gebhart/patrepeval huggingface dataset:
Use of an ipb-lux Fusion To Study Regulation of the Isopropylbenzene Catabolism Operon of Pseudomonas putida RE204 and To Detect Hydrophobic Pollutants in the Environment (1996)

A DNA segment involved in the regulation of the isopropylbenzene (cumene) catabolism operon (ipb) of plasmid pRE4 from Pseudomonas putida RE204 and the Vibrio fischeri luciferase genes, luxCDABE, were used to create an ipbRo/pA(prm1)-luxCDABE reporter fusion plasmid, pOS25. Escherichia coli HMS174(pOS25) produces light in the presence of inducers of the ipb operon. These inducers were shown to be hydrophobic compounds and to include monoalkylbenzenes, substituted benzenes and toluenes, some alkanes and cycloalkanes, chlorinated solvents, and naphthalenes. Complex hydrocarbon mixtures, such as gasoline, diesel fuel, jet fuels (JP-4 and JP-5), and creosote, were also inducers of ipb-lux. Bacteria carrying the ipb-lux reporter may be useful as bioindicators of hydrocarbon pollution in the environment and may be particularly valuable for examining the bioavailability of inducing pollutants.
Ligand-independent Dimerization of CXCR4, a Principal HIV-1 Coreceptor (2003)

CXCR4, a member of the G protein-coupled receptor family of proteins, is the receptor for stromal cell-derived factor (SDF-1 alpha) and is a principal coreceptor for human immunodeficiency virus type 1 (HIV-1). CXCR4 has also been implicated in breast cancer metastasis. We examined the ability of CXCR4 to homomultimerize in detergent-solubilized cell lysates and in the membranes of intact cells. CXCR4 was found to multimerize in cell lysates containing the detergents CHAPSO or Cymal-7 but not other detergents that have been shown to disrupt the native conformation of CXCR4. CXCR4 expression levels did not affect the observed multimerization and differentially tagged CXCR4 molecules associated only when coexpressed in the same cell. CXCR4 did not interact with CCR5, the other principal HIV-1 coreceptor, when the two proteins were coexpressed. Using bioluminescence resonance energy transfer (BRET(2)), we demonstrated that CXCR4 multimers are found naturally in the intact cell membrane, in both the presence and absence of multiple CXCR4 ligands. Ligand binding did not significantly alter the observed BRET(2) signal, suggesting that CXCR4 exists as a constitutive oligomer. In cell lysates prepared with non-denaturing detergents, CXCR4 sedimented in a manner consistent with a dimer, whereas CCR5 sedimented as a monomer under these conditions. The stable, constitutive dimerization of CXCR4 may contribute to its biological functions in chemokine binding, signaling, and HIV-1 entry.
Analysis of luminescent samples using subtracted shifted Raman spectroscopy (1998)

A novel method of obtaining high-quality Raman spectra of luminescent samples was tested using cyclohexane solutions which had been treated with a fluorescent dye. The method involves removing the fixed pattern irregularity found in the spectra taken with CCD detectors by subtracting spectra taken at several different, closely spaced spectrometer positions. It is conceptually similar to SERDS (shifted excitation Raman difference spectroscopy) but has the distinct experimental advantage that it does not require a tunable laser source. The subtracted spectra obtained as the raw data are converted into a more recognisable and conventional form by iterative fitting of appropriate double Lorentzian functions whose peak parameters are then used to ‘reconstruct’ a conventional representation of the spectrum. Importantly, it is shown that the degree of uncertainty in the resultant ‘reconstructed’ spectra can be gauged reliably by comparing reconstructed spectra obtained at two different spectrometer shifts (δ and 2δ). The method was illustrated and validated using a solvent (cyclohexane) the spectrum of which is well known and which contains both regions with complex overlapping bands and regions with isolated bands. Possible sources of error are discussed and it is shown that, provided the degree of uncertainty in the data is correctly characterised, it is completely valid to draw conclusions about the spectra of the sample on the basis of the reconstructed data. The acronym SSRS (subtracted shifted Raman spectroscopy; pronounced scissors) is proposed for this method, to distinguish it from the SERDS technique.
ON THE CONTROL OF THE DISTRIBUTION OF MEIOTIC EXCHANGE IN DROSOPHILA MELANOGASTER (1982)

The effects of eight recombination-defective meiotic mutants on crossing over within the X heterochromatin were examined. Since none permit substantial frequencies of exchange within heterochromatin although six lessen or abolish constraints on the location of exchanges within euchromatin, the systems that prohibit exchange within heterochromatin and that govern where exchanges will occur in euchromatin are under separate genetic control.-A minor component of the effects of mei-218 is the production of nonhomologous exchanges; of mei-9 is the recovery of deleted chromatids; and of mei-41 is the recovery of deleted chromatids and/or a low frequency of heterochromatic exchanges.
The Interaction Between Coronary Endothelial Dysfunction, Local Oxidative Stress, and Endogenous Nitric Oxide in Humans (2007)

In vitro and animal studies suggest that oxidative stress is associated with endothelial dysfunction. We tested whether local oxidative stress and nitric oxide (NO) bioavailability in the coronary circulation is associated with coronary endothelial dysfunction in humans. Blood samples were obtained simultaneously from the left main coronary artery and the coronary sinus for measurement of F2-isoprostanes, myeloperoxidase, nitrotyrosine, and superoxide dismutase in 20 patients without significant coronary disease. Afterward, coronary blood flow and the vascular response to intracoronary acetylcholine and NG-monomethyl-L-arginine (L-NMMA) were assessed. The gradient of isoprostanes between the arterial levels and coronary sinus correlated with the change in coronary artery diameter in response to acetylcholine (r=-0.79, P<0.0001). Isoprostanes net production across the left anterior descending artery territory correlated with a decrease in superoxide dismutase activity (r=0.66, P=0.002) and decrease in coronary artery diameter in response to L-NMMA (rs=0.48, P<0.05). Myeloperoxidase and nitrotyrosine gradients were similar in patients with endothelial dysfunction and controls. The effect of L-NMMA was similar in both groups. We conclude that coronary endothelial dysfunction in humans is characterized by local enhancement of oxidative stress without a decrease in basal NO release. This study supports the hypothesis that local oxidative stress has a role in reduction of NO bioavailability in humans with coronary endothelial dysfunction.
IL-17A Modulates Oxidant Stress-Induced Airway Hyperresponsiveness but Not Emphysema (2013)

IL-17A induces the release of pro-inflammatory cytokines and of reactive oxygen species which could lead to neutrophilic inflammation. We determined the role of IL-17 receptor (IL-17R) signalling in oxidant-induced lung emphysema and airway hyperresponsiveness. IL-17R(-/-) and wild-type C57/BL6 mice were exposed to ozone (3 ppm; 3 hours) for 12 times over 6 weeks. Bronchial responsiveness to acetylcholine was measured, and lungs were retrieved. Mean linear intercept (Lm) and isometric contractile responses of intrapulmonary airways to acetylcholine were determined. In wild-type mice but not in IL-17R(-/-), chronic ozone exposure caused airway hyperresponsiveness. The increase in Lm after chronic ozone exposure of wild-type mice was also observed in IL-17R(-/-) mice. The increased maximal contractile response to acetylcholine seen in airways of wild-type mice exposed to ozone was abolished in IL-17R(-/-) mice. p38-mitogen-activated protein kinase (MAPK) and dexamethasone-dependent increase in contractile response was reduced in airways from IL-17R(-/-) ozone-exposed mice. Lung inflammation scores were not altered in IL-17R(-/-) mice exposed to ozone compared to wild-type mice. The increased release of IL-17 and IL-1β, and the activation of p38 MAPK in the lungs of ozone-exposed mice was reduced in IL-17R(-/-) mice. IL-17R signalling underlies the increase in airway hyperresponsiveness seen after ozone exposure, mediated by the increased contractility of airway smooth muscle. The emphysema and lung inflammation induced by ozone is not dependent on IL-17.
Outgrowth of Drug-Resistant Carcinomas Expressing Markers of Tumor Aggression after Long-term TβRI/II Kinase Inhibition with LY2109761 (2011)

TGF-β is produced excessively by many solid tumors and can drive malignant progression through multiple effects on the tumor cell and microenvironment. TGF-β signaling pathway inhibitors have shown efficacy in preclinical models of metastatic cancer. Here, we investigated the effect of systemic LY2109761, a TGF-β type I/II receptor (TβRI/TβRII) kinase inhibitor, in both a tumor allograft model and the mouse skin model of de novo chemically induced carcinogenesis in vivo. Systemic LY2109761 administration disrupted tumor vascular architecture and reduced myofibroblast differentiation of E4 skin carcinoma cells in a tumor allograft. In the 7,12-dimethyl-benzanthracene plus phorbol myristate acetate-induced skin chemical carcinogenesis model, acute dosing of established naive primary carcinomas with LY2109761 (100 mg/kg) every 8 hours for 10 days (100 mg/kg) diminished phospho-Smad2 (P-Smad2) levels and marginally decreased the expression of inflammatory and invasive markers. Sustained exposure to LY2109761 (100 mg/kg/d) throughout the tumor outgrowth phase had no effect on carcinoma latency or incidence. However, molecular analysis of resultant carcinomas by microarray gene expression, Western blotting, and immunohistochemistry suggests that long-term LY2109761 exposure leads to the outgrowth of carcinomas with elevated P-Smad2 levels that do not respond to drug. This is the first description of acquired resistance to a small-molecule inhibitor of the TβRI/TβRII kinase. Resultant carcinomas were more aggressive and inflammatory in nature, with delocalized E-cadherin and elevated expression of Il23a, laminin V, and matrix metalloproteinases. Therefore, TGF-β inhibitors might be clinically useful for applications requiring acute administration, but long-term patient exposure to such drugs should be undertaken with caution.
A mechanism for slow release of biomagnified cyanobacterial neurotoxins and neurodegenerative disease in Guam (2004)

As root symbionts of cycad trees, cyanobacteria of the genus Nostoc produce beta-methylamino-l-alanine (BMAA), a neurotoxic nonprotein amino acid. The biomagnification of BMAA through the Guam ecosystem fits a classic triangle of increasing concentrations of toxic compounds up the food chain. However, because BMAA is polar and nonlipophilic, a mechanism for its biomagnification through increasing trophic levels has been unclear. We report that BMAA occurs not only as a free amino acid in the Guam ecosystem but also can be released from a bound form by acid hydrolysis. After first removing free amino acids from tissue samples of various trophic levels (cyanobacteria, root symbioses, cycad seeds, cycad flour, flying foxes eaten by the Chamorro people, and brain tissues of Chamorros who died from amyotrophic lateral sclerosis/Parkinsonism dementia complex), we then hydrolyzed the remaining fraction and found BMAA concentrations increased 10- to 240-fold. This bound form of BMAA may function as an endogenous neurotoxic reservoir, accumulating and being transported between trophic levels and subsequently being released during digestion and protein metabolism. Within brain tissues, the endogenous neurotoxic reservoir can slowly release free BMAA, thereby causing incipient and recurrent neurological damage over years or even decades, which may explain the observed long latency period for neurological disease onset among the Chamorro people. The presence of BMAA in brain tissues from Canadian patients who died of Alzheimer's disease suggests that exposure to cyanobacterial neurotoxins occurs outside of Guam.
Adaptation of a Microimmunofluorescence Test to the Study of Human Rickettsia Tsutsugamushi Antibody (1976)

A microimmunofluorescence (micro-IFA) test has been adapted to the study of naturally occurring antibody to Rickettsia tsutsugamushi in humans. The micro-IFA test was comparable to the present immlnofluorescent assay in sensitivity and reproducibility, but offered distinct advantages in the quantity of reagents necessary. Also the micro-IFA could be used to simultaneously titer a serum to as many as nine strains of the organism resulting in a great saving of time.
Tight junction proteins claudin-3 and claudin-4 are frequently overexpressed in ovarian cancer but not in ovarian cystadenomas. (2003)

These results show that CLDN3 and CLDN4 are frequently up-regulated in ovarian tumors and cell lines and may represent novel markers for this disease. Overexpression of these genes in ovarian cancer also suggests interesting scenarios for the involvement of TJ in tumorigenesis. A better knowledge of the mechanisms underlying ovarian tumorigenesis will likely result in the development of novel approaches for the diagnosis and therapy of this deadly disease.
Synthesis of Carbonated Fatty Methyl Esters Using Supercritical Carbon Dioxide (2005)

The two-step syntheses of the cyclic carbonates carbonated methyl oleate (CMO) and carbonated methyl linoleate (CML) are reported. First, synthesis of epoxides through well-precedented chemical reactions of unsaturated fatty methyl esters with hydrogen peroxide and formic acid was accomplished. Next, a carbonation reaction with a simple tetrabutylammonium bromide catalyst was performed, allowing the direct incorporation of carbon dioxide into the oleochemical. These syntheses avoid the use of the environmentally unfriendly phosgene. The carbonated products are characterized by IR, 1H NMR, and 13C NMR spectroscopy and studied by thermogravimetric analysis (TGA). Also reported is the synthesis of a similar cyclic carbonate from the commercially available 2-ethylhexyl epoxy soyate. These carbonates show properties that may make them useful as petrochemical replacements or as biobased industrial product precursors.
Characterization of the heat shock response in Mycobacterium bovis BCG (1991)

We have for the first time characterized the heat shock response in mycobacteria both at the level of transcription, by RNA extraction, Northern (RNA) blotting, and hybridization with gene-specific probes for the Mycobacterium tuberculosis 65- and 71-kDa heat shock proteins (HSPs), and at the level of translation, by [35S]methionine labelling, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and autoradiography. We observed increased synthesis of 40-, 65-, 71-, and 90-kDa proteins, which appear to be major HSPs in mycobacteria. The 40-, 71-, and 90-kDa HSPs are coordinately regulated in terms of temperature requirements and kinetics of induction but differ in the levels of expression. The 65- and 71-kDa HSPs are differentially regulated in response to temperature, with different kinetics and levels of induction. mRNA transcript sizes for the 71-, 65-, 40-, and 30-kDa proteins were found to be broadly consistent with DNA sequence open reading frames. A maximum increase of about 69-fold in the levels of mRNA for the 71-kDa HSP after 45 min of heat shock at 45 degrees C was observed, whereas the 65-kDa HSP mRNA increased only 5-fold. It was also found that in M. bovis BCG, as in Escherichia coli, a major control mechanism of the heat shock response is operative at the level of transcription. An ability to characterize the heat shock response in mycobacteria provides an experimental model with which to study environmentally regulated gene expression and an opportunity to identify virulence genes, which may coregulate as part of the heat shock regulon.
Functional Characterization of Enzymes Forming Volatile Esters from Strawberry and Banana (2004)

Volatile esters are flavor components of the majority of fruits. The last step in their biosynthesis is catalyzed by alcohol acyltransferases (AATs), which link alcohols to acyl moieties. Full-length cDNAs putatively encoding AATs were isolated from fruit of wild strawberry (Fragaria vesca) and banana (Musa sapientum) and compared to the previously isolated SAAT gene from the cultivated strawberry (Fragaria x ananassa). The potential role of these enzymes in fruit flavor formation was assessed. To this end, recombinant enzymes were produced in Escherichia coli, and their activities were analyzed for a variety of alcohol and acyl-CoA substrates. When the results of these activity assays were compared to a phylogenetic analysis of the various members of the acyltransferase family, it was clear that substrate preference could not be predicted on the basis of sequence similarity. In addition, the substrate preference of recombinant enzymes was not necessarily reflected in the representation of esters in the corresponding fruit volatile profiles. This suggests that the specific profile of a given fruit species is to a significant extent determined by the supply of precursors. To study the in planta activity of an alcohol acyltransferase and to assess the potential for metabolic engineering of ester production, we generated transgenic petunia (Petunia hybrida) plants overexpressing the SAAT gene. While the expression of SAAT and the activity of the corresponding enzyme were readily detected in transgenic plants, the volatile profile was found to be unaltered. Feeding of isoamyl alcohol to explants of transgenic lines resulted in the emission of the corresponding acetyl ester. This confirmed that the availability of alcohol substrates is an important parameter to consider when engineering volatile ester formation in plants.
Time constants in thermal laser medicine (1989)

Temperature rise of laser-irradiated tissue due to direct absorption of laser light is related to laser parameters (power, spot size, irradiation time, and repetition rate) and tissue parameters (absorption and scattering coefficients, density, heat capacity, and thermal conductivity). Solutions to the bio-heat equation are approximated by introducing axial (z) and radial (r) time constants for heat conduction that represent two parallel channels for heat conduction. These axial (tau z) and radial (tau r) time constants are found proportional to squared distances (z02, r02) that represent the extent of axial and radial temperatures respectively. For convenience, z0 and r0 are approximated to the axial and radial extent of laser light in the tissue. The resulting solution of the bio-heat equation, expressed as temperature rise as function of time and position, is obviously exact for irradiation times short compared to ta z, tau r (adiabatic heating), but is also a quite reasonable approximation up to irradiation times three times the overall time constant. Comparison with (exact) numerical computations show that this holds for all ratios of (light) penetration depth to laser-beam radius; for strongly scattering materials, smaller laser beams give better predictions than do larger laser beams. Several examples of clinical relevance are discussed, such as multiple-laser-pulse irradiation of high- and low-absorbing tissues and laser treatment of port-wine stains, with some unexpected results that also show potential clinical relevance.
Surface-normal emission of a high-Q resonator using a subwavelength high-contrast grating (2008)

We report a novel high-quality (Q) factor optical resonator using a subwavelength high-contrast grating (HCG) with in-plane resonance and surface-normal emission. We show that the in-plane resonance is manifested is by a sharp, asymmetric lineshape in the surface-normal reflectivity spectrum. The simulated Q factor of the resonator is shown to be as high as 500,000. A HCG-resonator was fabricated with an InGaAs quantum well active region sandwiched in-between AlGaAs layers and a Q factor of >14,000 was inferred from the photoluminescence linewidth of 0.07 nm, which is currently limited by instrumentation. The novel HCG resonator design will serve as a potential platform for many devices including surface emitting lasers, optical filters, and biological or chemical sensors.
Synthesis and characterization of derivatized capped porphyrins (1992)

The syntheses of porphyrins carrying either a fully hydrophobic cavity with a benzene moiety (32a,b) or a polar cavity with an amidobenzene (32c–d) are described. Terephthaldehyde (1) was converted to benzene-bisalkanoic acids (8, 10) and nitrobenzene-bisalkanoic acids (13 and 16) by using standard methods. The corresponding diacid chlorides 17a–d were used to acylate two equivalents of a β-unsubstituted pyrrole, and the ketonic groups were reduced by diborane. Following the transformation of the nitro function to the acetamide, appropriate modifications of the ethyl ester functions afforded the key bisformylpyrroles 25a–d. The cyanoacrylate-protected formyl pyrrole derivatives were mono-chlorinated at the α-methyl groups and condensed with two equivalents of an α-unsubstitutued pyrrole to give the dipyrromethane dimers. Strong aqueous alkali caused saponification of the two ester groups and deprotection of the formyl functions to produce the dipyrromethane dimer 30, which, after thermal decarboxylation, was cyclized intramolecularly in acidic medium to give the porphyrins 32 (n = 4 or 5, X = H or NHCOCH 3 ).
Soluble Human Complement Receptor Type 1: In Vivo Inhibitor of Complement Suppressing Post-Ischemic Myocardial Inflammation and Necrosis (1990)

The complement system is an important mediator of the acute inflammatory response, and an effective inhibitor would suppress tissue damage in many autoimmune and inflammatory diseases. Such an inhibitor might be found among the endogenous regulatory proteins of complement that block the enzymes that activate C3 and C5. Of these proteins, complement receptor type 1 (CR1; CD35) has the most inhibitory potential, but its restriction to a few cell types limits its function in vivo. This limitation was overcome by the recombinant, soluble human CR1, sCR1, which lacks the transmembrane and cytoplasmic domains. The sCR1 bivalently bound dimeric forms of its ligands, C3b and methylamine-treated C4 (C4-ma), and promoted their inactivation by factor I. In nanomolar concentrations, sCR1 blocked complement activation in human serum by the two pathways. The sCR1 had complement inhibitory and anti-inflammatory activities in a rat model of reperfusion injury of ischemic myocardium, reducing myocardial infarction size by 44 percent. These findings identify sCR1 as a potential agent for the suppression of complement-dependent tissue injury in autoimmune and inflammatory diseases.
A New TwIST: Two-Step Iterative Shrinkage/Thresholding Algorithms for Image Restoration (2007)

Iterative shrinkage/thresholding (IST) algorithms have been recently proposed to handle a class of convex unconstrained optimization problems arising in image restoration and other linear inverse problems. This class of problems results from combining a linear observation model with a nonquadratic regularizer (e.g., total variation or wavelet-based regularization). It happens that the convergence rate of these IST algorithms depends heavily on the linear observation operator, becoming very slow when this operator is ill-conditioned or ill-posed. In this paper, we introduce two-step IST (TwIST) algorithms, exhibiting much faster convergence rate than IST for ill-conditioned problems. For a vast class of nonquadratic convex regularizers (l(p) norms, some Besov norms, and total variation), we show that TwIST converges to a minimizer of the objective function, for a given range of values of its parameters. For noninvertible observation operators, we introduce a monotonic version of TwIST (MTwIST); although the convergence proof does not apply to this scenario, we give experimental evidence that MTwIST exhibits similar speed gains over IST. The effectiveness of the new methods are experimentally confirmed on problems of image deconvolution and of restoration with missing samples.