gebhart/patrepeval huggingface dataset:
A novel lysine 2,3-aminomutase encoded by the yodO gene of Bacillus subtilis: characterization and the observation of organic radical intermediates (2000)

The yodO gene product of Bacillus subtilis has been cloned and overexpressed in Escherichia coli and purified. The nucleotide sequence encodes a protein of 471 amino acids with a calculated molecular mass of 54071 Da. The translated amino acid sequence is more than 60% identical to that of the lysine 2,3-aminomutase from Clostridium subterminale SB4. Analytical HPLC gel-permeation chromatography leads to an estimate of an over all molecular mass of 224000+/-21000 Da, which corresponds to a tetrameric protein. The purified protein contains iron, sulphide and pyridoxal 5'-phosphate (PLP) and displays an optical absorption band extending to 700 nm, suggesting the presence of an iron-sulphide cluster. After reductive incubation with L-cysteine anaerobically, the protein catalyses the transformation of L-lysine into beta-lysine in the presence of S-adenosylmethionine (AdoMet) and sodium dithionite. The K(m) value for L-lysine is estimated to be 8.0+/-2.2 mM. The iron-sulphur centre is stable in air,allowing aerobic purification. EPR spectroscopy at 10 K of the purified enzyme revealed an EPR signal similar to that of the [4Fe-4S](3+) cluster observed in the clostridial lysine 2, 3-aminomutase. Incubation with cysteine under anaerobic conditions converts the iron-sulphur centre into the EPR-silent [4Fe-4S](2+). Unlike the clostridial enzyme, the fully reduced [4Fe-4S](+) could not be characterized by further reduction with dithionite in the presence of AdoMet, although both dithionite and AdoMet were required to activate the enzyme. Upon addition of L-lysine, dithionite and AdoMet to the reduced enzyme and freezing the solution to 77 K, the EPR spectrum revealed the presence of an organic free-radical signal (g=2.0023), which displayed multiple hyperfine transitions very similar to the spectrum of the beta-lysine-related radical in the mechanism of the clostridial lysine 2,3-aminomutase. Experiments with isotopically substituted L-lysine and lysine analogues verified the association of spin density with the carbon skeleton of lysine. The data indicate that the protein encoded by the yodO gene of B. subtilis is a novel lysine 2,3-aminomutase. The E. coli homologue of clostridial lysine 2,3-aminomutase was also expressed in E. coli and purified. This protein contained ironand sulphide but not PLP, it did not display lysine 2,3-aminomutase activity, and addition of PLP did not induce 2,3-aminomutase activity.
Quantum nondemolition measurement of the photon number via the optical Kerr effect (1985)

This paper proposes a quantum nondemolition measurement scheme for the photon number. The signal and probe optical waves interact via the optical Kerr effect. The optical phase of the probe wave is selected as the readout observable for the measurement of the photon number of the signal wave. The measurement accuracy \ensuremath{\Delta}n and the imposed phase noise \ensuremath{\Delta}\ensuremath{\varphi} of the signal wave satisfy Heisenberg's uncertainty principle with an equality sign, 〈(\ensuremath{\Delta}n${)}^{2}$〉〈(\ensuremath{\Delta}\ensuremath{\varphi}${)}^{2}$〉=(1/4). .AE
Characterization of Resistance to Non-obligate Chain-terminating Ribonucleoside Analogs That Inhibit Hepatitis C Virus Replication in Vitro (2003)

The urgent need for efficacious drugs to treat chronic hepatitis C virus (HCV) infection requires a concerted effort to develop inhibitors specific for virally encoded enzymes. We demonstrate that 2'-C-methyl ribonucleosides are efficient chain-terminating inhibitors of HCV genome replication. Characterization of drug-resistant HCV replicons defined a single S282T mutation within the active site of the viral polymerase that conferred loss of sensitivity to structurally related compounds in both replicon and isolated polymerase assays. Biochemical analyses demonstrated that resistance at the level of the enzyme results from a combination of reduced affinity of the mutant polymerase for the drug and an increased ability to extend the incorporated nucleoside analog. Importantly, the combination of these agents with interferon-alpha results in synergistic inhibition of HCV genome replication in cell culture. Furthermore, 2'-C-methyl-substituted ribonucleosides also inhibited replication of genetically related viruses such as bovine diarrhea virus, yellow fever, and West African Nile viruses. These observations, together with the finding that 2'-C-methyl-guanosine in particular has a favorable pharmacological profile, suggest that this class of compounds may have broad utility in the treatment of HCV and other flavivirus infections.
Robust and Porous β-Diketiminate-Functionalized Metal–Organic Frameworks for Earth-Abundant-Metal-Catalyzed C–H Amination and Hydrogenation (2016)

We have designed a strategy for postsynthesis installation of the β-diketiminate (NacNac) functionality in a metal-organic framework (MOF) of UiO-topology. Metalation of the NacNac-MOF (I) with earth-abundant metal salts afforded the desired MOF-supported NacNac-M complexes (M = Fe, Cu, and Co) with coordination environments established by detailed EXAFS studies. The NacNac-Fe-MOF catalyst, I•Fe(Me), efficiently catalyzed the challenging intramolecular sp(3) C-H amination of a series of alkyl azides to afford α-substituted pyrrolidines. The NacNac-Cu-MOF catalyst, I•Cu(THF), was effective in promoting the intermolecular sp(3) C-H amination of cyclohexene using unprotected anilines to provide access to secondary amines in excellent selectivity. Finally, the NacNac-Co-MOF catalyst, I•Co(H), was used to catalyze alkene hydrogenation with turnover numbers (TONs) as high as 700,000. All of the NacNac-M-MOF catalysts were more effective than their analogous homogeneous catalysts and could be recycled and reused without a noticeable decrease in yield. The NacNac-MOFs thus provide a novel platform for engineering recyclable earth-abundant-element-based single-site solid catalysts for many important organic transformations.
Intelligent compounds which read DNA base sequences (1995)

Abstract We have studied the DNA binding and DNA cleavage specificities of two novel classes of synthetic DNA breakage agents. One class comprises redox-activated metalloporphyrins, the other uses the photoactivable p-nitrobenzoyl group as the DNA breaking moiety linked covalently to a DNA recognizing entity such as an oligo N-methylpyrrolecarboxamide or oligothiazole group. Studies of DNA cleavage using end-labeled DNA restriction fragments and high resolution sequencing gel electrophoresis have allowed DNA break sites to be identified at the nucleotide level. This work in conjunction with induced CD spectroscopy has shown that these compounds, especially photoactive agents containing thiazole units, display high sequence specificity. The mechanism of sequence recognition appears to be quite different for the two series of compounds.
Low-multiplicity infection of Moloney murine leukemia virus in mouse cells: effect on number of viral DNA copies and virus production in producer cells (1978)

Mouse cells infected with Moloney murine leukemia virus (M-MuLV) were prepared by two methods, and the number of M-MuLV-specific DNA copies in the infected cells was measured. The number of M-MuLV-specific DNA copies detected varied from one to eight per infected cell in different cell lines. Cells in which multiple rounds of viral infection occurred during establishment had on the average more viral DNA copies than cells in which infection at low multiplicity was performed, followed by cloning of the cells. However, even in cells derived by the low multiplicity of infection method, most cell lines carried more than one copy of M-MuLV-specific DNA. Virus production per cell was also measured, and no strict correlation was observed between the number of M-MuLV DNA copies present and the amount of virus produced.
Liquid Chromatography-Tandem Mass Spectrometry – Application in the Clinical Laboratory (2003)

This review provides a concise survey of liquid chromatography-tandem mass spectrometry (LC-TMS) as an emerging technology in clinical chemistry. The combination of two mass spectrometers with an interposed collision cell characterizes LC-TMS as an analytical technology on its own and not just as a more specific detector for HPLC compared with conventional techniques. In LC-TMS, liquid chromatography is rather used for sample preparation but not for complete resolution of compounds of interest. The instrument technology of LC-TMS is complex and comparatively expensive; however, in routine use, methods are far more rugged compared to conventional chromatographic techniques and enable high-throughput analyses with very limited manual handling steps. Moreover, compared to both gas chromatography-mass spectrometry (GC-MS) and conventional HPLC techniques, LC-TMS is substantially more versatile with respect to the spectrum of analyzable compounds. For these reasons it is likely that LC-TMS will gain far more widespread use in the clinical laboratory than HPLC and GC-MS ever did. In this article, the key features of LC-TMS are described, method development is explained, typical fields of application are discussed, and personal experiences are related.
Intracellular adhesion molecule-1 modulates β-chemokines and directly costimulates T cells in vivo (1999)

The potential roles of adhesion molecules in the expansion of T cell-mediated immune responses in the periphery were examined using DNA immunogen constructs as model antigens. We coimmunized cDNA expression cassettes encoding the adhesion molecules intracellular adhesion molecule-1 (ICAM-1), lymphocyte function associated-3 (LFA-3), and vascular cell adhesion molecule-1 (VCAM-1) along with DNA immunogens, and we analyzed the resulting antigen-specific immune responses. We observed that antigen-specific T-cell responses can be enhanced by the coexpression of DNA immunogen and adhesion molecules ICAM-1 and LFA-3. Coexpression of ICAM-1 or LFA-3 molecules along with DNA immunogens resulted in a significant enhancement of T-helper cell proliferative responses. In addition, coimmunization with pCICAM-1 (and more moderately with pCLFA-3) resulted in a dramatic enhancement of CD8-restricted cytotoxic T-lymphocyte responses. Although VCAM-1 and ICAM-1 are similar in size, VCAM-1 coimmunization did not have any measurable effect on cell-mediated responses. These results suggest that ICAM-1 and LFA-3 provide direct T-cell costimulation. These observations are further supported by the finding that coinjection with ICAM-1 dramatically enhanced the level of interferon-gamma (IFN-gamma) and beta-chemokines macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, and regulated on activation normal T-cell expression and secreted (RANTES) produced by stimulated T cells. Through comparative studies, we observed that ICAM-1/LFA-1 T-cell costimulatory pathways are independent of CD86/CD28 pathways and that they may synergistically expand T-cell responses in vivo.
The time sequence of electrical and mechanical activation during spontaneous beating and ectopic stimulation (1992)

The relation between the sequence of electrical (E) and mechanical (M) activation was studied at the LV anterior wall of open-chest dogs (n = 11). M activation was defined as the onset of epicardial fibre shortening, as measured with a recently developed video technique. E activation was determined with a brush of extracellular electrodes. The delay between activation of basal and apical regions was consistently larger for M activation than for E activation: during spontaneous beating: 20.5 +/- 7.30 ms vs 8.8 +/- 3.31 ms, during right ventricular outflow tract pacing: 50.3 +/- 7.69 ms vs 39.0 +/- 5.31 ms and during left ventricular apex pacing 40.1 +/- 10.03 ms vs 25.4 +/- 9.30 ms, respectively (P less than 0.05 in all cases). The E-M time interval was consistently shorter in early than in late activated regions: 32 +/- 10 vs 41 +/- 8 ms during RV outflow tract pacing (P = 0.09) and 24 +/- 30 vs 40 +/- 24 ms during LV apex pacing (P less than 0.05). Electrical asynchronies larger than 40 ms resulted in decreases of systolic blood pressure and stroke volume. This study shows that the asynchrony of cardiac motion exceeds that of electrical activation because the time interval between electrical activation and onset of fibre shortening is larger the later a particular region is activated. Possible explanations for this phenomenon are discussed.
Optical coherence tomography using a frequency-tunable optical source (1997)

We have developed a simple, wide-optical-bandwidth, high-resolution system for performing rapid optical frequency domain reflectometry measurements and applied it to multidimensional tomographic imaging. The source is a grating-tuned external cavity semiconductor laser with a tuning capability of 25 nm in 100 ms. We discuss system performance and show a two-dimensional optical coherence tomography image of a thin glass sandwich structure as a preliminary demonstration of the systems depth and resolution capabilities.
Infliximab Therapy for the Treatment of Refractory Ocular Inflammatory Disease (2007)

We found a high rate of ocular inflammation control with infliximab therapy. The incidence of adverse effects in this study was low.
Mass Production Method for Rice Protein Isolate and Nutritional Evaluation (1993)

ABSTRACT We developed a method for mass production of rice protein isolate (RPI) and evaluated its nutritional quality in rats. To obtain thick slurry, rice flour was mixed with a 0.6% Termamyl 120L‐solution (1:2, w/v) at room temperature (∼23°C). The slurry was heated at 97°C for 2 hr with stirring. Gelatinization and liquefaction occurred simultaneously. RPI obtained by filtration and washing with boiling water, was more than 90% pure protein (dry matter basis). It also contained 6.4% dietary fiber, 1.3% ash, and 1.1% carbohydrate. RPI diets (40–50%) allowed the maximum growth in rats comparable to that with 25% casein diet.
Remote Ischemic Limb Preconditioning After Subarachnoid Hemorrhage (2011)

We found limb preconditioning to be safe and well tolerated, even at ischemia times of 10 minutes, in critically ill patients with subarachnoid hemorrhage.
Programmable imaging using a digital micromirror array (2004)

We introduce the notion of a programmable imaging system. Such an imaging system provides a human user or a vision system significant control over the radiometric and geometric characteristics of the system. This flexibility is achieved using a programmable array of micro-mirrors. The orientations of the mirrors of the array can be controlled with high precision over space and time. This enables the system to select and modulate rays from the light field based on the needs of the application at hand. We have implemented a programmable imaging system that uses a digital micro-mirror device (DMD), which is used in digital light processing. Although the mirrors of this device can only be positioned in one of two states, we show that our system can be used to implement a wide variety of imaging functions, including, high dynamic range imaging, feature detection, and object recognition. We conclude with a discussion on how a micro-mirror array can be used to efficiently control field of view without the use of moving parts.
Preclinical Evaluation of Chimeric L6 Antibody for the Treatment of Kaposi's Sarcoma with Radioimmunotherapy (1999)

L6 is a murine IgG2a monoclonal antibody with panadenocarcinoma reactivity. Chimeric L6 (ChL6), the variable region of murine L6 combined with a human IgG1 constant region, has been used in clinical trials for the delivery of radioimmunotherapy to patients with breast cancer. AIDS-associated Kaposi's sarcoma (KS), a malignancy of vascular endothelium, may be an excellent candidate for systemic radioimmunotherapy because KS is well vascularized and radioresponsive. Because ChL6 has been noted to bind vascular endothelium, our hypothesis was that ChL6 will recognize and bind KS tumors making this a potentially useful antibody for the treatment of KS with radioimmunotherapy. To test this hypothesis, 4 human KS spindle cell cultures established from cutaneous punch biopsy specimens (KS-MR, KS-NO, KS-JD and KS 6-3E) and one well-characterized human KS cell line (KS Y-1) were assessed for L6 immunoreactivity. All 5 cell cultures were L6 positive by immunohistochemistry. KS Y-1 cells grown as nude mouse xenografts were also L6 positive by immunohistochemistry. Competitive binding assays performed on the KS Y-1 and KS 6-3E cell cultures showed high density and high affinity cell binding. Biodistribution experiments performed on nude mice with KS Y-1 xenografts demonstrate tumor targeting by ChL6. These findings indicate that ChL6 may be a useful antibody for the radioimmunotherapy of KS. Future experiments will assess the therapeutic efficacy of radiolabeled ChL6 with and without concurrent systemic radiosensitizing chemotherapy.
Chemical composition of tobacco seeds (Nicotiana tabacum L.) (1991)

Chemical characterization of tobacco seeds is supposed to be an interesting tool in order to extend the knowledge on alternative products of this crop which is of great economic interest. This paper describes chemical composition of meals, fat, ash, protein, fiber and nitrogen‐free‐extract; furthermore, particular emphasis is given to the composition of lipid fraction, with a complete characterization of triglycerides, fatty acids, and unsaponifiable matter. Trilinolein and palmitodilinolein are the main triglycerides, while linoleic is the main fatty acid. Cholesterol, as in other Solanaceae , is present in the sterol fraction. Cycloartenol is the main component of the triterpenic alcohols fraction. Amino acids and glucides composition is also reported.
Human Anti-Animal Antibody Interferences in Immunological Assays (1999)

Human anti-animal antibodies often go unnoticed, to the detriment of patient care. A heightened awareness on the part of laboratory staff and clinicians of the problems caused by this type of interference in routine immunoassay tests is desirable. Efforts should be directed at improving methods for identifying and eliminating this type of analytical interference.
Characterization of a Borna disease virus glycoprotein, gp18 (1994)

Borna disease virus is a nonsegmented negative-strand RNA virus that causes neurologic disease in a wide variety of animal hosts. Here we describe identification and characterization of the first glycoprotein in this viral system. The 18-kDa glycoprotein, gp18, has been purified from infected rat brain. Isolation and microsequencing of this protein allowed identification of a 16.2-kDa open reading frame in the viral antigenome. Lectin binding and endoglycosidase sensitivity assays indicate that gp18 is an unusual N-linked glycoprotein.
SecDF of Bacillus subtilis, a Molecular Siamese Twin Required for the Efficient Secretion of Proteins (1998)

In the present studies, we show that the SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of Escherichia coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps. Strains lacking intact SecDF showed a cold-sensitive phenotype, which was exacerbated by high level production of secretory proteins, indicating that protein translocation in B. subtilis is intrinsically cold-sensitive. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters. Our data suggest that SecDF of B. subtilis represents a novel type of the SecD and SecF proteins, which seems to be present in at least two other organisms.
Clusterin Facilitates COMMD1 and I-κB Degradation to Enhance NF-κB Activity in Prostate Cancer Cells (2010)

Secretory clusterin (sCLU) is a stress-activated, cytoprotective chaperone that confers broad-spectrum cancer treatment resistance, and its targeted inhibitor (OGX-011) is currently in phase II trials for prostate, lung, and breast cancer. However, the molecular mechanisms by which sCLU inhibits treatment-induced apoptosis in prostate cancer remain incompletely defined. We report that sCLU increases NF-kappaB nuclear translocation and transcriptional activity by serving as a ubiquitin-binding protein that enhances COMMD1 and I-kappaB proteasomal degradation by interacting with members of the SCF-betaTrCP E3 ligase family. Knockdown of sCLU in prostate cancer cells stabilizes COMMD1 and I-kappaB, thereby sequestrating NF-kappaB in the cytoplasm and decreasing NF-kappaB transcriptional activity. Comparative microarray profiling of sCLU-overexpressing and sCLU-knockdown prostate cancer cells confirmed that the expression of many NF-kappaB-regulated genes positively correlates with sCLU levels. We propose that elevated levels of sCLU promote prostate cancer cell survival by facilitating degradation of COMMD1 and I-kappaB, thereby activating the canonical NF-kappaB pathway.
4-Aminoethylene derivatives of 2-methylbenzotriazole (1990)

N-Methylation of 4(7)-nitrobenzotriazole ( I ) afforded a mixture of three isomers; one of them, 4-nitro-2-methylbenzotriazole ( II ) could easily be isolated. Catalytical hydrogenation of II led to the corresponding amine which in turn, afforded products of nucleophilic substitution IVa-IVi on reaction with alkoxymethylene derivatives IIIa-IIIi . Thermal cyclocondensation of IVi yielded 7-ethoxycarbonyl-6,9-dihydro-6-oxo-2-methyl-2 H -triazolo[4,5- h ]quinoline ( V ). The structure of all products was deduced from the IR, UV, 1 H and 13 C NMR spectral data.
Uniform InFlow Completion System Extends Economic Field Life: A Field Case Study and Technology Overview (2006)

Abstract Horizontal wells on a global basis continue to serve as a primary well type for improving recovery efficiency, increasing reservoir drainage area, delaying water and gas coning and increasing production rate. However, in longer, highly deviated and horizontal wells, non-uniform flow profiles can result in premature water or gas breakthrough, screen plugging and erosion, which can shorten well life and decrease well profitability. This paper describes historical and new applications of a proven production technology system that optimizes production, delays water and gas coning, minimizes annular flow to prevent erosion and ensures uniform inflow along the lateral at the cost of a minute pressure drop in high-rate horizontal wells. Case histories will be presented from the Norwegian Sector of the North Sea and offshore Saudi Arabia, where this production technology, combined with sand-control technology, has resulted in significant savings for the operator and improved production in horizontal offshore oil wells.