gebhart/patrepeval huggingface dataset:
Molecular analysis of DNA and construction of genomic libraries of Mycobacterium leprae (1985)

Molecular analysis of DNA from Mycobacterium leprae, "Mycobacterium lufu," and Mycobacterium vaccae has demonstrated that the G + C (guanine plus cytosine) contents of the DNAs are 56, 61, and 65%, respectively, and that the genome sizes are 2.2 X 10(9), 3.1 X 10(9), and 3.1 X 10(9) daltons, respectively. Because of the significant differences in both G + C content and genome size among M. leprae, "M. lufu," and M. vaccae DNAs, these species are not related, although hybridization experiments under nonstringent conditions, with two separate cloned M. leprae DNA inserts as probes, indicate that there are some conserved sequences among the DNAs. The G + C content of Dasypus novemcinctus (armadillo, the animal of choice for cultivating M. leprae) DNA was determined to be 36%. Genomic libraries potentially representing more than 99.99% of each genome were prepared by cloning into the cosmid vector, pHC79, in Escherichia coli K-12. A genomic library representing approximately 95% of the genome of M. vaccae was prepared in pBR322. M. leprae DNA was subcloned from the pHC79::M. leprae library into an expression vector, pYA626. This vector is a 3.8-kilobase derivative of pBR322 in which the promoter region of the asd (aspartate semialdehyde dehydrogenase) gene from Streptococcus mutans has been inserted in place of the EcoRI-to-PstI fragment of pBR322. Several (44% of those tested) pYA626::M. leprae recombinants and one pBR322::M. vaccae recombinant synthesized new polypeptides in minicells of E. coli, indicating that mycobacterial DNA can be expressed in E. coli K-12, although expression is probably dependent upon use of nonmycobacterial promoters recognized by the E. coli transcription-translation apparatus.
Evaluation of predictive value of CLIP, Okuda, TNM and JIS staging systems for hepatocellular carcinoma patients undergoing surgery (2005)

Both the Okuda and CLIP systems are not superior to TNM staging for HCC patients who undergo surgical resection. Whether JIS score is feasible for those patients with advanced HCC needs further evaluation.
Cross-linking of laminin-nidogen complexes by tissue transglutaminase. A novel mechanism for basement membrane stabilization (1991)

The laminin-nidogen complex, a major component of basement membranes, incorporates [3H]putrescine and monodansylcadaverine in the presence of guinea pig liver transglutaminase. Label was detected in nidogen in the isolated, as well as in the complexed form, but not in laminin. The incorporation proceeds in a time-dependent manner at a rate similar to that achieved with N,N-dimethylcasein, a well characterized transglutaminase substrate. Saturation of incorporation site(s), as well as comparison with the incorporation level in reference proteins, indicated the presence of one high affinity amine acceptor site in nidogen. Electron microscopy of the reaction products showed that the laminin-nidogen complexes become stabilized in a head-to-head arrangement, characteristic of Ca(2+)-induced self-aggregation. Indirect immunofluorescence and detection of transglutaminase activity on unfixed cryosections revealed an extracellular distribution of tissue transglutaminase. Intensive staining was observed in collagen-rich connective tissue. Codistribution with nidogen was not a ubiquitous feature, but was observed in many locations.
A latent s‐chelated ruthenium benzylidene initiator for ring‐opening metathesis polymerization (2009)

Herein, we present the first results on the use of sulfur chelated ruthenium olefin metathesis catalysts in ring-opening metathesis polymerization (ROMP). By the use of these slow initiators, monomer consumption, undetectable at room temperature, could be reversibly turned on and off as desired by heating and cooling cycles, respectively. Significantly, polymer size essentially remained constant throughout reaction progress, irrespective of catalyst loading. The polymers produced presented monomodal high molecular weights (>105 g/mol) with relatively low polydispersities (<1.4). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.] Additional Supporting Information may be found in the online version of this article. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mapping of HLA class I binding motifs in forty-four fusion proteins involved in human cancers. (1997)

Chromosomal translocations coding for abnormal proteins are present in several human cancers. The junctional region of fusion proteins represents a potential target for a T cell-mediated antitumor response. T lymphocytes recognize antigens in the form of short peptides that must bind to HLA molecules. Different HLA specificities can bind different peptides, thus depicting different "peptide binding motifs." It would be useful to know whether a certain fusion protein presents, within its fusion region, the binding motif(s) for a certain HLA molecule. This information would allow a more focused immunological analysis. Here we present data obtained from the screening of the fusion regions of 44 different fusion proteins for the presence of binding motifs to 34 class I HLA molecules, including all of the most frequently encountered specificities. A total of 201 independent peptides was identified (range, 0-11 peptides/fusion protein). A marked heterogeneity among the 44 different fusion proteins analyzed is evident. For example, the pml/RARalpha fusion protein present in acute promyelocytic leukemia presents no binding motif (BCR 3) at all or to a single HLA molecule (Cw*0301, BCR 1). Alternatively, the fusion proteins BCR/ABL, ALL1/AF-6, EWS/ATF-1, or NPM/ALK exhibit motifs for several common HLA specificities. Heterogeneity is also present inside a single translocation (in ALL1/ENL, for example, different subtypes match motifs with cumulative frequencies in the population from 108 to 0%). In two cases where the relative frequency of different fusion protein subtypes was available, a tendency toward an inverse relationship between frequency and the percentage of population covered by the identified binding motifs was observed. Peptides with motifs for HLA A*0201, A3, and Cw*0702 were also tested for actual binding using a stabilization assay; 13-40% showed significant HLA binding, using this assay. However, fewer fusion protein-derived peptides bound to HLA A*0201 and A3 than non-fusion protein-derived peptides. These data provide the first list of peptides derived from fusion proteins that may be assessed as potential tumor-specific antigens.
Gain and the threshold of three-dimensional quantum-box lasers (1986)

Gain and threshold current density are analyzed for quantum-box lasers where electrons are confined in quantum well three-dimensionally, based on the density-matrix theory of semiconductor lasers with relaxation broadening. The electronic dipole moment and its polarization dependence are first analyzed, and it is shown that the gain becomes maximum when the electric field of light is parallel to the longest side of the quantum box. Calculated gain is about 10 times that of bulk crystal for 100 Å × 100 Å × 100 Å GaAs/Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.8</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</inf> As quantum box, and 15 times for Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> As/InP quantum box with the same size, respectively. The threshold current density are 45 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 62 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for GRINSCH GaAs/(Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.8</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</inf> As-Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.4</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</inf> As) and Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</inf> In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</inf> As/(Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.28</inf> In <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.72</inf> As <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</inf> P <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.4</inf> -InP), respectively, where for the GaInAs/ GaInAsP/InP system the intervalence band absorption and nonradiative recombinations have been assumed to be the same as those obtained for bulk crystals experimentally. These results show the possibility of remarkable reduction in the laser threshold by the quantum-box structures.
Complementary and alternative therapies as treatment approaches for interstitial cystitis. (2002)

The management of interstitial cystitis (IC) is predominantly the reduction of the symptoms of frequency, urgency, and pain. Multimodal treatment approaches for IC are helpful in customizing therapy for individual patients. Complementary and alternative therapies are a quintessential addition to the therapeutic armamentarium and frequently include dietary modification, nutraceuticals, bladder training, neuromodulation, stress reduction, and sex therapy. Dietary modification involves elimination of bladder irritants, fluid regulation, and a bowel regimen. Nutraceuticals studied for the treatment of IC include calcium glycerophosphate, L-arginine, mucopolysaccharides, bioflavinoids, and Chinese herbs. Bladder training is effective after pain reduction. The neuromodulation of high-tone pelvic-floor muscle dysfunction is achieved with physical therapy and acupuncture. Stress reduction and sex therapy are best administered by a qualified stress manager and sex therapist. Multimodal, nonconventional management may add efficacy to the treatment of IC.
A high throughput supra-wavelength plasmonic bull’s eye photon sorter spatially and spectrally multiplexed on silica optical fiber facet (2013)

This paper presents a plasmonic bull's eye consisting of a micron-sized hole and a concentric nano-antenna metallic ring surrounded by periodic circular grooves on a thin gold film. The unique metallic nano-ring imbedded in the supra-wavelength-sized hole acts as an amplifying and filtering component to simultaneously provide a significantly lower spectral noise and a higher power transmission at the resonance wavelength, in comparison to prior sub-wavelength bull's eyes. Systematic numerical analyses based on finite-difference time-domain method were carried out to find the impacts of the structural parameters. Experimentally we integrated three proposed plasmonic structure on a cleaved facet of an optical fiber that can act as a spatially and spectrally multiplexed photon sorter. Transmission characteristics of the proposed devices were characterized in terms of the spectral response and signal to noise ratio. Potential applications of the fiber optic photon sorter were also discussed.
Comparison of contact lens overrefraction and standard keratometry for measuring corneal curvature in eyes with lenticular opacity (1999)

In eyes of patients with good visual acuity (20/20 to 20/40), corneal power measurements by CLO and keratometry were similar. The accuracy of the CLO-derived value decreased with increasing media opacity but was still acceptable with acuity of 20/70. Contact lens overrefraction may be a viable alternative to refractive history and videokeratography for estimating true corneal power in patients with surgically altered or irregular corneas.
Metabolism of mitomycin C by DT-diaphorase: role in mitomycin C-induced DNA damage and cytotoxicity in human colon carcinoma cells. (1990)

The role of DT-diaphorase in bioreductive activation of mitomycin C was examined using HT-29 and BE human carcinoma cells which have high and low levels of DT-diaphorase activity, respectively. HT-29 cells were more sensitive to mitomycin C-induced cytotoxicity than the DT-diaphorase-deficient BE cell line. Mitomycin C induced DNA interstrand cross-linking in HT-29 cells but not in BE cells. Both mitomycin C-induced cytotoxicity and induction of DNA interstrand cross-links could be inhibited by pretreatment of HT-29 cells with dicoumarol. Metabolism of mitomycin C by HT-29 cell cytosol was pH dependent and increased as the pH was lowered to 5.8, the lowest pH tested. Metabolism of mitomycin C by HT-29 cytosol was inhibited by prior boiling of cytosol or by the inclusion of dicoumarol. Little metabolism was detected in BE cytosols. When purified rat hepatic DT-diaphorase was used, metabolism of mitomycin C increased as the pH was decreased and could be detected at pH 5.8, 6.4, 7.0, 7.4, but not at 7.8. Metabolism of mitomycin C was NADH dependent and inhibited by dicoumarol or by prior boiling of enzyme. An approximate 1:1 stoichiometry between NADH and mitomycin C removal was demonstrated and no oxygen consumption could be detected. Metabolism of mitomycin C by purified HT-29 DT-diaphorase was also dicoumarol inhibitable and pH dependent. The major metabolite formed during metabolism of mitomycin C by HT-29 cytosol, purified HT-29, and rat hepatic DT-diaphorase was characterized as 2,7-diaminomitosene. These data suggest that two-electron reduction of mitomycin C by DT-diaphorase may be an important determinant of mitomycin C-induced genotoxicity and cytotoxicity.
Immunosuppressive effect of mesenchymal stem cells favors tumor growth in allogeneic animals (2003)

Mesenchymal stem cells (MSCs) are largely studied for their potential clinical use. Recently, they have gained further interest after demonstration of an immunosuppressive role. In this study, we investigated whether in vivo injection of MSCs could display side effects related to systemic immunosuppression favoring tumor growth. We first showed in vitro that the murine C3H10T1/2 (C3) MSC line and primary MSCs exhibit immunosuppressive properties in mixed lymphocyte reaction. We demonstrated that this effect is mediated by soluble factors, secreted only on "activation" of MSCs in the presence of splenocytes. Moreover, the immunosuppression is mediated by CD8+ regulatory cells responsible for the inhibition of allogeneic lymphocyte proliferation. We then demonstrated that the C3 MSCs expressing the human bone morphogenetic protein 2 (hBMP-2) differentiation factor were not rejected when implanted in various allogeneic immunocompetent mice and were still able to differentiate into bone. Importantly, using a murine melanoma tumor model, we showed that the subcutaneous injection of B16 melanoma cells led to tumor growth in allogeneic recipients only when MSCs were coinjected. Although the potential side effects of immunosuppression induced by MSCs have to be considered in further clinical studies, the usefulness of MSCs for various therapeutic applications still remains of great interest.
Role of neuropeptides in autism and their relationships with classical neurotransmitters (1990)

Treatment of hypertension increasingly requires association of drugs. Among them, the association of calcium antagonists with angiotensin converting enzyme inhibitors is a new tempting approach since the two pharmaceutical classes have synergistic effects on blood pressure lowering and target organ protection whereas their effect is antagonistic for adverse events. Numerous large randomized clinical trials have validated this treatment strategy, and new fixed association are being developed. They apply to hypertensive patients, but also to coronary artery disease patients and more generally speaking to high cardiovascular risk subjects.
Protein Ligand Design:  From Phage Display to Synthetic Protein Epitope Mimetics in Human Antibody Fc-Binding Peptidomimetics (2006)

Phage display is a powerful method for selecting peptides with novel binding functions. Synthetic peptidomimetic chemistry is a powerful tool for creating structural diversity in ligands as a means to establish structure-activity relationships. Here we illustrate a method of bridging these two methodologies, by starting with a disulfide bridged phage display peptide which binds a human antibody Fc fragment (Delano et al. Science 2000, 287, 1279) and creating a backbone cyclic beta-hairpin peptidomimetic with 80-fold higher affinity for the Fc domain. The peptidomimetic is shown to adopt a well-defined beta-hairpin conformation in aqueous solution, with a bulge in one beta-strand, as seen in the crystal structure of the phage peptide bound to the Fc domain. The higher binding affinity of the peptidomimetic presumably reflects the effect of constraining the free ligand into the conformation required for binding, thus highlighting in this example the influence that ligand flexibility has on the binding energy. Since phage display peptides against a wide variety of different proteins are now accessible, this approach to synthetic ligand design might be applied to many other medicinally and biotechnologically interesting target proteins.
Direct evidence for tonic sympathetic support of resting metabolic rate in healthy adult humans (2001)

The sympathetic nervous system (SNS) plays an important role in the regulation of energy expenditure. However, whether tonic SNS activity contributes to resting metabolic rate (RMR) in healthy adult humans is controversial, with the majority of studies showing no effect. We hypothesized that an intravenous propranolol infusion designed to achieve complete beta-adrenergic blockade would result in a significant acute decrease in RMR in healthy adults. RMR (ventilated hood, indirect calorimetry) was measured in 29 healthy adults (15 males, 14 females) before and during complete beta-adrenergic blockade documented by plasma propranolol concentrations > or =100 ng/ml, lack of heart rate response to isoproterenol, and a plateau in RMR with increased doses of propranolol. Propranolol infusion evoked an acute decrease in RMR (-71 +/- 11 kcal/day; -5 +/- 0.7%, P < 0.0001), whereas RMR was unchanged from baseline levels during a saline control infusion (P > 0.05). The response to propranolol differed from the response to saline control (P < 0.01). The absolute and percent decreases in RMR with propranolol were modestly related to baseline plasma concentration of norepinephrine (r = 0.38, P = 0.05; r = 0.44, P = 0.02, respectively). These findings provide direct evidence for the concept of tonic sympathetic beta-adrenergic support of RMR in healthy nonobese adults.
Positive allosteric modulation of native and recombinant gamma-aminobutyric acid(B) receptors by 2,6-Di-tert-butyl-4-(3-hydroxy-2,2-dimethyl-propyl)-phenol (CGP7930) and its aldehyde analog CGP13501. (2001)

The compounds CGP7930 [2,6-Di-tert-butyl-4-(3-hydroxy-2,2-dimethyl-propyl)-phenol] and its close analog CGP13501 were identified as positive modulators of gamma-aminobutyric acid(B) (GABA(B)) receptor function. They potentiate GABA-stimulated guanosine 5'-O-(3-[(35)S]thiotriphosphate) (GTP gamma[(35)S]) binding to membranes from a GABA(B(1b/2)) expressing Chinese hamster ovary (CHO) cell line at low micromolar concentrations and are ineffective in the absence of GABA. The structurally related compounds propofol and malonoben are inactive. Similar effects of CGP7930 are seen in a GTP gamma[(35)S] binding assay using a native GABA(B) receptor preparation (rat brain membranes). Receptor selectivity is demonstrated because no modulation of glutamate-induced GTP gamma[(35)S] binding is seen in a CHO cell line expressing the metabotropic glutamate receptor subtype 2. Dose-response curves with GABA in the presence of different fixed concentrations of CGP7930 reveal an increase of both the potency and maximal efficacy of GABA at the GABA(B(1b/2)) heteromer. Radioligand binding studies show that CGP7930 increases the affinity of agonists but acts at a site different from the agonist binding site. Agonist affinity is not modulated by CGP7930 at homomeric GABA(B(1b)) receptors. In addition to GTP gamma[(35)S] binding, we show that CGP7930 also has modulatory effects in cellular assays such as GABA(B) receptor-mediated activation of inwardly rectifying potassium channels in Xenopus laevis oocytes and Ca(2+) signaling in human embryonic kidney 293 cells. Furthermore, we show that CGP7930 enhances the inhibitory effect of L-baclofen on the oscillatory activity of cultured cortical neurons. This first demonstration of positive allosteric modulation at GABA(B) receptors may represent a novel means of therapeutic interference with the GABA-ergic system.
Glucosamine synthetase from Escherichia coli: purification, properties, and glutamine-utilizing site location (1987)

L-Glutamine:D-fructose-6-phosphate amidotransferase (glucosamine synthetase) has been purified to homogeneity from Escherichia coli. A subunit molecular weight of 70,800 was estimated by gel electrophoresis in sodium dodecyl sulfate. Pure glucosamine synthetase did not exhibit detectable NH3-dependent activity and did not catalyze the reverse reaction, as reported for more impure preparations [Gosh, S., Blumenthal, H. J., Davidson, E., & Roseman, S. (1960) J. Biol. Chem. 235, 1265]. The enzyme has a Km of 2 mM for fructose 6-phosphate, a Km of 0.4 mM for glutamine, and a turnover number of 1140 min-1. The amino-terminal sequence confirmed the identification of residues 2-26 of the translated E. coli glmS sequence [Walker, J. E., Gay, J., Saraste, M., & Eberle, N. (1984) Biochem. J. 224, 799]. Methionine-1 is therefore removed by processing in vivo, leaving cysteine as the NH2-terminal residue. The enzyme was inactivated by the glutamine analogue 6-diazo-5-oxo-L-norleucine (DON) and by iodoacetamide. Glucosamine synthetase exhibited half-of-the-sites reactivity when incubated with DON in the absence of fructose 6-phosphate. In its presence, inactivation with [6-14C]DON was accompanied by incorporation of 1 equiv of inhibitor per enzyme subunit. From this behavior, a dimeric structure was tentatively assigned to the native enzyme. The site of reaction with DON was the NH2-terminal cysteine residue as shown by Edman degradation.