gebhart/patrepeval huggingface dataset:
Identification of amino acid residues involved in the binding of Huperzine A to cholinesterases (1994)

Huperzine A, a potential agent for therapy in Alzheimer's disease and for prophylaxis of organophosphate toxicity, has recently been characterized as a reversible inhibitor of cholinesterases. To examine the specificity of this novel compound in more detail, we have examined the interaction of the 2 stereoisomers of Huperzine A with cholinesterases and site-specific mutants that detail the involvement of specific amino acid residues. Inhibition of fetal bovine serum acetylcholinesterase by (-)-Huperzine A was 35-fold more potent than (+)-Huperzine A, with KI values of 6.2 nM and 210 nM, respectively. In addition, (-)-Huperzine A was 88-fold more potent in inhibiting Torpedo acetylcholinesterase than (+)-Huperzine A, with KI values of 0.25 microM and 22 microM, respectively. Far larger KI values that did not differ between the 2 stereoisomers were observed with horse and human serum butyrylcholinesterases. Mammalian acetylcholinesterase, Torpedo acetylcholinesterase, and mammalian butyrylcholinesterase can be distinguished by the amino acid Tyr, Phe, or Ala in the 330 position, respectively. Studies with mouse acetylcholinesterase mutants, Tyr 337 (330) Phe and Tyr 337 (330) Ala yielded a difference in reactivity that closely mimicked the native enzymes. In contrast, mutation of the conserved Glu 199 residue to Gln in Torpedo acetylcholinesterase produced only a 3-fold increase in KI value for the binding of Huperzine A.(ABSTRACT TRUNCATED AT 250 WORDS)
Myocardial contractile reserve and perfusion defect severity with rest and stress dobutamine (99m)Tc-sestamibi SPECT in canine stunning and subendocardial infarction. (2002)

Defect severity for stunned myocardium and SEMI was mild and was not significantly different. Contractile reserve was significantly different in stunned myocardium and SEMI. (99m)Tc-Sestamibi SPECT at rest and with low-dose dobutamine is a promising new technique to simultaneously assess myocardial perfusion and contractile reserve.
The Identification, Characterization, and Distribution of Guinea Pig CCR4 and Epitope Mapping of a Blocking Antibody (2002)

Th2 lymphocytes play a central role in the control and maintenance of allergic inflammation. The chemokine receptor CCR4 is preferentially expressed on the surface of Th2 lymphocytes polarised in vitro. However, CCR4 is found on the surface of a significant proportion of circulating memory T lymphocytes, some of which are capable of producing the Th1-associated cytokine interferon . To investigate the function of CCR4 on guinea pig (gp) T lymphocytes, we identified the open-reading frame of gpCCR4, which encodes a 361-amino acid protein with 88 and 81% amino acid identity to human and murine CCR4 sequences, respectively. Cells transfected with gpCCR4 migrated toward the human and murine orthologues of the CCR4 ligands, macrophage-derived chemokine and thymus and activation-regulated chemokine. Surface expression of CCR4, using an anti-human CCR4 monoclonal antibody, 10E4, was detected on 12% of guinea pig peripheral blood T helper cells, and CCR4 guinea pig thymocytes were detected in low numbers. However, CCR4 T helper cells constituted 9% of the T lymphocyte population within the normal guinea pig lung and 52% of the guinea pig bronchoalveolar lavage fluid, which is consistent with a role for CCR4 in T lymphocyte development and trafficking through normal tissues. Subsequent analysis of chimeric chemokine receptors indicated that 10E4, a functional inhibitor of gpCCR4 responses, recognized the amino terminus of CCR4.
Detection by Time Reversal: Single Antenna (2006)

This paper studies the binary hypothesis test of detecting the presence or absence of a target in a highly cluttered environment by using time reversal. In time reversal, the backscatter of a signal transmitted into a scattering environment is recorded, delayed, energy normalized, and retransmitted through the medium. We consider two versions of the test-target channel frequency response assumed known or unknown-and, for each version, contrast two approaches: conventional detection (where no time reversal occurs) and time reversal detection. This leads to four alternative formulations for which we derive the optimal detector and the generalized likelihood ratio test, when the target channel frequency response is known or unknown, respectively. We derive analytical expressions for the error probabilities and the threshold for all detectors, with the exception of the time reversal generalized likelihood ratio test. Experiments with real-world electromagnetic data for two channels (free space with a target immersed in 20 scatterers and a duct channel) confirm the analytical results and show that time reversal detection provides significant gains over conventional detection. This gain is explained by the empirical distribution or type of the target channel frequency response-richer scattering channels induce types with heavier tails and larger time reversal detection gains
Ethylene biosynthesis: Identification of 1-aminocyclopropane-1-carboxylic acid as an intermediate in the conversion of methionine to ethylene (1979)

L-[U-(14)C]Methionine fed to apple tissue was efficiently converted to ethylene when the tissue was incubated in air. In nitrogen, however, it was not metabolized to ethylene but was instead converted to 1-aminocyclopropane-1-carboxylic acid (ACC). When apple tissues were fed with L-[methyl-(14)C]methionine or L-[(35)S]methionine and incubated in nitrogen, radioactivity was found subsequently in methylthioribose. This suggests that methionine is first converted to S-adenosylmethionine which is in turn fragmented to ACC and methylthioadenosine. Methylthioadenosine is then hydrolyzed to methylthioribose. The conclusion that ACC is an intermediate in the conversion of methionine to ethylene is based on the following observations: Labeled ACC was efficiently converted to ethylene by apple tissue incubated in air; the conversion of labeled methionine to ethylene was greatly decreased in the presence of unlabeled ACC, but the conversion of labeled ACC to ethylene was little affected by the presence of unlabeled methionine; and 2-amino-4-(2'-aminoethoxy)trans-3-butenoic acid, a potent inhibitor of pyridoxal phosphate-mediated enzyme reactions, greatly inhibited the conversion of methionine to ethylene but did not inhibit conversion of ACC to ethylene. These data indicate the following sequence for the pathway of ethylene biosynthesis in apple tissue: methionine --> S-adenosylmethionine --> ACC --> ethylene. A possible mechanism accounting for these reactions is presented.
Further Studies on Leydig Cell Function in Old Age (1974)

Pathophysiological mechanisms leading to a decreased Leydig cell function in old males were studied. Increased basal plasma LH and FSH levels, an increased pituitary reaction to LHRH 200 μg iv, and a decreased responsiveness of the Leydig cells to hCG stimulation, lead to the conclusion that the decreased Leydig cell function in old age has a primary testicular origin. The plasma estrone and estradiol levels are slightly but significantly increased in elderly males, the free estradiol concentration is however unchanged. There exists a highly significant correlation between the (log transformed) apparent free testosterone concentration and LH and FSH levels suggesting that the feedback of the gonadotropin secretion is regulated via the free rather than via total testosterone levels.
L-29, an endogenous lectin, binds to glycoconjugate ligands with positive cooperativity (1993)

The soluble mammalian lactose-binding lectins L-14-I and L-29 are both secreted and bind to oligosaccharides on laminin, a large extracellular matrix glycoprotein containing polylactosamine chains. Because of the potential functional significance of these lectin-laminin interactions, we compared quantitative aspects of L-14-I and L-29 binding to immobilized laminin using recombinant lectins labeled with 125I. We report that the concentration-dependent binding of L-29 exhibits positive cooperativity whereas binding of L-14-I does not. Cooperative binding of L-29 can also occur on glycoconjugate substrates other than laminin and is not dependent on cystine bond formation or aggregation in solution. L-29 contains repetitive sequences within the N-terminal domain not present in L-14-I. This domain is not required for binding activity, but is required for positive cooperativity. Though the precise mechanism of interaction of L-29 with laminin remains to be determined, it apparently results in assembly of a lectin aggregate on the substrate surface, which could have important functional consequences.
Detection, identification, and quantification of oxidative protein modifications (2019)

Exposure of biological molecules to oxidants is inevitable and therefore commonplace. Oxidative stress in cells arises from both external agents and endogenous processes that generate reactive species, either purposely (<i>e.g.</i> during pathogen killing or enzymatic reactions) or accidentally (<i>e.g.</i> exposure to radiation, pollutants, drugs, or chemicals). As proteins are highly abundant and react rapidly with many oxidants, they are highly susceptible to, and major targets of, oxidative damage. This can result in changes to protein structure, function, and turnover and to loss or (occasional) gain of activity. Accumulation of oxidatively-modified proteins, due to either increased generation or decreased removal, has been associated with both aging and multiple diseases. Different oxidants generate a broad, and sometimes characteristic, spectrum of post-translational modifications. The kinetics (rates) of damage formation also vary dramatically. There is a pressing need for reliable and robust methods that can detect, identify, and quantify the products formed on amino acids, peptides, and proteins, especially in complex systems. This review summarizes several advances in our understanding of this complex chemistry and highlights methods that are available to detect oxidative modifications-at the amino acid, peptide, or protein level-and their nature, quantity, and position within a peptide sequence. Although considerable progress has been made in the development and application of new techniques, it is clear that further development is required to fully assess the relative importance of protein oxidation and to determine whether an oxidation is a cause, or merely a consequence, of injurious processes.
Limited up-regulation of DNA methyltransferase in human colon cancer reflecting increased cell proliferation. (1996)

Epigenetic alterations in the genome of tumor cells have attracted considerable attention since the discovery of widespread alterations in DNA methylation of colorectal cancers over 10 years ago. However, the mechanism of these changes has remained obscure. el-Deiry and coworkers [el-Deiry, W. S., Nelkin, B. D., Celano, P., Yen, R. C., Falco, J. P., Hamilton, S. R. & Baylin, S. B. (1991) Proc. Natl. Acad. Sci. USA 88, 3470-3474], using a quantitative reverse transcription-PCR assay, reported 15-fold increased expression of DNA methyltransferase (MTase) in colon cancer, compared with matched normal colon mucosa, and a 200-fold increase in MTase mRNA levels compared with mucosa of unaffected patients. These authors suggested that increases in MTase mRNA levels play a direct pathogenetic role in colon carcinogenesis. To test this hypothesis, we developed a sensitive quantitative RNase protection assay of MTase, linear over three orders of magnitude. Using this assay on 12 colorectal carcinomas and matched normal mucosal specimens, we observed a 1.8- to 2.5-fold increase in MTase mRNA levels in colon carcinoma compared with levels in normal mucosa from the same patients. There was no significant difference between the normal mucosa of affected and unaffected patients. Furthermore, when the assay was normalized to histone H4 expression, a measure of S-phase-specific expression, the moderate increase in tumor MTase mRNA levels was no longer observed. These data are in contrast to the previously reported results, and they indicate that changes in MTase mRNA levels in colon cancer are nonspecific and compatible with other markers of cell proliferation.
Breast cancer screening by impedance measurements. (1990)

More efficient screening for breast cancer can lead to a reduction in the need for radical surgery and improved survival rates. Modern technology, particularly electronics and computerized instrumentation, makes such improvement feasible. We have developed an instrument for screening for breast cancer based on measuring the dielectric properties of tissues. An image of the electric properties of the breast is presented on a monitoring screen, using 512 'pixels', from which it is possible to distinguish pathological tissue. The image can be recalled on the monitor at will. The test can be performed by paramedical personnel. In the present study 6000 patients were tested with this instrument; 745 of these have undergone biopsy and these had been tested with all available instrumentation. A number of cases were found in which only this instrument detected a pathology which proved malignant. Instruments of such a type could become an additional part of breast cancer clinics.
Clinical trials referral resource. Clinical trials and NCI resources for cancer in HIV-positive patients. (2002)

The association between HIV infection and the development of cancer was noted early in the acquired immunodeficiency syndrome (AIDS) epidemic. The AIDS-defining malignancies are Kaposi’s sarcoma, intermediate- or high-grade B-cell non-Hodgkin’s lymphoma (NHL), and cervical cancer. All of these cancers feature specific infectious agents in their etiology. These agents are human herpesvirus 8/Kaposi’s sarcoma-associated herpesvirus, or HHV-8/KSHV (implicated in Kaposi’s sarcoma), Epstein-Barr virus, or EBV (in primary central nervous system lymphoma and a subset of systemic B-cell NHL) and human papillomavirus, or HPV (in cervical cancer).[1]
Isolation, Fractionation, and Identification of Sucrose Esters from Various Oriental Tobaccos Employing Supercritical Fluids (2008)

Abstract Isolation, fractionation, and identification of sucrose esters from aged oriental tobacco employing supercritical fluids have been completed. Underivatized sucrose ester-rich extracts were obtained using supercritical CO 2 at densities greater than 0.73 g/mL. Lower density CO 2 provided extracts with notable amounts of tobacco derived material; yet, no detectable sucrose ester content. Preparative supercritical fluid chromatography (SFC) provided for an additional purification of the sucrose ester-enriched fraction after column optimization. Structural assignments of the SFC fractions were facilitated using gas chromatography/mass spectrometry (GC/MS) accompanied by N, O-bis(trimethylsilyl)trifluoroacetamide-dimethylformamide (BSTFA-DMF) derivatization of the free hydroxyl groups and high performance-liquid chromatography/mass spectrometry (HPLC/MS). From a relative quantitative perspective regardless of tobacco type, sucrose esters having an acetyl group on C 6 of the glucose function (Group III) were in higher concentration compared to both the concentration observed for sucrose ester of Group I (acetyl group on C 3 of fructose) and sucrose ester of Group II (no acetyl group on either glucose or fructose). Saturated fatty acid constituents were found to range from a maximum total of 18 carbons to a minimum total of 13 carbons. Unsaturated and isomeric fatty acid homologues were detected within the Group II sucrose ester.
Fuzzy Web ad selector based on Web usage mining (2003)

Internet and Web technologies are widely available, making it easier for companies to conduct business and transfer information to customers. Moreover, they speed up financial transactions efficiently, reducing the transaction costs of commercial activities that businesses would normally incur. So, Internet business has created a competitive environment, a successful company wanting to survive and gain a competitive advantage must provide an acceptable bundle of customized services that satisfy customers' needs. Despite the Internet's obvious benefits as a new communication medium its advertising gives the same advertising messages to all customers and so has suffered from poor responses. To raise a Web ad's effectiveness, we propose a Web ad selector that personalizes advertising messages for customers based on their preferences and interests. The Web ad selection system divides Web site customers with similar preferences into several segments through Web usage mining. It uses fuzzy rules that express customer segments' surfing patterns on the basis of expert advice, and recommends appropriate ads by fuzzy inference.
Neomycin Resistance as a Dominant Selectable Marker for Selection and Isolation of Vaccinia Virus Recombinants (1985)

The antibiotic G418 was shown to be an effective inhibitor of vaccinia virus replication when an appropriate concentration of it was added to cell monolayers 48 h before infection. Genetic engineering techniques were used in concert with DNA transfection protocols to construct vaccinia virus recombinants containing the neomycin resistance gene (neo) from transposon Tn5. These recombinants contained the neo gene linked in either the correct or incorrect orientation relative to the vaccinia virus 7.5-kilodalton gene promoter which is expressed constitutively throughout the course of infection. The vaccinia virus recombinant containing the chimeric neo gene in the proper orientation was able to grow and form plaques in the presence of G418, whereas both the wild-type and the recombinant virus with the neo gene in the opposite polarity were inhibited by more than 98%. The effect of G418 on virus growth may be mediated at least in part by selective inhibition of the synthesis of a subset of late viral proteins. These results are discussed with reference to using this system, the conferral of resistance to G418 with neo as a positive selectable marker, to facilitate constructing vaccinia virus recombinants which contain foreign genes of interest.
Erythropoietin production by interstitial cells of hypoxic monkey kidneys (1996)

Previous studies which demonstrated that interstitial cells of the peritubular capillary bed of the kidneys are the site of erythropoietin (Epo) production have been performed in non-primate species. In this study, kidneys from adult rhesus monkeys exposed to 18 h hypoxia (0.42 atm) with high serum (5685 mU/ml) and kidney (814 mU/g. includes serum EPO in the kidney) levels of Epo were compared with a kidney from a nonhypoxic normal rhesus monkey. Localization of Epo mRNA by in situ hybridization was carried out with either anti-sense or sense RNA probes generated from a 645 base pair KpnI-BgIII fragment of a monkey Epo cDNA. Epo mRNA was demonstrated only in interstitial cells in the peritubular capillary bed of the hypoxic and normal monkey kidneys utilizing the antisense probe. The finding that the same type of cell that produces EPO in mice, rats and sheep also produces EPO in a higher primate species strongly supports the contention that renal interstitial cells also produce EPO in the human.
<title>Step and flash imprint lithography for sub-100-nm patterning</title> (2000)

Step and Flash Imprint Lithography (SFIL) is an alternative to photolithography that efficiently generates high aspect-ratio, sub-micron patterns in resist materials. Other imprint lithography techniques based on physical deformation of a polymer to generate surface relief structures have produced features in PMMA as small as 10 nm, but it is very difficult to imprint large depressed features or to imprint a thick films of resist with high aspect-ratio features by these techniques. SFIL overcomes these difficulties by exploiting the selectivity and anisotropy of reactive ion etch (RIE). First, a thick organic 'transfer' layer (0.3 micrometer to 1.1 micrometer) is spin coated to planarize the wafer surface. A low viscosity, liquid organosilicon photopolymer precursor is then applied to the substrate and a quartz template applied at 2 psi. Once the master is in contact with the organosilicon solution, a crosslinking photopolymerization is initiated via backside illumination with broadband UV light. When the layer is cured the template is removed. This process relies on being able to imprint the photopolymer while leaving the minimal residual material in the depressed areas. Any excess material is etched away using a CHF<SUB>3</SUB>/He/O<SUB>2</SUB> RIE. The exposed transfer layer is then etched with O<SUB>2</SUB> RIE. The silicon incorporated in the photopolymer allows amplification of the low aspect ratio relief structure in the silylated resist into a high aspect ratio feature in the transfer layer. The aspect ratio is limited only by the mechanical stability of the transfer layer material and the O<SUB>2</SUB> RIE selectivity and anisotropy. This method has produced 60 nm features with 6:1 aspect ratios. This lithography process was also used to fabricate alternating arrays of 100 nm Ti lines on a 200 nm pitch that function as efficient micropolarizers. Several types of optical devices including gratings, polarizers, and sub-wavelength structures can be easily patterned by SFIL.
Controlling a Polymer Adhesive Using Light and a Molecular Switch (2014)

A thermally remendable polymer was synthesized by the Diels-Alder reaction between dithienylfuran and maleimide monomers to generate a photoresponsive diarylethene. UV light (312 nm) and visible light (>435 nm) "gate" the reversibility of the Diels-Alder reaction and turn the self-healing properties of the polymer "off" and "on", respectively. After exposure to UV light, the strength of the polymer as an adhesive is enhanced. Visible light weakens the adhesive.
A glutamine-amidotransferase-like protein modulates FixT anti-kinase activity in Sinorhizobium meliloti (2001)

Isolation of the asnO mutant argues for the existence of a physiological regulation associated with fixT and makes it unlikely that fixT serves a mere homeostatic function in S. meliloti. Our data suggest that asnO might control activity of the FixT protein, in a way that remains to be elucidated. A proposed role for asnO might be to couple nitrogen fixation gene expression in S. meliloti to the nitrogen needs of the cells.
In vitro differentiation of embryonic stem cells into glial cells and functional neurons (1995)

Mouse embryonic stem cells were induced to differentiate in culture with retinoic acid. Putative precursors of neurons and glial cells (nestin-positive cells) were clearly identified as early as three days after the onset of differentiation. At day 6, neuron-like cells could be clearly identified, either as isolated cells or as cellular networks. Some of these cells were positive for astrocyte- or oligodendrocyte-specific antigens (GFAP or O4 antigens, respectively). Other cells were positive for neuron-specific antigens (cytoskeleton proteins MAP2, MAP5 and NF200, as well as synaptophysin). Some neuronal-like cells were also positive for acetylcholinesterase activity or glutamic acid decarboxylase expression, indicating that ES cells could differentiate into GABAergic and possibly cholinergic neurons. Electrophysiological analyses performed in voltage clamp conditions showed that cell membranes contained voltage-dependent channels. Overshooting action potentials could be triggered by current injection. Taken together, these data provide evidence that embryonic stem cells can differentiate first into neuron-glia progenitors, and later into glial cells and functional neurons, in vitro. This technique provides an unique system to study early steps of neuronal differentiation in vitro.