gebhart/patrepeval huggingface dataset:
Biosynthesis of carotenes in higher plants (1986)

Abstract Information is presented on various aspects of carotenoid biosynthesis in higher plants. These include the pathways of conversion of acetyl CoA to isopentenyl pyrophosphate, the formation of phytoene and, from the latter compound, the conversion of phytoene to lycopene and cylcic carotenes and the modifications of acyclic and cyclic carotenes to yield alicyclic xanthophylls, epoxycarotenoids, cyclopentenyl ketones, allenic and acetylenic carotenoids, and methyl‐oxidized carotenoids. Other subjects covered in this review are the stereochemistry and mechanism of synthesis for various carotenoids. Insofar as possible, information on the enzymes that catalyze the synthesis of carotenes is given. This includes their separation from other proteins, the products of their action, and the properties of each. Emphasis in this review is placed upon the newer findings on carotenoid biosynthesis and their significance. Some emphasis is also placed upon unsolved problems.
Amiodarone versus Sotalol for Atrial Fibrillation (2005)

Amiodarone and sotalol are equally efficacious in converting atrial fibrillation to sinus rhythm. Amiodarone is superior for maintaining sinus rhythm, but both drugs have similar efficacy in patients with ischemic heart disease. Sustained sinus rhythm is associated with an improved quality of life and improved exercise performance.
A New MF59-Adjuvanted Influenza Vaccine Enhances the Immune Response in the Elderly with Chronic Diseases: Results from an Immunogenicity Meta-Analysis (2003)

The MF59-adjuvanted influenza vaccine is more immunogenic in elderly subjects than conventional non-adjuvanted influenza vaccines and especially so in those with chronic disease. Therefore, since its safety profile is clinically acceptable, this adjuvanted vaccine represents an excellent option for influenza immunization of elderly subjects at highest risk of complications.
Display adaptive tone mapping (2008)

We propose a tone mapping operator that can minimize visible contrast distortions for a range of output devices, ranging from e-paper to HDR displays. The operator weights contrast distortions according to their visibility predicted by the model of the human visual system. The distortions are minimized given a display model that enforces constraints on the solution. We show that the problem can be solved very efficiently by employing higher order image statistics and quadratic programming. Our tone mapping technique can adjust image or video content for optimum contrast visibility taking into account ambient illumination and display characteristics. We discuss the differences between our method and previous approaches to the tone mapping problem.
Presence of donor-and-recipient-derived DNA microchimerism in the cell-free blood samples of renal transplantation recipients associates with the acceptance of transplanted kidneys (2006)

These results suggest that plasma DNA microchimerism present in certain patients following renal transplantation and measurement of plasma DNA microchimerism using quantitative RT-PCR might be a useful predictor for the acceptance of transplanted kidneys.
Isothiocyanate E‐4IB induces MAPK activation, delayed cell cycle transition and apoptosis (2007)

These findings suggest that the activation of mitogen-activated protein kinases signalling pathways, followed by the induction cell cycle arrest and apoptosis, might be responsible for anticancer activities of E-4IB.
Effects of nitrate and nitrite on dissimilatory iron reduction by Shewanella putrefaciens 200 (1992)

The inhibitory effects of nitrate (NO3-) and nitrite (NO2-) on dissimilatory iron (FE3+) reduction were examined in a series of electron acceptor competition experiments using Shewanella putrefaciens 200 as a model iron-reducing microorganism. S. putrefaciens 200 was found to express low-rate nitrate reductase, nitrite reductase, and ferrireductase activity after growth under highly aerobic conditions and greatly elevated rates of each reductase activity after growth under microaerobic conditions. The effects of NO3- and NO2- on the Fe3+ reduction activity of both aerobically and microaerobically grown cells appeared to follow a consistent pattern; in the presence of Fe3+ and either NO3- or NO2-, dissimilatory Fe3+ and nitrogen oxide reduction occurred simultaneously. Nitrogen oxide reduction was not affected by the presence of Fe3+, suggesting that S. putrefaciens 200 expressed a set of at least three physiologically distinct terminal reductases that served as electron donors to NO3-, NO2-, and Fe3+. However, Fe3+ reduction was partially inhibited by the presence of either NO3- or NO2-. An in situ ferrozine assay was used to distinguish the biological and chemical components of the observed inhibitory effects. Rate data indicated that neither NO3- nor NO2- acted as a chemical oxidant of bacterially produced Fe2+. In addition, the decrease in Fe3+ reduction activity observed in the presence of both NO3- and NO2- was identical to the decrease observed in the presence of NO2- alone. These results suggest that bacterially produced NO2- is responsible for inhibiting electron transport to Fe3+.
Cytochemical Identification of Monocytes and Granulocytes (1971)

Cytochemical methods for chloroacetate esterase, nonspecific esterase, peroxidase, and metachromasia were used to identify monocytes and neutrophilic, basophilic, or eosinophilic granulocytes. These methods are very simple, sensitive, and easily reproducible. Their reaction products are highly chromogenic and insoluble in most organic solvents. Any of these methods may be used independently or in combination with another cytochemical method to demonstrate a particular type of cell as desired. The specific aims and possible areas for clinical application of these cytochemical methods are discussed.
Computer Guided Instructional Design. (1984)

Ubiquitin-mediated proteasomal degradation is an important mechanism to control protein load in the cells. Ubiquitin binds to a protein on lysine residue and usually promotes its degradation through 26S proteasome system. Abnormal proteins and regulators of many processes, are targeted for degradation by the ubiquitin-proteasome system. It allows cells to maintain the response to cellular level signals and altered environmental conditions. The ubiquitin-mediated proteasomal degradation system plays a key role in the plant biology, including abiotic stress, immunity, and hormonal signaling by interfering with key components of these pathways. The involvement of the ubiquitin system in many vital processes led scientists to explore more about the ubiquitin machinery and most importantly its targets. In this review, we have summarized recent discoveries of the plant ubiquitin system and its involvement in critical processes of plant biology.
Mechanism of the Clostridium thermoaceticum Pyruvate:Ferredoxin Oxidoreductase:  Evidence for the Common Catalytic Intermediacy of the Hydroxyethylthiamine Pyropyrosphate Radical (1997)

The cofactor content and mechanism of pyruvate:ferredoxin oxidoreductase (PFOR) are controversial. By using rapid freeze-quench EPR and stopped-flow spectroscopy, the elementary steps that constitute the first half-reaction of the Clostridiumthermoaceticum PFOR mechanism were elucidated. A hydroxyethyl-TPP (HE-TPP) radical was identified and characterized as a transient intermediate, and for the first time, the kinetic competence of this substrate-derived radical was demonstrated. When the C. thermoaceticum PFOR was reacted with pyruvate and CoA, it had a lifetime of only approximately 100 ms. The results described here suggest that this radical intermediate is often not detected in studies of alpha-ketoacid oxidoreductases because it rapidly decays. It is postulated here that the HE-TPP radical is an intermediate in the mechanism of all PFORs irrespective of the number of 4Fe-4S clusters and will be detected in all PFORs when rapid mixing methods are used. The C. thermoaceticum PFOR was shown to contain two 4Fe-4S clusters, as concluded earlier [Wahl, R. C., & Orme-Johnson, W. H. (1987) J. Biol. Chem. 262, 10489-10496]. The first reductive half-reaction was shown to involve the following steps: (i) reaction with pyruvate with PFOR to form the hydroxyethylidene-TPP intermediate; (ii) one-electron transfer to reduce one of the two Fe4S4 clusters and yield the HE-TPP radical; and, (iii) reaction with CoA resulting in formation of acetyl-CoA, rapid decay of the HE-TPP radical intermediate, and reduction of the second Fe4S4 cluster. Thus, at the end of the first half-reaction, the two Fe4S4 clusters are fully reduced. The rate of the third step was found to depend on the CoA concentration (k = 35 per s at saturating concentrations of CoA); however, in its absence, this step was slower by approximately 4400-fold.
High-Resolution MALDI Fourier Transform Mass Spectrometry of Oligonucleotides (1996)

The matrix-assisted laser desorption/ionization (MALDI) method has been used with an external ion source Fourier transform mass spectrometer (FIMS) to analyze single-stranded, mixed-base oligomers of DNA. It is demonstrated that ultrahigh mass resolution (830 000 fwhm) can be achieved for small oligomers, and high resolution (136 000 fwhm) can be achieved for a 25-mer at m/z 7634. MALDI-FTMS can clearly separate the molecular ion peaks from analyte-matrix adduct peaks and alkali metal-containing species that result from replacement of hydrogen ions with sodium or potassium ions at multiple sites along the phosphate backbone. Previous MALDI-FTMS studies of oligonucleotides had two limitations: (1) low sensitivity due to difficulty in trapping the high kinetic energy ions made by the laser and (2) fragmentation of the ions due to the long delay (tens to hundreds of milliseconds) between their formation and detection. Both of these problems are alleviated in the present study. With the external ion source FTMS instrument, ions made by MALDI are injected at low energy into the analyzer cell by a rf-only quadrupole ion guide, captured by gating the voltage on the trapping plates, and cooled by a 0.5-s pulse of argon gas. Under these conditions, fragmentation is minimized, and DNA ions can be trapped in the FTMS analyzer cell for greater than 50 s. Sensitivity is also improved, as demonstrated by detection of 1 pmol of a single-stranded, mixed-base 20-mer of DNA, with a signal-to-noise ratio greater than 20:1.
Integrated out-of-plane nanoelectrospray thruster arrays for spacecraft propulsion (2009)

Nanoelectrosprays, well known for their use in sample injection for the mass spectrometry of large biomolecules, can also be used in other applications such as spacecraft propulsion. The thrust generated by a single electrospray emitter is well below 1 N, which is several orders of magnitude below the required thrust for planned formation flying missions. This paper presents the process flow and the microfabrication of large 2D arrays of out-of-plane nanoelectrospray capillary emitters with integrated extractor electrodes as well as electrospray results. The capillaries, 70 m high and with 24 m inner diameter, are etched from one silicon-on-insulator wafer. The extractor electrodes are from another silicon-on-insulator wafer. Both parts are passively aligned to within 2 m, centering each capillary under one extractor electrode, thus ensuring highly uniform emitter characteristics over large arrays. Low hydraulic impedance has been a major problem in out-of-plane electrospray designs in the past, which is solved here by adding a post-processing step in which the capillaries are filled with 5 m silica microspheres fixed in place by silanization. Finally, this paper reports on successful spray tests carried out under vacuum conditions with single and arrays of capillaries spraying the ionic liquid EMI-Tf 2 N demonstrating the operation of our nanoelectrospray thrusters in an ionic mode.
CMP-N-acetylneuraminic acid synthetase of Escherichia coli: high level expression, purification and use in the enzymatic synthesis of CMP-N-acetylneuraminic acid and CMP-neuraminic acid derivatives (1991)

The gene encoding CMP-N-acetylneuraminic acid (CMP-NeuAc) synthetase (EC 2.7.7.43) in Escherichia coil serotype 07 K1 was isolated and overexpressed in E.coli W3110. Maximum expression of 8–10% of the soluble E.coli protein was achieved by placing the gene with an engineered 5'-terminus and Shine-Dalgarno sequence into a pKK223 vector derivative behind the tac promoter. The overexpressed synthetase was purified to >95% homogeneity in a single step by chromatography on high titre Orange A Matrex ™ dye resin. Enzyme purified by this method was used directly for the synthesis of CMP-NeuAc and derivatives. The enzymatic synthesis of CMP-NeuAc was carried out on a multigram scale using equimolar CTP and N-acetylneuraminic acid as substrates. The resultant CMP-NeuAc, isolated as its disodium salt by ethanol precipitation, was prepared in an overall yield of 94% and was judged to be >95% pure by 1HNMR analysis. N-Carbomethoxyneuraminic acid and N-carbobenzyloxyneuraminic acid were also found to be substrates of the enzyme; 5-azidoneuraminic acid was not a substrate of the enzyme. N-Carbomethoxyneuraminic acid was coupled to CMP at a rate similar to that observed with NeuAc, whereas N-carbobenzyloxyneuraminic acid was coupled > 100-fold more slowly. The high level of expression achieved with the E.coli synthetase, together with the high degree of purity readily obtainable from crude cell extracts, make the recombinant bacterial enzyme the preferred catalyst for the enzymatic synthesis of CMP-N-acetylneuraminic acid.
Comparison of coagulation factor Xa and des-(1-44)factor Xa in the assembly of prothrombinase. (1984)

The gamma-carboxyglutamic acid (Gla)-domain region of factor X (residues 1-44 of the light chain) was selectively removed by limited proteolysis with alpha-chymotrypsin. The Gla-domainless factor X was then activated by the factor X coagulant protein of Russell's viper venom. Apparent dissociation constants Kd' values for the interaction of factor Va with either factor Xa or Gla-domainless factor Xa were determined kinetically using prothrombin as the substrate. In the absence of phospholipid, factor Va interacted with Gla-domainless factor Xa with lower affinity (Kd' 4 X 10(-6) M) than with factor Xa (Kd' = 5 X 10(-8) M). At saturating concentrations of factor Va, maximal rates of thrombin formation were similar for either enzyme. The addition of phospholipid increased the affinity of factor Va for factor Xa approximately 75-fold (Kd' = 3.3 X 10(-10) M). In contrast, phospholipid had no effect on the affinity of Gla-domainless factor Xa for factor Va (Kd' = 4 X 10(-6) M). The maximal rate of thrombin formation increased approximately 300-fold with the addition of phospholipid to the factor Xa-factor Va system. Under the same conditions, phospholipid had no effect on the rate of thrombin formation when Gla-domainless factor Xa was the enzymatic moiety. These results demonstrate phospholipid has little or no effect on factor Va function when factor Xa has lost its Gla-mediated Ca2+-binding sites.
Clinical Validation of Integrated Nucleic Acid and Protein Detection on an Electrochemical Biosensor Array for Urinary Tract Infection Diagnosis (2011)

We successfully demonstrate simultaneous detection of nucleic acid and host immune marker on a single biosensor array in clinical samples. This platform can be used for multiplexed detection of nucleic acid and protein as the next generation of urinary tract infection diagnostics.
Defect Engineering in Ce-Doped Aluminum Garnet Single Crystal Scintillators (2014)

Mg-codoped Lu3Al5O12:Ce single crystal scintillators were prepared by a micropulling down method in a wide concentration range from 0 to 3000 ppm of Mg codopant. Their structure and chemical composition were checked by X-ray diffraction and electron probe microanalysis techniques. Absorption and luminescence spectra, photoluminescence decays, and thermoluminescence glow curves were measured together with several other scintillation characteristics, namely, the scintillation decay, light yield, afterglow, and radiation damage to reveal the effect of Mg codoping. Several material characteristics manifest a beneficial effect of Mg codopant. We propose a model explaining the mechanism of material improvement which is based on the stabilization of a part of the cerium dopant in the tetravalent charge state. The stable Ce4+ center provides an additional fast radiative recombination pathway in the scintillation mechanism and efficiently competes with electron traps in garnet scintillators.
SCP-1 cancer/testis antigen is a prognostic indicator and a candidate target for immunotherapy in epithelial ovarian cancer. (2004)

SCP-1 is a novel tumor antigen that belongs to the growing family of cancer/testis (CT) antigens, and it is a potential target for immunotherapy. In an effort to determine the expression of SCP-1 in epithelial ovarian cancer (EOC), one-step RT-PCR was performed with RNA from epithelial ovarian tumor tissues and with two normal ovarian surface epithelial cell lines. We used immunohistochemistry (IHC) to investigate SCP-1 expression in paraffin-fixed EOC samples and ELISA to test sera from a subgroup of patients for SCP-1 antibody. SCP-1 was expressed in 15 out of 100 (15%) primary tumors, as determined by RT-PCR. The normal ovarian surface epithelial cell lines were negative for SCP-1 expression, as were a panel of other normal tissues. None of the patients whose tumors were determined to be SCP-1 positive by RT-PCR expressed the antigen by IHC or demonstrated a humoral immune response by ELISA. Tumors that expressed SCP-1 mRNA tended to have a higher grade than those that did not (P = 0.03). There was a significant decrease in survival time (P = 0.004) for patients with SCP-1 mRNA-positive tumors compared to those with SCP-1 mRNA-negative tumors [median 25 mo, 95% confidence interval (CI) 0-56 mo; and median 97 mo, CI 32-162 mo, respectively]. The present study shows that SCP-1 mRNA expression in patients with EOC is associated with a poorer chance of survival. These findings imply that further evaluation of SCP-1 as a potential target for vaccine therapy in EOC is warranted.
Subset languages for conversing with collaborative interface agents (2002)

This paper reports on experiments with subjects who must learn to use a small artificially constructed subset language (of English) to interact with a conversational spoken language system. The subjects converse with a collaborative interface agent about tasks involving TV recording and schedule navigation. The subjects perform their tasks in two conditions, one with contextually appropriate help on what to say always available on the screen and those with only a help sheet that they request to see. Our experiments indicate that users can perform their tasks in either condition, but demonstrate limits in remembering the language in a subsequent session.
Recognition of Lysophosphatidylcholine by Type II NKT Cells and Protection from an Inflammatory Liver Disease (2014)

Lipids presented by the MHC class I-like molecule, CD1d, are recognized by NK T (NKT) cells, which can be broadly categorized into two subsets. The well-characterized type I NKT cells express a semi-invariant TCR and can recognize both α- and β-linked glycolipids, whereas type II NKT cells are less well studied, express a relatively diverse TCR repertoire, and recognize β-linked lipids. Recent structural studies have shown a distinct mode of recognition of a self-glycolipid sulfatide bound to CD1d by a type II NKT TCR. To further characterize Ag recognition by these cells, we have used the structural data and screened other small molecules able to bind to CD1d and activate type II NKT cells. Using plate-bound CD1d and APC-based Ag presentation assay, we found that phospholipids such as lysophosphatidylcholine (LPC) can stimulate the sulfatide-reactive type II NKT hybridoma Hy19.3 in a CD1d-dependent manner. Using plasmon resonance studies, we found that this type II NKT TCR binds with CD1d-bound LPC with micromolar affinities similar to that for sulfatide. Furthermore, LPC-mediated activation of type II NKT cells leads to anergy induction in type I NKT cells and affords protection from Con A-induced hepatitis. These data indicate that, in addition to self-glycolipids, self-lysophospholipids are also recognized by type II NKT cells. Because lysophospholipids are involved during inflammation, our findings have implications for not only understanding activation of type II NKT cells in physiological settings, but also for the development of immune intervention in inflammatory diseases.
Chimeric tick-borne encephalitis and dengue type 4 viruses: effects of mutations on neurovirulence in mice (1993)

Two new chimeric flaviviruses were constructed from full-length cDNAs that contained tick-borne encephalitis virus (TBEV) CME or ME structural protein genes and the remaining genes derived from dengue type 4 virus (DEN4). Studies involving mice inoculated intracerebrally with the ME chimeric virus indicated that it retained the neurovirulence of its TBEV parent from which its pre-M and E genes were derived. However, unlike parental TBEV, the chimeric virus did not produce encephalitis when mice were inoculated peripherally, indicating a loss of neuroinvasiveness. In the present study, the ME chimeric virus (vME) was subjected to mutational analysis in an attempt to reduce or ablate neurovirulence measured by direct inoculation of virus into the brain. We identified three distinct mutations that were each associated independently with a significant reduction of mouse neurovirulence of vME. These mutations ablated (i) the TBEV pre-M cleavage site, (ii) the TBEV E glycosylation site, or (iii) the first DEN4 NS1 glycosylation site. In contrast, ablation of the second DEN4 NS1 glycosylation site or the TBE pre-M glycosylation site or amino acid substitution at two positions in the TBEV E protein increased neurovirulence. The only conserved feature of the three attenuated mutants was restriction of virus yield in both simian and mosquito cells. Following parenteral inoculation, these attenuated mutants induced complete resistance in mice to fatal encephalitis caused by the highly neurovirulent vME.
The Study of Molecular Interactions by AFM Force Spectroscopy (2001)

Recent progress in atomic force microscopy (AFM) technology has allowed the measurement of inter- and intramolecular forces at the level of individual molecules. The mechanical manipulation of single polymer chains immobilized on solid substrates has become possible in solution, as they are spanned and stretched between the tip of an AFM cantilever and the substrate surface. This investigation of polymer chains far from their maximum entropy configurations has stimulated the refinement of existing polymer theories. From the measured force-distance curves quantitative information can be obtained on the elasticity of single macromolecules in solution, on conformational transitions along the chains, about the mechanical stability of chemical bonds and on secondary structures, as well as on the desorption of individual polymer molecules from solid substrates. Recent applications of AFM single molecule force spectroscopy reach from the study of dynamic processes in complex biological systems and intermolecular forces in colloidal systems to the investigation of new functional materials capable of performing energy transductions on the level of individual macromolecules. In this article, we present a detailed description of the experimental procedure, followed by an overview of the development, the success and the current challenges of this technique during the past five years, in which it has rapidly evolved from the first proof of principle to a highly active field of research.