both fibromodulin and biglycan appeared to specifically label early articular cartilage as opposed to epiphyseal or growth plate cartilage. All 3 small PGs become preferentially distributed to the upper half of the adult articular cartilage depth. Similarly, delta di-6S, delta di-4S oligosaccharide 'stubs', KS and epitope 7D4 were variably distributed during development but all were again preferentially located to the upper depth of the mature tissue. The epitope recognised by antibody 3B3[-] was extensively distributed in the neonate, but became more restricted to hypertrophic chondrocytes by day 19. It was not detected in the adult tissue. These data suggest that in Monodelphis, proteoglycans are preferentially synthesised and elaborated in the upper half of the tissue depth and contrasts with the patterns observed in eutherian mammals. The data also pose questions as to the functional significance of these molecules within the tissues and to the idea that global patterns of matrix components exist in mammalian articular cartilages.
A stable bifunctional antisense transcript inhibiting gene expression in transgenic plants (1988)

Tobacco plants expressing constitutive chloramphenicol acetyltransferase (CAT; EC 2.3.1.28) activity were obtained by transformation with a chimeric CAT gene driven by the cauliflower mosaic virus 19S promoter. Plants expressing different levels of CAT activity were retransformed with vectors containing CAT sequences transcriptionally fused in the antisense orientation between the coding region of the hygromycin-resistance gene and the 3' end of the nopaline synthase gene. Several plants regenerated on high concentrations of hygromycin exhibited a loss of CAT activity, whereas plants retransformed with a vector conferring hygromycin resistance but lacking the antisense CAT sequence showed no reduction in CAT activity. RNA blot analysis revealed a strong correlation between the degree of CAT gene inactivation and the levels of stable antisense transcripts accumulated. The possibility that CAT gene inactivation was due to transferred DNA instability was discounted since a kanamycin-resistance gene contiguous with the CAT gene was expressed normally, and DNA blot analysis indicated no loss or rearrangements of the transferred DNA fragments. Thus, the imposed selection pressure enabled the selection of plants expressing high levels of stable bifunctional antisense transcripts that inhibited the activity of the targeted gene.
Liquid crystal quantized GRIN lens and its application to AF systems (2008)

Liquid crystal devices are suitable for spatial light modulators, since their half-wave voltage is only a few volts and can be driven directly by CMOS ICs. In this paper, we describe liquid crystal GRIN lens with segmented ITO patterns. So ITO patterns are like zone plates. ITO segments are connected with smaller, highly resistive ITO links that produce voltage drops between the larger ITO segments. The voltage distribution causes a phase distribution across the modulator that can be generated by a simple 3-terminal input. Variable focus range of from plus-minus 150mm to infinity with 1.64mm diameter and good image quality is achieved.
Construction of Bordetella pertussis strains that overproduce genetically inactivated pertussis toxin (1992)

Nontoxic analogs of pertussis toxin (PT), produced by in vitro mutagenesis of the tox operon, are immunogenic and protective against infection by Bordetella pertussis. The moderate levels of PT production by B. pertussis, however, make it the limiting antigen in the formulation of multicomponent, acellular, recombinant whooping cough vaccines. To increase production of the highly detoxified Lys9Gly129 PT analog by B. pertussis, additional copies of the mutated tox operon were integrated into the bacterial chromosome at the tox or fha locus by unmarked allelic exchange. Recombinant strains produced in this way secreted elevated levels of the PT analog proportional to gene dosage. The strains were stable during 10-liter fermentations, and yields of up to 80 mg of PT analog per liter were obtained under production-scale conditions. The nontoxic analog was purified and shown to be indistinguishable from material obtained from a B. pertussis strain that contained only a single copy of the toxLys9Gly129 operon. Such strains are therefore suitable for large-scale, industrial production of an acellular whooping cough vaccine containing a genetically detoxified PT analog.
Silicon nitride three-mode division multiplexing and wavelength-division multiplexing using asymmetrical directional couplers and microring resonators (2014)

We demonstrate silicon nitride mode-division multiplexing (MDM) and wavelength-division multiplexing (WDM) using asymmetrical directional couplers and microring resonators. Our experiments reveal three-mode multiplexing and demultiplexing. We demonstrate 30Gb/s open eye diagrams with an extinction ratio of ~9 dB for each of the three modes. We observe the worst-case modal crosstalk of ~-10 dB. Our analysis of the measured transmission spectra suggests three contributions to the observed crosstalks, with the dominant cause being a compromised input-coupling at the directional couplers in the multiplexer.
Preparation of Modified Red Mud-Supported Fe Catalysts for Hydrogen Production by Catalytic Methane Decomposition (2017)

A modified red mud- (MRM-) supported Fe catalyst (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:math>Fe/MRM) was prepared using the homogeneous precipitation method and applied to methane decomposition to produce hydrogen. The TEM and SEM-EDX results suggested that the particle sizes of the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:math>Fe/MRM catalysts were much smaller than that of raw red mud (RM), and the active metal Fe was evenly distributed over the catalyst structure. Moreover, BET results indicated that the surface areas and pore volumes of the catalysts were significantly improved, and the pore sizes of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:math>Fe/MRM were distributed from 5 to 12 nm, which is typical for a mesoporous material. The activities of those catalysts for the catalytic decomposition of methane were studied at atmospheric pressure at a moderate temperature of 650°C; the results showed that the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M4"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:math>Fe/MRM catalysts were more active than RM and MRM. The methane conversion curves of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M5"><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:math>Fe/MRM catalysts exhibited similar variation tendencies (three-step) during the reaction despite different Fe contents, and the loading amount of Fe clearly affected the activity of the catalysts.
Control of pore structure and size in freeze‐dried collagen sponges (2001)

Because of many suitable properties, collagen sponges are used as an acellular implant or a biomaterial in the field of tissue engineering. Generally, the inner three-dimensional structure of the sponges influences the behavior of cells. To investigate this influence, it is necessary to develop a process to produce sponges with a defined, adjustable, and homogeneous pore structure. Collagen sponges can be produced by freeze-drying of collagen suspensions. The pore structure of the freeze-dried sponges mirrors the ice-crystal morphology after freezing. In industrial production, the collagen suspensions are solidified under time- and space-dependent freezing conditions, resulting in an inhomogeneous pore structure. In this investigation, unidirectional solidification was applied during the freezing process to produce collagen sponges with a homogeneous pore structure. Using this technique the entire sample can be solidified under thermally constant freezing conditions. The ice-crystal morphology and size can be adjusted by varying the solute concentration in the collagen suspension. Collagen sponges with a very uniform and defined pore structure can be produced. Furthermore, the pore size can be adjusted between 20–40 μm. The thickness of the sponges prepared during this research was 10 mm. © 2001 John Wiley & Sons, Inc. J Biomed Mater Res (Appl Biomater) 58: 352–357, 2001
Pathogenesis of shigella diarrhea. XI. Isolation of a shigella toxin-binding glycolipid from rabbit jejunum and HeLa cells and its identification as globotriaosylceramide. (1986)

A glycolipid that specifically binds shigella toxin was isolated from both HeLa cells and rabbit jejunal mucosa and identified as globotriaosylceramide (Gb3) by its identical mobility on HPTLC to authentic erythrocyte Gb3. Toxin also bound to a band tentatively identified as alpha-hydroxylated Gb3. In addition, toxin bound to P1 antigen present in group B human erythrocyte glycolipid extracts. The common feature of the three binding glycolipids is a terminal Gal alpha 1----4Gal disaccharide linked beta 1----4 to either Glc or GlcNAc. Globoisotriaosylceramide, which differs from Gb3 only in possessing a Gal alpha 1----3Gal terminal disaccharide, and LacCer, which lacks the terminal Gal residue of Gb3, were incapable of binding the toxin. Binding was shown to be mediated by the B subunit by the use of isolated toxin A and B subunits and monoclonal subunit-specific antibodies. Gb3-containing liposomes competitively inhibited the binding of toxin to HeLa cell monolayers but did not inhibit toxin-induced cytotoxicity. These studies show an identical carbohydrate-specific glycolipid receptor for shigella toxin in gut and in HeLa cells. The toxin B subunit that mediates this binding has also been shown to recognize a glycoprotein receptor with different sugar specificity. Thus, we have demonstrated that the same small (Mr 6,500) B subunit polypeptide has two distinctive carbohydrate-specific binding sites. The Gal alpha 1----4Gal disaccharide of the glycolipid toxin receptor is also recognized by the Gal-Gal pilus of uropathogenic E. coli. This suggests the possibility that the pilus and toxin B subunit contain homologous sequences. If this is true, it may be possible to use the purified Gal-Gal pilus to produce toxin-neutralizing antibodies.
Morphometry of pig coronary arterial trees (1993)

To establish a mathematical model of the tree like arteries for the purpose of hemodynamic analysis, a complete set of morphometric data of pig coronary arteries is presented. For the purpose of mathematical modeling, three innovations in morphometry are introduced: 1) a rule for assigning the order numbers of the vessels on the basis of diameter ranges, 2) a connectivity matrix to describe asymmetric branching, and 3) a measurement of the fraction of vessel segments connected in series. The morphometric measurements were made with the silicone elastomer-casting method. Data on smaller vessels were obtained from histological specimens by optical sectioning. Data on larger vessels were obtained from vascular casts. The order number, diameter, length, connectivity matrix, and fractions of the vessels of a given order connected in series were measured for all orders of vessels of the right coronary artery and the left anterior descending and left circumflex branches. The data can be used to analyze the longitudinal distribution of blood pressure and volume and spatial distribution of perfusion in myocardium.
In-situ hybridization using digoxigenin-labelled probes in human skin (1991)

This study demonstrated that in‐situ hybridization using digoxigenin‐labelled oligonucleotide poIy‐T probes and digoxigenin‐labelled riboprobes for keratin 14 is possible on routinely fixed paraffin‐embedded sections. The resolution and time course of the detection system compared favourably with isotopically labelled probes. Major differences were shown in keratinocyte messenger RNA content with differentiating cells expressing high levels when compared with the basal layers. Previous work on the distribution of keratin 14 messenger RNA was confirmed and we were able to show that using non‐isotopic in‐situ hybridization, sensitive and accurate cellular localization was feasible in skin sections.
Nickel-Dependent Oxidative Cross-Linking of a Protein (1997)

A model protein, ribonuclease A (bovine pancreas), was examined for its ability to coordinate Ni2+ and promote selective oxidation. In the presence of a peracid such as monopersulfate, HSO5-, nickel induced the monomeric RNase A to form dimers, trimers, tetramers, and higher oligomers without producing fragmentation of the polypeptide backbone. Co2+ and to a lesser extent Cu2+ exhibited similar activity. The nickel-dependent reaction appeared to result from a specific association between the protein and Ni2+ that allowed for transient and in situ oxidation of the bound nickel to yield intermolecular tyrosine-tyrosine cross-links. Macrocylic nickel complexes that had previously been shown to promote guanine oxidation were unable to mimic the activity of the free metal salt. Amino acid analysis of the protein dimer confirmed the expected consumption of one tyrosine per polypeptide and formation of dityrosine. The presence of excess tyrosine efficiently inhibited formation of the protein dimer and produced instead a ribonuclease-tyrosine cross-link. In contrast, high concentrations of the hydroxyl radical quenching agent mannitol only partially inhibited ribonuclease dimerization. The polypeptide-mediated activation of nickel and its subsequent reactivity mimic a process that could contribute to the adverse effects of nickel in vivo.
The Immunological Synapse (2001)

The adaptive immune response is initiated by the interaction of T cell antigen receptors with major histocompatibility complex molecule-peptide complexes in the nanometer scale gap between a T cell and an antigen-presenting cell, referred to as an immunological synapse. In this review we focus on the concept of immunological synapse formation as it relates to membrane structure, T cell polarity, signaling pathways, and the antigen-presenting cell. Membrane domains provide an organizational principle for compartmentalization within the immunological synapse. T cell polarization by chemokines increases T cell sensitivity to antigen. The current model is that signaling and formation of the immunological synapse are tightly interwoven in mature T cells. We also extend this model to natural killer cell activation, where the inhibitory NK synapse provides a striking example in which inhibition of signaling leaves the synapse in its nascent, inverted state. The APC may also play an active role in immunological synapse formation, particularly for activation of naïve T cells.
Intracellular recording from myenteric neurons of the guinea‐pig ileum that respond to stretch (1998)

1. Isolated longitudinal muscle-myenteric plexus preparations from guinea-pig ileum were used to investigate the activity of myenteric neurons when the tissue was stretched in the circumferential direction. Membrane potentials were recorded via flexibly mounted intracellular recording electrodes containing Neurobiotin in 1 M KCl. The preparations were stretched to constant widths (+20% and +40% beyond slack width). 2. Multipolar neurons (Dogiel type II morphology) discharged spontaneous action potentials and proximal process potentials during maintained stretching, three of twenty-one at +20% stretch and seven of nine at +40% stretch. At the maximum extent of stretch tried, +40% beyond slack tissue width, action potentials in Dogiel type II neurons occurred at 10-33 Hz. Neurons with other morphologies were all uniaxonal. Some displayed spontaneous fast EPSPs or action potentials, three of forty one at +20% stretch and seven of nineteen at +40% stretch. 3. In seven of eight Dogiel type II neurons, action potentials or proximal process potentials persisted when membrane hyperpolarization was imposed via the recording electrode. Action potential discharge was abolished by hyperpolarization in seven of nine uniaxonal neurons; the exceptions were two orally projecting neurons. 4. Dogiel type II and uniaxonal neurons were classified as rapidly accommodating if they discharged action potentials only at the beginning of a 500 ms intracellular depolarizing pulse and slowly accommodating if they discharged for more than 250 ms. For Dogiel type II neurons, three of thirteen were slowly accommodating at +20% stretch and two of four at 40% stretch. For uniaxonal neurons the corresponding data were twelve of twenty-six and fifteen of nineteen neurons. The slowly accommodating state was associated with increased cell input resistance in uniaxonal neurons. 5. The spontaneous action potential discharge in Dogiel type II and uniaxonal neurons ceased when the muscle was relaxed pharmacologically by nicardipine (3 microM) or isoprenaline (1 microM), although the applied stretch was maintained. At the same time, evoked spike discharge became rapidly accommodating. 6. We conclude that many Dogiel type II neurons, and possibly some orally projecting uniaxonal neurons, are intrinsic, stretch-sensitive, primary afferent neurons that respond to muscle tension with sustained action potential discharge.
Dilator actions of arginine in human peripheral vasculature (1991)

1. L-Arginine is the physiological precursor for the formation of endothelium-derived nitric oxide. The synthesis of nitric oxide is stereospecific: D-arginine is not a substrate for nitric oxide synthase. It is possible that the provision of excess L-arginine substrate might increase the vascular synthesis of nitric oxide. We have examined this possibility by studying the effects of local infusion of L- and D-arginine in the forearm resistance bed and the superficial dorsal hand veins of healthy subjects. 2. Drugs were either infused locally into a vein on the back of the hand and then the vein diameter was measured using a linear displacement technique, or into the brachial artery and then the forearm blood flow was measured by venous occlusion plethysmography. 3. In the superficial hand veins, L- and D-arginine free base and L- and D-arginine hydrochloride (all four preparations at a dose of 5 mumol/min) all caused a significant increase in venous diameter. The responses of the L- and D-enantiomers did not differ significantly from one another. 4. In the forearm resistance bed, L- and D-arginine free base and L- and D-arginine hydrochloride were without effect at doses of 10 and 40 mumol/min. However, at doses of 160 mumol/min all three preparations of arginine caused a significant increase in forearm blood flow compared with control values. The responses to the three preparations of arginine did not differ significantly from one another. 5. These results show that arginine in high dose is a vasodilator in both human resistance vessels and superficial veins in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)
Per‐oral transgastric abdominal surgery (2006)

Laparoscopic surgery has several advantages over traditional surgery because it has been shown to be less invasive. The next logical step in the evolution of minimally invasive surgery may be to eliminate all abdominal incisions. The natural orifices provide a port of entry via the gastrointestinal tract to the peritoneal cavity. This approach would require the creation of a perforation, which is considered to be a major complication of endoscopy with significant morbidity and mortality. However, there are several recent studies that have described the technical feasibility and safety of a per-oral transgastric approach to the peritoneal cavity using conventional endoscopes. Theoretically, this approach could reduce postoperative abdominal wall pain, wound infection, hernia formation, and adhesions. This article aims to summarize the current status of transgastric surgery, currently referred to as natural orifice transluminal endoscopic surgery (NOTES), and to address some of its future challenges.
Theoretical Bounds on the Estimation of Transverse Displacement, Transverse Strain and Poisson's Ratio in Elastography (2000)

The Cramér-Rao Lower Bounds (CRLB) are derived for the displacement and strain estimation in directions orthogonal to the ultrasonic beam axis, using a previously-described recorrelation method of axial, lateral and elevational motion estimation. We also compare it to the lateral tracking method that involves the sole use of the axial signal in the transverse direction. Our theoretical results, verified with simulations and phantom experiments, show that elastography is capable of measuring axial and transverse strain at up to 10% axially applied compression. Finally, we predict the performance of the estimation of the Poisson's ratio using decoupled axial and lateral estimates that result from the recorrelation method.