gebhart/patrepeval huggingface dataset:
A Kazal-Type Inhibitor of Human Mast Cell Tryptase: Isolation from the Medical LeechHirudo medicinalis, Characterization, and Sequence Analysis (1994)

Human tryptase, a tetrameric proteinase expressed by mast cells, is virtually unique among the serine proteinases as it is not inhibited by any proteinaceous inhibitor tested so far. We have now isolated, sequenced, and characterized an inhibitor of human tryptase from the medical leech Hirudo medicinalis. LDTI (Leech-Derived Tryptase Inhibitor) was purified to apparent homogeneity by cation exchange and affinity chromatography. Amino acid sequencing of the protein consisting of 46 residues (M(r) 4738) revealed a high degree of similarity to the non-classical Kazal-type inhibitors bdellin B-3 and rhodniin, inhibitors isolated from the medical leech and the insect Rhodnius prolixus, respectively. LDTI is a tight-binding and relatively specific inhibitor of human tryptase; it inhibits only trypsin (EC 3.4.21.4) and chymotrypsin (EC 3.4.21.1) with similar affinities. Inhibition studies using small chromogenic substrates revealed that LDTI inhibits the amidolytic activity of tryptase by approximately 50%, suggesting that most likely due to steric hindrance LDTI binds to and inhibits only 2 of 4 active sites of tryptase. LDTI appears useful as a prototype of inhibitors of human tryptase and as a pharmacological tool for the investigation of the role of tryptase in health and disease.
Effect of Ionic Strength on Initial Interactions of Escherichia coli with Surfaces, Studied On-Line by a Novel Quartz Crystal Microbalance Technique (1999)

A novel quartz crystal microbalance (QCM) technique was used to study the adhesion of nonfimbriated and fimbriated Escherichia coli mutant strains to hydrophilic and hydrophobic surfaces at different ionic strengths. This technique enabled us to measure both frequency shifts (Deltaf), i.e., the increase in mass on the surface, and dissipation shifts (DeltaD), i.e., the viscoelastic energy losses on the surface. Changes in the parameters measured by the extended QCM technique reflect the dynamic character of the adhesion process. We were able to show clear differences in the viscoelastic behavior of fimbriated and nonfimbriated cells attached to surfaces. The interactions between bacterial cells and quartz crystal surfaces at various ionic strengths followed different trends, depending on the cell surface structures in direct contact with the surface. While Deltaf and DeltaD per attached cell increased for nonfimbriated cells with increasing ionic strengths (particularly on hydrophobic surfaces), the adhesion of the fimbriated strain caused only low-level frequency and dissipation shifts on both kinds of surfaces at all ionic strengths tested. We propose that nonfimbriated cells may get better contact with increasing ionic strengths due to an increased area of contact between the cell and the surface, whereas fimbriated cells seem to have a flexible contact with the surface at all ionic strengths tested. The area of contact between fimbriated cells and the surface does not increase with increasing ionic strengths, but on hydrophobic surfaces each contact point seems to contribute relatively more to the total energy loss. Independent of ionic strength, attached cells undergo time-dependent interactions with the surface leading to increased contact area and viscoelastic losses per cell, which may be due to the establishment of a more intimate contact between the cell and the surface. Hence, the extended QCM technique provides new qualitative information about the direct contact of bacterial cells to surfaces and the adhesion mechanisms involved.
Differential Interaction of the Cyclin-dependent Kinase (Cdk) Inhibitor p27Kip1 with Cyclin A-Cdk2 and Cyclin D2-Cdk4 (1997)

Although p27(Kip1) has been considered a general inhibitor of G1 and S phase cyclin-dependent kinases, we report that the interaction of p27 with two such kinases, cyclin A-Cdk2 and cyclin D-Cdk4, is different. In Mv1Lu cells containing a p27 inducible system, a 6-fold increase over the basal p27 level completely inhibited Cdk2 and cell cycle progression. In contrast, the same or a larger increase in p27 levels did not inhibit Cdk4 or its homologue Cdk6, despite extensive binding to these kinases. A p27-cyclin A-Cdk2 complex formed in vitro was essentially inactive, whereas a p27-cyclin D2-Cdk4 complex was active as a retinoblastoma kinase and served as a substrate for the Cdk-activating kinase Cak. High concentrations of p27 inhibited cyclin D2-Cdk4, apparently by conversion of active complexes into inactive ones by the binding of additional p27 molecules. In contrast to their differential interaction, cyclin A-Cdk2 and cyclin D2-Cdk4 were similarly inhibited by bound p21(Cip1/Waf1). Roles of cyclin A-Cdk2 as a p27 target and cyclin D2-Cdk4 as a p27 reservoir may result from the differential ability of bound p27 to inhibit the kinase subunit in these complexes.
Selenium direct-converter structure for static and dynamic x-ray detection in medical imaging applications (1998)

Digital x-ray imaging techniques of today require electronic detectors that can be applied to all modalities of medical imaging. This paper presents work showing that selenium, when used as a direct converter, can be competitive with present day scintillator technologies targeting mammographic, radiographic and fluoroscopic applications. In this work, supporting results are presented on the dark currents, lag and ghosting effects and also on the theoretical and experimental x-ray absorption and sensitivity of selenium layers. Measurements were carried out on suitably alloyed selenium layers where the electronic transport properties have been optimized. Measured values for dark currents were below 100 pA/cm<SUP>2</SUP> at operating fields up to 20 V/micrometer. Experimental measurement of the intrinsic lag in selenium has shown it to be less than 0.5% after 30 milliseconds under a dose of 50 mR at 55 keV mean beam energy, which is very low compared with present day image intensifiers. Similar measurements on ghosting, using multiple radiographic pulses, indicate that the magnitude of the ghost image after a few seconds is around 2000 electrons, which is comparable to the electronic noise of most read out systems. Measured sensitivity of a 200 micrometer selenium layer under a mammographic spectrum was around 230 pC/mR/cm<SUP>2</SUP> at an operating field of 20 V/micrometer, which is significantly higher than that reported for competing technologies. Sensitivity for 1000 micrometer selenium was also measured with an 80 kVp spectrum and 20 mm Al filtration and was found to be around 3400 pC/mR/cm<SUP>2</SUP> which is in close agreement with theoretically calculated values. Theoretical estimations for MTF and DQE are also given to assess the potential imaging performance of a selenium-based detector for various applications.
Stereoselective Reduction of Ethyl 4-Chloro-3-Oxobutanoate by a Microbial Aldehyde Reductase in an Organic Solvent-Water Diphasic System (1990)

Enzyme-catalyzed asymmetric reduction of ethyl 4-chloro-3-oxobutanoate in an organic solvent-water diphasic system was studied. NADPH-dependent aldehyde reductase isolated from Sporobolomyces salmonicolor AKU4429 and glucose dehydrogenase were used as catalysts for reduction of ethyl 4-chloro-3-oxobutanoate and recycling of NADPH, respectively, in this system. In an aqueous system, the substrate was unstable. Inhibition of the reaction and inactivation of the enzymes by the substrate and the product were also observed. An n-butyl acetate-water diphasic system very efficiently overcame these limitations. In a 1,600-ml-1,600-ml scale diphasic reaction, ethyl (R)-4-chloro-3-hydroxybutanoate (0.80 mol; 86% enantiomeric excess) was produced from the corresponding oxoester in a molar yield of 95.4% with an NADPH turnover of 5,500 mol/mol.
Evolutionary approach to the question of immunoglobulin heavy chain switching: evidence from cloned human and mouse genes. (1980)

We have used cloned mouse and human heavy chain genes to identify regions of conserved homology between mouse and man and between mu and alpha genes. Using heteroduplex mapping, we find that coding segments for homologous domains appear to have been well conserved between the two species, but the short intervening sequences that separate domains have diverged considerably. These studies also identify extensive regions of homology 5' to both mu and alpha constant region genes that are conserved between the two genes as well as between mouse and man. These segments encompass regions in which mu/alpha recombination occurs during the heavy chain class switch, and their extensive homology may be relevant to this process.
Identification of epitope‐like consensus motifs using mRNA display (2002)

The mRNA display approach to in vitro protein selection is based upon the puromycin-mediated formation of a covalent bond between an mRNA and its gene product. This technique can be used to identify peptide sequences involved in macromolecular recognition, including those identical or homologous to natural ligand epitopes. To demonstrate this approach, we determined the peptide sequences recognized by the trypsin active site, and by the anti-c-Myc antibody, 9E10. Here we describe the use of two peptide libraries of different diversities, one a constrained library based on the trypsin inhibitor EETI-II, where only the six residues in the first loop were randomized (6.4 x 10(7) possible sequences, 6.0 x 10(11) sequences in the library), the other a linear-peptide library with 27 randomized amino acids (1.3 x 10(35) possible sequences, 2 x 10(13) sequences in the library). The constrained library was screened against the natural target of wild-type EETI, bovine trypsin, and the linear library was screened against the anti-c-myc antibody, 9E10. The analysis of selected sequences revealed minimal consensus sequences of PR(I,L,V)L for the first loop of EETI-II and LISE for the 9E10 epitope. The wild-type sequences, PRILMR for the first loop of EETI-II and QKLISE for the 9E10 epitope, were selected with the highest frequency, and in each case the complete wild-type epitope was selected from the library.
Minihepcidins prevent iron overload in a hepcidin-deficient mouse model of severe hemochromatosis (2012)

The deficiency of hepcidin, the hormone that controls iron absorption and its tissue distribution, is the cause of iron overload in nearly all forms of hereditary hemochromatosis and in untransfused iron-loading anemias. In a recent study, we reported the development of minihepcidins, small drug-like hepcidin agonists. Here we explore the feasibility of using minihepcidins for the prevention and treatment of iron overload in hepcidin-deficient mice. An optimized minihepcidin (PR65) was developed that had superior potency and duration of action compared with natural hepcidin or other minihepcidins, and favorable cost of synthesis. PR65 was administered by subcutaneous injection daily for 2 weeks to iron-depleted or iron-loaded hepcidin knockout mice. PR65 administration to iron-depleted mice prevented liver iron loading, decreased heart iron levels, and caused the expected iron retention in the spleen and duodenum. At high doses, PR65 treatment also caused anemia because of profound iron restriction. PR65 administration to hepcidin knockout mice with pre-existing iron overload had a more moderate effect and caused partial redistribution of iron from the liver to the spleen. Our study demonstrates that minihepcidins could be beneficial in iron overload disorders either used alone for prevention or possibly as adjunctive therapy with phlebotomy or chelation.
Directed assembly of copolymer materials on patterned substrates: Balance of simple symmetries in complex structures (2006)

Abstract The self‐assembly of a lamella‐forming blend of a diblock copolymer and its respective homopolymers on periodically patterned substrates is investigated by a concerted experimental and theoretical approach. The substrate pattern consists of square arrays of spots that preferentially attract one component of the blend. The mismatch between the lamellar equilibrium morphology of the copolymer material and the substrate pattern results in the formation of a bicontinuous morphology. At the substrate, a quadratically perforated lamella (QPL) assembles in perfect registry with the substrate pattern. From this, QPL necks emanate and reach the top surface of the film. The detailed structure of these cylindrical nanochannels is analyzed using Voronoi tessellation, orientation correlation functions, and the structure factor of the neck positions on the top surface. The surface morphology is dictated by the antagonism of the square symmetry of the substrate pattern and the tendency of the necks to locally pack in a hexagonal arrangement. The analogy and differences to a system of adsorbed monolayer on corrugated substrates is explored by comparing the arrangement of the necks on the film's top surface with the structure of a soft disk model on a quadratically corrugated substrate. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2589–2604, 2006
Specular surface inspection using structured highlight and Gaussian images (1990)

The structured highlight inspection method uses an array of point sources to illuminate a specular object surface. The point sources are scanned, and highlights on the object surface resulting from each source are used to derive local surface orientation information. The extended Gaussian image (EGI) is obtained by placing at each point on a Gaussian sphere a mass proportional to the area of elements on the object surface that have a specific orientation. The EGI summarizes shape properties of the object surface and can be efficiently calculated from structured highlight data without surface reconstruction. Features of the estimated EGI including areas, moments, principal axes, homogeneity measures, and polygonality can be used as the basis for classification and inspection. The structured highlight inspection system (SHINY) has been implemented using a hemisphere of 127 point sources. The SHINY system uses a binary coding scheme to make the scanning of point sources efficient. Experiments have used the SHINY system and EGI features for the inspection and classification of surface-mounted-solder joints.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interactions between a Polystyrene Particle and Hydrophilic and Hydrophobic Surfaces in Aqueous Solutions (2008)

The interaction between a colloidal polystyrene particle mounted on an AFM cantilever and a hydrophilic and a hydrophobic surface in aqueous solution is investigated. Despite the apparent simplicity of these two types of systems a variety of different types of interactions are observed. The system containing the polystyrene particle and a hydrophilic surface shows DLVO-like interactions characteristic of forces between charged surfaces. However, when the surface is hydrophobized the interaction changes dramatically and shows evidence of a bridging air bubble being formed between the particle and the surface. For both sets of systems, plateaus of constant force in the force curves are obtained when the particle is retracted from the surface after being in contact. These events are interpreted as a number of individual polystyrene molecules that are bridging the polystyrene particle and the surface. The plateaus of constant force are expected for pulling a hydrophobic polymer in a bad (hydrophilic) solvent. The plateau heights are found to be of uniform spacing and independent of the type of surface, which suggests a model by which collapsed polymers are extended into the aqueous medium. This model is supported by a full stretching curve showing also the backbone elasticity and a stretching curve obtained in pentanol, where the plateau changes to a nonlinear force response, which is typical for a polymer in a good or neutral solvent. We suggest that these polymer bridges are important in particular for the interaction between polystyrene and the hydrophilic surface, where they to some extent counteract the long-range electrostatic repulsion.
Combinatorial therapeutic activation with heparin and AICAR stimulates additive effects on utrophin A expression in dystrophic muscles (2015)

Upregulation of utrophin A is an attractive therapeutic strategy for treating Duchenne muscular dystrophy (DMD). Over the years, several studies revealed that utrophin A is regulated by multiple transcriptional and post-transcriptional mechanisms, and that pharmacological modulation of these pathways stimulates utrophin A expression in dystrophic muscle. In particular, we recently showed that activation of p38 signaling causes an increase in the levels of utrophin A mRNAs and protein by decreasing the functional availability of the destabilizing RNA-binding protein called K-homology splicing regulatory protein, thereby resulting in increases in the stability of existing mRNAs. Here, we treated 6-week-old mdx mice for 4 weeks with the clinically used anticoagulant drug heparin known to activate p38 mitogen-activated protein kinase, and determined the impact of this pharmacological intervention on the dystrophic phenotype. Our results show that heparin treatment of mdx mice caused a significant ∼1.5- to 3-fold increase in utrophin A expression in diaphragm, extensor digitorum longus and tibialis anterior (TA) muscles. In agreement with these findings, heparin-treated diaphragm and TA muscle fibers showed an accumulation of utrophin A and β-dystroglycan along their sarcolemma and displayed improved morphology and structural integrity. Moreover, combinatorial drug treatment using both heparin and 5-amino-4-imidazolecarboxamide riboside (AICAR), the latter targeting 5' adenosine monophosphate-activated protein kinase and the transcriptional activation of utrophin A, caused an additive effect on utrophin A expression in dystrophic muscle. These findings establish that heparin is a relevant therapeutic agent for treating DMD, and illustrate that combinatorial treatment of heparin with AICAR may serve as an effective strategy to further increase utrophin A expression in dystrophic muscle via activation of distinct signaling pathways.
Bionic epidural stimulation restores arterial pressure regulation during orthostasis (2004)

A bionic baroreflex system (BBS) is a computer-assisted intelligent feedback system to control arterial pressure (AP) for the treatment of baroreflex failure. To apply this system clinically, an appropriate efferent neural (sympathetic vasomotor) interface has to be explored. We examined whether the spinal cord is a candidate site for such interface. In six anesthetized and baroreflex-deafferentiated cats, a multielectrode catheter was inserted into the epidural space to deliver epidural spinal cord stimulation (ESCS). Stepwise changes in ESCS rate revealed a linear correlation between ESCS rate and AP for ESCS rates of 2 pulses/s and above (r2, 0.876-0.979; slope, 14.3 +/- 5.8 mmHg.pulses(-1).s; pressure axis intercept, 35.7 +/- 25.9 mmHg). Random changes in ESCS rate with a white noise sequence revealed dynamic transfer function of peripheral effectors. The transfer function resembled a second-order, low-pass filter with a lag time (gain, 16.7 +/- 8.3 mmHg.pulses(-1).s; natural frequency, 0.022 +/- 0.007 Hz; damping coefficient, 2.40 +/- 1.07; lag time, 1.06 +/- 0.41 s). On the basis of the transfer function, we designed an artificial vasomotor center to attenuate hypotension. We evaluated the performance of the BBS against hypotension induced by 60 degrees head-up tilt. In the cats with baroreflex failure, head-up tilt dropped AP by 37 +/- 5 mmHg in 5 s and 59 +/- 11 mmHg in 30 s. BBS with optimized feedback parameters attenuated hypotension to 21 +/- 2 mmHg in 5 s (P < 0.05) and 8 +/- 4 mmHg in 30 s (P < 0.05). These results indicate that ESCS-mediated BBS prevents orthostatic hypotension. Because epidural stimulation is a clinically feasible procedure, this BBS can be applied clinically to combat hypotension associated with various pathophysiologies.
Acute intermittent porphyria in Sweden. Molecular, functional and clinical consequences of some new mutations found in the porphobilinogen deaminase gene (2002)

Acute intermittent porphyria (AIP) is an autosomal dominant disorder caused by a partial deficit of porphobilinogen deaminase (PBGD), the third of eight enzymes in the haem biosynthetic pathway. The overt disease is characterized by neuropsychiatric symptoms that are often triggered by exogenous factors such as certain drugs, stress, and alcohol. The aim of this work has been to identify the underlying genetic defect in each AIP-affected family in order to provide early counselling to assist in the avoidance of precipitating factors. The prevalence of AIP in Sweden is in the order of 1:10 000. The major mutation in Sweden, W198X, is due to a founder effect in the northern part of the country. This mutation, together with a further 11 mutations, have been reported previously. The present communication encompasses the great majority of AIP kindreds in Sweden and includes a further 27 mutations within the PBGD gene. This includes 14 completely new mutations, as well as 11 known mutations detected for the first time in Sweden. The majority of the mutations are located in exons 10 and 12 with fewer in exon 7. The clinical and biochemical outcomes in some patients are described. We also use the three-dimensional structure of the porphobilinogen deaminase enzyme to predict the possible molecular and functional consequences of the new Swedish missense and nonsense mutations.
Functional Characterization of Nine Norway Spruce TPS Genes and Evolution of Gymnosperm Terpene Synthases of the TPS-d Subfamily (2004)

Constitutive and induced terpenoids are important defense compounds for many plants against potential herbivores and pathogens. In Norway spruce (Picea abies L. Karst), treatment with methyl jasmonate induces complex chemical and biochemical terpenoid defense responses associated with traumatic resin duct development in stems and volatile terpenoid emissions in needles. The cloning of (+)-3-carene synthase was the first step in characterizing this system at the molecular genetic level. Here we report the isolation and functional characterization of nine additional terpene synthase (TPS) cDNAs from Norway spruce. These cDNAs encode four monoterpene synthases, myrcene synthase, (-)-limonene synthase, (-)-alpha/beta-pinene synthase, and (-)-linalool synthase; three sesquiterpene synthases, longifolene synthase, E,E-alpha-farnesene synthase, and E-alpha-bisabolene synthase; and two diterpene synthases, isopimara-7,15-diene synthase and levopimaradiene/abietadiene synthase, each with a unique product profile. To our knowledge, genes encoding isopimara-7,15-diene synthase and longifolene synthase have not been previously described, and this linalool synthase is the first described from a gymnosperm. These functionally diverse TPS account for much of the structural diversity of constitutive and methyl jasmonate-induced terpenoids in foliage, xylem, bark, and volatile emissions from needles of Norway spruce. Phylogenetic analyses based on the inclusion of these TPS into the TPS-d subfamily revealed that functional specialization of conifer TPS occurred before speciation of Pinaceae. Furthermore, based on TPS enclaves created by distinct branching patterns, the TPS-d subfamily is divided into three groups according to sequence similarities and functional assessment. Similarities of TPS evolution in angiosperms and modeling of TPS protein structures are discussed.