gebhart/patrepeval huggingface dataset:
Purification and properties of fructosyl-amino acid oxidase from Corynebacterium sp. 2-4-1. (1989)

A new enzyme, fructosyl-amino acid oxidase (fructosyl-α-L-amino acid: oxygen oxidoreductase (defructosylating)) was found, which decomposes Amadori rearrangement compounds of α-L-amino acids to the corresponding α-ketoaldehydes and α-L-amino acids. The enzyme was purified from a strain of Corynebacterium sp. about 38.9-fold to a single protein band with an overall yield of 35 % from the crude extract, and crystallized in rhombic plates. The molecular weight of the enzyme was about 88, 000 on gel filtration and 44, 000 on SDS-poIyacrylamide gel electrophoresis. Non-covalently bound FAD was the prosthetic group. Its isoelectric point was pH 4.6. The optimum pH of the enzyme reaction in potassium phosphate buffer was about 8.3. Fructosyl-α-L-amino acid was the substrate having the highest susceptibility to the enzyme, but N-fructosyl derivatives of other materials, such as β-amino acids, L-imino acids, D-amino acids, alkyl amines, and ammonia, showed almost no susceptibility. The apparent Km values for fructosyl-glycine and fructosyl-phen via la nine were 0.74 mM and 0.71 mM, respectively. The enzyme was inhibited by Hg2+ and Pb2+.
Analysis of the Growth Mechanism of Coprecipitated Spherical and Dense Nickel, Manganese, and Cobalt-Containing Hydroxides in the Presence of Aqueous Ammonia (2009)

Spherical and dense metal hydroxides were synthesized with a coprecipitation reaction in the presence of aqueous ammonia. The growth of the particles was studied by tracking the tap density and morphology with reaction time. The dependence of pH on the tap density and morphology of the particles synthesized in the coprecipitation reaction was determined for Ni(OH)2, Ni1/2Mn1/2(OH)2, and Ni1/3Mn1/3Co1/3(OH)2 The pH range at which particle growth occurred varied for the different metal hydroxides. Solving the chemical equilibria present in the coprecipitation reaction revealed that the pH range at which spherical particle growth occurred was due to the presence of metal coordinated with ammonia. On the basis of the experiments and analysis presented here, the metal hydroxide particle growth occurs by a dissolution−recrystallization type mechanism during synthesis.
Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (2005)

Dietary reference intakes for energy,carbohydrate,fiber,fat,fatty acids,cholesterol,protein,and amino acids , Dietary reference intakes for energy,carbohydrate,fiber,fat,fatty acids,cholesterol,protein,and amin... , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Interaction of von Willebrand Factor with the Extracellular Matrix and Glycocalicin under Static Conditions (1997)

The binding of human von Willebrand factor (vWF) to a variety of extracellular matrix components immobilized on plates and the binding of vWF to platelet glycoprotein Ib (GPIb) after interacting with these matrix components were examined by means of an enzyme-linked immunosorbent assay. vWF preferably bound to type III collagen, whereas it did not significantly bind to type I, IV, V, or VI collagen, fibronectin, laminin, elastin, or proteoglycans. Soluble type III collagen did not bind to vWF coated on plates and showed a little effect on the vWF binding to the immobilized collagen, suggesting that solid-phase collagen is important for the interaction with vWF. When glycocalicin, the N-terminal carbohydrate-rich extracellular domain of GPIb alpha exhibiting the vWF-binding activity, was added to vWF bound to collagen type III, no significant binding of glycocalicin was observed, but it bound to vWF in the presence of botrocetin, a vWF modulator protein isolated from Bothrops jararaca snake venom. These results indicate that vWF immobilized on collagen can interact with GPIb but that binding of vWF to the collagen matrix alone is insufficient for modulating vWF so that it interacts with GPIb under static conditions. Another unknown physiological modulator functionally mimicking botrocetin or high-shear stress may be involved in the platelet adhesion to extracellular matrix in the early stage of hemostasis.
Cell Mediators of Inflammation in the Alzheimer Disease Brain (2000)

Lesions of Alzheimer disease are associated with low-grade but sustained inflammatory responses. Activated microglia agglomerate in the center of senile plaques. Reactive astrocytes marginate the amyloid beta-protein (A beta) deposits and extend their processes toward the center of plaques. Both microglia and astrocytes are known to secrete a wide variety of molecules involved in inflammation and are potential sources of proinflammatory elements in the brain. Dystrophic neurites occur in senile plaques with such glial reactions, suggesting the relevance of inflammatory responses to the neuronal degeneration in Alzheimer disease. Activated glial cells are, therefore, targets of anti-inflammatory therapy of Alzheimer disease. However, evidence also indicates that these cells eliminate A beta from the brain. A beta is produced continuously in both the normal and the AD brain. Under normal conditions, A beta is removed successfully before it accumulates as extracellular amyloid fibrils. Even in Alzheimer disease, a large portion of A beta may be cleared from the brain with a small portion being left and deposited as neurotoxic senile plaques. Both in vivo and in vitro studies showed the effective uptake of A beta by microglia. Before clinical application, it must be determined whether the treatment that suppresses glial activation and inflammatory responses inhibits A beta removal by glial cells.
Distinct Effects of Guanidine Thiocyanate on the Structure of Superfolder GFP (2012)

Having a high folding efficiency and a low tendency to aggregate, the superfolder GFP (sfGFP) offers a unique opportunity to study the folding of proteins that have a β-barrel topology. Here, we studied the unfolding-refolding of sfGFP that was induced by guanidine thiocyanate (GTC), which is a stronger denaturing agent than GdnHCl or urea. Structural perturbations of sfGFP were studied by spectroscopic methods (absorbance, fluorescence, and circular dichroism), by acrylamide quenching of tryptophan and green chromophore fluorescence, and by size-exclusion chromatography. Low concentrations of GTC (up to 0.1 M) induce subtle changes in the sfGFP structure. The pronounced changes in the visible absorption spectrum of sfGFP which are accompanied by a dramatic decrease in tryptophan and green chromophore fluorescence was recorded in the range 0-0.7 M GNC. These alterations of sfGFP characteristics that erroneously can be mixed up with appearance of intermediate state in fact have pure spectroscopic but not structural nature. Higher concentrations of GTC (from 0.7 to 1.7 M), induce a disruption of the sfGFP structure, that is manifested in simultaneous changes of all of the detected parameters. Full recovery of native properties of denaturated sfGFP was observed after denaturant removal. The refolding of sfGFP passes through the accumulation of the off-pathway intermediate state, in which inner alpha-helix and hence green chromophore and Trp57 are still not tuned up to (properly integrated into) the already formed β-barrel scaffold of protein. Incorporation of the chromophore in the β-barrel in the pathway of refolding and restoration of its ability to fluoresce occur in a narrow range of GTC concentrations from 1.0 to 0.7 M, and a correct insertion of Trp 57 occurs at concentrations ranging from 0.7 to 0 M GTC. These two processes determine the hysteresis of protein unfolding and refolding.
Mussel Adhesive Protein Mimetic Polymers for the Preparation of Nonfouling Surfaces (2003)

A new biomimetic strategy for modification of biomaterial surfaces with poly(ethylene glycol) (PEG) was developed. The strategy exploits the adhesive characteristics of 3,4-dihydroxyphenylalanine (DOPA), an important component of mussel adhesive proteins, to anchor PEG onto surfaces, rendering the surfaces resistant to cell attachment. Linear monomethoxy-terminated PEGs were conjugated either to a single DOPA residue (mPEG-DOPA) or to the N-terminus of Ala-Lys-Pro-Ser-Tyr-Hyp-Hyp-Thr-DOPA-Lys (mPEG-MAPD), a decapeptide analogue of a protein found in Mytilus edulis adhesive plaques. Gold and titanium surfaces were modified by adsorption of mPEG-DOPA and mPEG-MAPD from solution, after which surface analysis by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectroscopy confirmed the presence of immobilized PEG on the surface. The ability of modified surfaces to resist cell attachment was examined by culturing 3T3 fibroblasts on the surfaces for up to 14 days. Quantitative image analysis revealed that cell adhesion to mPEG-DOPA and mPEG-MAPD modified surfaces decreased by as much as 98% compared to control surfaces. Modified Ti surfaces exhibited low cell adhesion for up to 2 weeks in culture, indicating that the nonfouling properties of mPEG-DOPA and mPEG-MAPD treated surfaces persist for extended periods of time. This strategy paradoxically exploits the strong fouling characteristics of MAP analogues for antifouling purposes and may be broadly applied to medical implants and diagnostics, as well as numerous nonmedical applications in which the minimization of surface fouling is desired.
Effects of β‐adrenoceptor agonists in human bronchial smooth muscle (1993)

1. We have investigated the potency and duration of action of isoprenaline and a range of beta-adrenoceptor agonists as relaxants of inherent tone in human superfused, isolated bronchial smooth muscle, a tissue reported to contain a homogeneous population of beta 2-adrenoceptors. 2. All of the beta-adrenoceptor agonists caused concentration-related inhibition of inherent tone, with isoprenaline having an EC50 of 27 nM. The rank order of agonist potency was: formoterol > or = -salmeterol > or = clenbuterol > fenoterol = isoprenaline > terbutaline > or = salbutamol > quinprenaline. 3. Relaxant responses to salmeterol were fully reversed by the selective beta 2-adrenoceptor blocking drug, ICI 118551, demonstrating the involvement of beta 2-adrenoceptors. 4. Rt50, i.e. the time taken for 50% recovery from the effects of an EC50 concentration of agonist, differed considerably between the different beta 2-adrenoceptor agonists. Most agonists were short-acting, having Rt50 values less than 13 min. Quinprenaline was of moderate duration, with an Rt50 value of > or = 20 min. In contrast, salmeterol was extremely long-acting, with no sign of recovery within 4 h. 5. Estimates of relative potency and duration of action were similar to those previously determined for these agonists in the guinea-pig isolated trachea. These results suggest, therefore, that guinea-pig trachea is a suitable alternative to human bronchus for the evaluation of the actions of beta-adrenoceptor agonists on airways smooth muscle.
cGMP production of patient-specific iPSCs and photoreceptor precursor cells to treat retinal degenerative blindness (2016)

Immunologically-matched, induced pluripotent stem cell (iPSC)-derived photoreceptor precursor cells have the potential to restore vision to patients with retinal degenerative diseases like retinitis pigmentosa. The purpose of this study was to develop clinically-compatible methods for manufacturing photoreceptor precursor cells from adult skin in a non-profit cGMP environment. Biopsies were obtained from 35 adult patients with inherited retinal degeneration and fibroblast lines were established under ISO class 5 cGMP conditions. Patient-specific iPSCs were then generated, clonally expanded and validated. Post-mitotic photoreceptor precursor cells were generated using a stepwise cGMP-compliant 3D differentiation protocol. The recapitulation of the enhanced S-cone phenotype in retinal organoids generated from a patient with NR2E3 mutations demonstrated the fidelity of these protocols. Transplantation into immune compromised animals revealed no evidence of abnormal proliferation or tumor formation. These studies will enable clinical trials to test the safety and efficiency of patient-specific photoreceptor cell replacement in humans.
Building carbon–carbon bonds using a biocatalytic methanol condensation cycle (2014)

Methanol is an important intermediate in the utilization of natural gas for synthesizing other feedstock chemicals. Typically, chemical approaches for building C-C bonds from methanol require high temperature and pressure. Biological conversion of methanol to longer carbon chain compounds is feasible; however, the natural biological pathways for methanol utilization involve carbon dioxide loss or ATP expenditure. Here we demonstrated a biocatalytic pathway, termed the methanol condensation cycle (MCC), by combining the nonoxidative glycolysis with the ribulose monophosphate pathway to convert methanol to higher-chain alcohols or other acetyl-CoA derivatives using enzymatic reactions in a carbon-conserved and ATP-independent system. We investigated the robustness of MCC and identified operational regions. We confirmed that the pathway forms a catalytic cycle through (13)C-carbon labeling. With a cell-free system, we demonstrated the conversion of methanol to ethanol or n-butanol. The high carbon efficiency and low operating temperature are attractive for transforming natural gas-derived methanol to longer-chain liquid fuels and other chemical derivatives.
Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future (2000)

Synthetic molecules that can bind with high sequence specificity to a chosen target in a gene sequence are of major interest in medicinal and biotechnological contexts. They show promise for the development of gene therapeutic agents, diagnostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Peptide nucleic acid (PNA) is a nucleic acid analog in which the sugar phosphate backbone of natural nucleic acid has been replaced by a synthetic peptide backbone usually formed from N-(2-amino-ethyl)-glycine units, resulting in an achiral and uncharged mimic. It is chemically stable and resistant to hydrolytic (enzymatic) cleavage and thus not expected to be degraded inside a living cell. PNA is capable of sequence-specific recognition of DNA and RNA obeying the Watson-Crick hydrogen bonding scheme, and the hybrid complexes exhibit extraordinary thermal stability and unique ionic strength effects. It may also recognize duplex homopurine sequences of DNA to which it binds by strand invasion, forming a stable PNA-DNA-PNA triplex with a looped-out DNA strand. Since its discovery, PNA has attracted major attention at the interface of chemistry and biology because of its interesting chemical, physical, and biological properties and its potential to act as an active component for diagnostic as well as pharmaceutical applications. In vitro studies indicate that PNA could inhibit both transcription and translation of genes to which it has been targeted, which holds promise for its use for antigene and antisense therapy. However, as with other high molecular mass drugs, the delivery of PNA, involving passage through the cell membrane, appears to be a general problem.
Hyphenated HPLC‐NMR and its applications in drug discovery (2000)

Hyphenated HPLC-NMR is a fast growing technology, allowing rapid and detailed structural characterization of unknown mixtures. The technical aspects of the technology are reviewed on the basis of system configuration, operation, solvent suppression, HPLC and NMR optimization, and detection. The combined use of HPLC-NMR and HPLC-MS is also described and discussed. Various applications of HPLC-NMR and integrated HPLC-NMR-MS in drug discovery, especially in the separation and structure elucidation of drug impurities, reaction mixtures, degradation products, in vitro and in vivo metabolites, and combinatorial library samples, are illustrated. Copyright © 2000 John Wiley & Sons, Ltd. Abbreviations used: APCI atmospheric pressure chemical ionization API atmospheric pressure ionization CEC capillary electrochromatography ESI electrospray ionization IT ion trap Q quadrupole SFC supercritical fluid chromatography TOF time-of-flight
Oral Dosage Forms with Controlled Gastrointestinal Transit (1984)

The present investigation concerns the development of new dosage forms which, after oral administration, exert an active influence on their gastrointestinal transit. The dosage forms release excipients which aim to increase the lenght of time the drug spends in the absorbing section of the duodenum and small intestine. A delayed gastrointestinal transit is intended to achieve a more complete and longer lasting absorption of drugs with a limited duration of absorption. The present study examined whether, by incorporating triethanolamine myristate (165 mg) as an excipient in tablets containing riboflavine (20 mg) as an example of a drug with limited absorption, the gastrointestinal transit of riboflavine could be delayed and hence its absorption improved. Five subjects took part in the in vivo studies and a pH-telemetering device (Heidelberg capsule) was used to determine gastric residence time.The investigations showed that in 4 out of 5 subjects, the gastric residence time of the pH-telemetering capsule could be prolonged and the renal elimination of riboflavine increased The increase in renal elimination of riboflavine in the presence of triethanolamine myristate was statistically significant in the 4th urine collection period (0.05 > p> 0.0025).
Complexity-aware adaptive spatial pre-processing for ROI scalable video coding with dynamic transition region (2011)

We present a complexity-aware adaptive spatial pre- processing (pre-filtering) scheme for the efficient Region-of-Interest (ROI) Scalable Video Coding (SVC). According to the proposed approach, we adaptively vary various parameters of the SVC pre-filters, such as standard deviations, a number of filters for the dynamic pre-processing of a transition region between the ROI and background, etc., thereby enabling to dynamically adjust the desired SVC settings. In addition, our adaptive spatial pre-filtering system is based on an SVC computational complexity-rate-distortion (C-R-D) analysis, thereby adding a complexity dimension to the conventional Region-of-Interest SVC R-D analysis. As a result, the ROI SVC visual presentation quality is significantly improved, which can be especially useful for various resource-limited devices, such as mobile devices. The performance of the presented adaptive spatial ROI SVC pre-processing scheme is evaluated and tested in detail, further comparing it to the Joint Scalable Video Model reference software (JSVM 9.19) and demonstrating significant improvements.
Photonic band gaps and holography (1997)

Photonic band gap materials are holograms with extremely high refractive index contrasts. The refractive index function can be approximated by a small number of plane waves, as a consequence of the photonic crystal periodicity. Photonic crystals can hence be constructed with a simple holographic recording of a very small number of optical plane waves, and appear in this regard as the simplest holograms. Various photonic band gap structures are theoretically analysed and those concepts are illustrated experimentally with the fabrication of a two-dimensional triangular lattice in GaAs. The extension of the method to the three-dimensional diamond structure is discussed.
Vector for regulated expression of cloned genes in a wide range of gram-negative bacteria (1986)

A pKT231-based broad-host-range plasmid vector was constructed which enabled regulation of expression of cloned genes in a wide range of gram-negative bacteria. This vector, pNM185, contained upstream of its EcoRI, SstI, and SstII cloning sites the positively activated pm twin promoters of the TOL plasmid and xylS, the gene of the positive regulator of these promoters. Expression of cloned genes was induced with micromolar quantities of benzoate or m-toluate, the inexpensive coinducers of the pm promoters. Expression of a test gene, xylE, which specifies catechol 2,3-dioxygenase, cloned in this vector was tested in representative strains of a variety of gram-negative bacteria. Regulated expression of xylE was observed in most strains examined, and induced levels of enzyme representing up to 5% of total cellular protein and ratios of induced:noninduced levels of enzyme up to a factor of 600 were observed. The level of xylE gene expression in different bacteria tended to be correlated with their phylogenetic distance from Pseudomonas putida.
Detection of BRAF mutation in thyroid papillary carcinomas by mutant allele-specific PCR amplification (MASA) (2006)

BRAF(V600E) is present in PTC, both in the classic form and in follicular variant with similar prevalence. No correlation was found between BRAF mutation and aggressive clinical behavior. MASA-PCR proved to be a specific, sensitive and reliable method to detect BRAF T1799A in DNA extracted from different sources, including cytologic samples obtained either fresh or from archival glass slides. We propose this method as a useful tool to improve accuracy of preoperative diagnosis identifying PTC from biopsies with indeterminate cytologic findings.
Isolation of the human peroxisomal acyl-CoA oxidase gene: organization, promoter analysis, and chromosomal localization. (1994)

Peroxisomal acyl-CoA oxidase (ACOX; EC 1.3.3.6) is the first enzyme of the fatty acid beta-oxidation pathway, which catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs, and it donates electrons directly to molecular oxygen, thereby producing H2O2. The discovery of carcinogenic peroxisome proliferators, which markedly increase the levels of this H2O2-producing ACOX in rat and mouse liver, generated interest in peroxisomal beta-oxidation system genes. The present study deals with the structural organization of human ACOX gene. This gene spans approximately 33 kb and consists of 14 exons and 13 introns. Primer-extension analysis revealed three principal cap sites, which were mapped at 50, 52, and 53 nt upstream of the initiator methionine codon. The 5' flanking region of the ACOX gene was sequenced up to 500 bp upstream of the cap sites. This promoter region is G + C-rich and contains three copies of the "GC box" hexanucleotides. Multiple GC boxes are a characteristic feature of the rat ACOX and bifunctional protein genes of the beta-oxidation system. A + T-rich TATA-boxlike sequences, TTTATTT and TTATT, have also been identified in this human ACOX gene, but typical CCAAT motifs are absent. This ACOX gene has been mapped to chromosome 17q25 by in situ hybridization, using a biotinlabeled probe.