gebhart/patrepeval huggingface dataset:
Transient-State and Steady-State Kinetic Studies of the Mechanism of NADH-Dependent Aldehyde Reduction Catalyzed by Xylose Reductase from the Yeast <i>Candida tenuis</i> (2001)

Microbial xylose reductase, a representative aldo-keto reductase of primary sugar metabolism, catalyzes the NAD(P)H-dependent reduction of D-xylose with a turnover number approximately 100 times that of human aldose reductase for the same reaction. To determine the mechanistic basis for that physiologically relevant difference and pinpoint features that are unique to the microbial enzyme among other aldo/keto reductases, we carried out stopped-flow studies with wild-type xylose reductase from the yeast Candida tenuis. Analysis of transient kinetic data for binding of NAD(+) and NADH, and reduction of D-xylose and oxidation of xylitol at pH 7.0 and 25 degrees C provided estimates of rate constants for the following mechanism: E + NADH right arrow over left arrow E.NADH right arrow over left arrow E.NADH + D-xylose right arrow over left arrow E.NADH.D-xylose right arrow over left arrow E.NAD(+).xylitol right arrow over left arrow E.NAD(+) right arrow over left arrow E.NAD(+) right arrow over left arrow E + NAD(+). The net rate constant of dissociation of NAD(+) is approximately 90% rate limiting for k(cat) of D-xylose reduction. It is controlled by the conformational change which precedes nucleotide release and whose rate constant of 40 s(-)(1) is 200 times that of completely rate-limiting E.NADP(+) --> E.NADP(+) step in aldehyde reduction catalyzed by human aldose reductase [Grimshaw, C. E., et al. (1995) Biochemistry 34, 14356-14365]. Hydride transfer from NADH occurs with a rate constant of approximately 170 s(-1). In reverse reaction, the E.NADH --> E.NADH step takes place with a rate constant of 15 s(-1), and the rate constant of ternary-complex interconversion (3.8 s(-1)) largely determines xylitol turnover (0.9 s(-1)). The bound-state equilibrium constant for C. tenuis xylose reductase is estimated to be approximately 45 (=170/3.8), thus greatly favoring aldehyde reduction. Formation of productive complexes, E.NAD(+) and E.NADH, leads to a 7- and 9-fold decrease of dissociation constants of initial binary complexes, respectively, demonstrating that 12-fold differential binding of NADH (K(i) = 16 microM) vs NAD(+) (K(i) = 195 microM) chiefly reflects difference in stabilities of E.NADH and E.NAD(+). Primary deuterium isotope effects on k(cat) and k(cat)/K(xylose) were, respectively, 1.55 +/- 0.09 and 2.09 +/- 0.31 in H(2)O, and 1.26 +/- 0.06 and 1.58 +/- 0.17 in D(2)O. No deuterium solvent isotope effect on k(cat)/K(xylose) was observed. When deuteration of coenzyme selectively slowed the hydride transfer step, (D)()2(O)(k(cat)/K(xylose)) was inverse (0.89 +/- 0.14). The isotope effect data suggest a chemical mechanism of carbonyl reduction by xylose reductase in which transfer of hydride ion is a partially rate-limiting step and precedes the proton-transfer step.
Titanium Catalysis in the Ugi Reaction of α-Amino Acids with Aromatic Aldehydes (2004)

[reaction: see text] Ugi reaction between an (S)-alpha-amino acid, an aromatic aldehyde, and an isonitrile proceeds best under catalysis by TiCl(4) in MeOH. The sense of diastereoinduction is (S,S).
Low-temperature performance advantages for hydrodewaxed base stocks and products (1983)

Hydrodewaxing is more selective and more efficient than solvent dewaxing in the removal of paraffins to reduce lube oil pour point. The lower paraffin content of Mobil Lube Dewaxed (MLDW) oils results in lower VI values than solvent dewaxed (SDW) oils from the same source. Conventional interpretation of this lower VI is higher viscosity (poorer performance) at low temperatures and poorer viscosity-lubrication performance at high temperatures. However experiments show that VI is not a good indicator of viscometric performance at either low or high temperature extremes. In both viscometer and full-scale equipment tests, MLDW oils exhibit superior performance at low temperatures and equivalent performance at high temperatures to SDW oils. These results are a natural consequence of the composition differences between MLDW and SDW oils.
Contactless Optical Fiber Interferometric Sensor to Monitor Water Content in Ethanol (2018)

A simple contactless optical fiber interferometric sensor for real-time measurement of low-level of water content in ethanol is proposed and demonstrated. The sensing head consists of a multi-cavity Fabry-Pérot interferometer formed with a fiber tip in close contact with a quartz spectrophotometer cell. Ethanol-water solutions introduced into the cell cavity produce a change in the optical path length of one cavity of the interferometer. The increment of water content induces refractive index changes, but more important the absorption of the light increases. Both effects produce a significant change in the interference spectra that can be easily monitored and quantified in the Fourier domain. We demonstrate that our technique can detect water content (0%-60%) in ethanol with a detection limit as low as 0.5%.
Survey on categorical data for neural networks (2020)

Abstract This survey investigates current techniques for representing qualitative data for use as input to neural networks. Techniques for using qualitative data in neural networks are well known. However, researchers continue to discover new variations or entirely new methods for working with categorical data in neural networks. Our primary contribution is to cover these representation techniques in a single work. Practitioners working with big data often have a need to encode categorical values in their datasets in order to leverage machine learning algorithms. Moreover, the size of data sets we consider as big data may cause one to reject some encoding techniques as impractical, due to their running time complexity. Neural networks take vectors of real numbers as inputs. One must use a technique to map qualitative values to numerical values before using them as input to a neural network. These techniques are known as embeddings, encodings, representations, or distributed representations. Another contribution this work makes is to provide references for the source code of various techniques, where we are able to verify the authenticity of the source code. We cover recent research in several domains where researchers use categorical data in neural networks. Some of these domains are natural language processing, fraud detection, and clinical document automation. This study provides a starting point for research in determining which techniques for preparing qualitative data for use with neural networks are best. It is our intention that the reader should use these implementations as a starting point to design experiments to evaluate various techniques for working with qualitative data in neural networks. The third contribution we make in this work is a new perspective on techniques for using categorical data in neural networks. We organize techniques for using categorical data in neural networks into three categories. We find three distinct patterns in techniques that identify a technique as determined, algorithmic, or automated. The fourth contribution we make is to identify several opportunities for future research. The form of the data that one uses as an input to a neural network is crucial for using neural networks effectively. This work is a tool for researchers to find the most effective technique for working with categorical data in neural networks, in big data settings. To the best of our knowledge this is the first in-depth look at techniques for working with categorical data in neural networks.
Fidelity and Error Specificity of the α Catalytic Subunit of Escherichia coli DNA Polymerase III (1996)

Escherichia coli DNA polymerase III holoenzyme is the replicative enzyme primarily responsible for the duplication of the E. coli chromosome. This process occurs with high accuracy, less than 10(-9) to 10(-10) errors being committed per base pair per round of replication. As a first step in understanding the mechanisms responsible for the high fidelity of this process, we have purified the polymerase III alpha catalytic subunit, free of exonuclease activity, and analyzed its fidelity in vitro. We employed a newly developed gap-filling assay using the N-terminal 250 bases of the lacI gene as a forward mutational target. When synthesizing across this target, alpha subunit produced mutations at a frequency of 0.6%. DNA sequencing revealed that the mutants created in vitro consisted mostly of frameshift mutations, although some base substitutions were also observed. The frameshifts, occurring at more than 120-fold above the background, consisted largely of -1 deletions. Among them, about 80% were the deletion of a purine template base with a pyrimidine 5'-neighbor. These results suggest that the alpha subunit (i) has a relatively low ability to extend from misincorporated bases, accounting for the low level of observed base substitutions, and (ii) has a relatively high capability of extension after misalignment of a misincorporated base on the next (complementary) template base, accounting for the high level of frameshift mutations. This model is supported by an experiment in which alpha subunit was required to initiate DNA synthesis from a terminal mispair in a sequence context that allowed slippage on the next template base. Among the products of this reaction, frameshifts outnumbered base pair substitutions by greater than 70-fold. A comparison to in vivo mutational spectra suggests that the pol III accessory factors may play a major role in modulating the fidelity of DNA synthesis.
A Direct in Vivo Comparison of the Melanocortin Monovalent Agonist Ac-His-DPhe-Arg-Trp-NH<sub>2</sub> versus the Bivalent Agonist Ac-His-DPhe-Arg-Trp-PEDG20-His-DPhe-Arg-Trp-NH<sub>2</sub>: A Bivalent Advantage (2017)

Bivalent ligands targeting putative melanocortin receptor dimers have been developed and characterized in vitro; however, studies of their functional in vivo effects have been limited. The current report compares the effects of homobivalent ligand CJL-1-87, Ac-His-DPhe-Arg-Trp-PEDG20-His-DPhe-Arg-Trp-NH<sub>2</sub>, to monovalent ligand CJL-1-14, Ac-His-DPhe-Arg-Trp-NH<sub>2</sub>, on energy homeostasis in mice after central intracerebroventricular (ICV) administration into the lateral ventricle of the brain. Bivalent ligand CJL-1-87 had noteworthy advantages as an antiobesity probe over CJL-1-14 in a fasting-refeeding in vivo paradigm. Treatment with CJL-1-87 significantly decreased food intake compared to CJL-1-14 or saline (50% less intake 2-8 h after treatment). Furthermore, CJL-1-87 treatment decreased the respiratory exchange ratio (RER) without changing the energy expenditure indicating that fats were being burned as the primary fuel source. Additionally, CJL-1-87 treatment significantly lowered body fat mass percentage 6 h after administration (p < 0.05) without changing the lean mass percentage. The bivalent ligand significantly decreased insulin, C-peptide, leptin, GIP, and resistin plasma levels compared to levels after CJL-1-14 or saline treatments. Alternatively, ghrelin plasma levels were significantly increased. Serum stability of CJL-1-87 and CJL-1-14 (T<sub>1/2</sub> = 6.0 and 16.8 h, respectively) was sufficient to permit physiological effects. The differences in binding affinity of CJL-1-14 compared to CJL-1-87 are speculated as a possible mechanism for the bivalent ligand's unique effects. We also provide in vitro evidence for the formation of a MC3R-MC4R heterodimer complex, for the first time to our knowledge, that may be an unexploited neuronal molecular target. Regardless of the exact mechanism, the advantageous ability of CJL-1-87 compared to CJL-1-14 to increase in vitro binding affinity, increase the duration of action in spite of decreased serum stability, decrease in vivo food intake, decrease mice's body fat percent, and differentially affect mouse hormone levels demonstrates the distinct characteristics achieved from the current melanocortin agonist bivalent design strategy.
The evolution of DCS technology in access and core networks (2003)

A description is given of the function of and technology used in digital cross-connect systems (DCS) and the need for such a capability, which leads to broader aspects of network management. The potential overlap with real-time switching capability is discussed, together with the impact of the introduction of optical-fiber transmission in all parts of the network. It is shown how local network restructuring is leading to entirely new forms of DCS technology, as represented by the new Synchronous Optical Network (SONet) standards, which will bring a dynamic architecture to telecommunications networks, enabling bandwidth to be provided on demand, with much improved levels of supervision.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Feasibility study of micro-laser induced breakdown spectroscopy applied to lead identification in metal alloys and environmental matrices (1998)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1998.
Total Synthesis of Leustroducsin B (2003)

A convergent total synthesis of leustroducsin B (1), which is known to exhibit a variety of biological activities, was successfully carried out. Notable features of our synthesis include construction of the C8 stereocenter by lipase-mediated desymmetrization of meso-diol 4 (90.2% ee) and preparation of the C9-C11 anti-diol moiety by the addition of alkynylzinc reagent 20 to the aldehyde 19. Furthermore, a new diol protecting group, p-silyloxybenzylidene, was developed for the deprotection from densely functionalized substrates under weakly acidic conditions. The protecting group was easily removed in a two-step procedure ((HF)3.Et3N; AcOH-THF-H2O).
Recurrent intraocular inflammation after implantation of the Artiflex phakic intraocular lens for the correction of high myopia (2006)

We describe a 54-year old man who developed a severe cell deposition 1 week after implantation of a foldable Artiflex phakic intraocular lens (pIOL) (Ophtec B.V.) with a silicone optic and poly(methyl methacrylate) (PMMA) haptics in the left eye for the correction of high myopia. Nine months after implantation, many cell deposits remained visible on the posterior surface of the IOL, causing severe glare, especially during daylight conditions. We explanted the Artiflex pIOL and exchanged it for a PMMA Artisan pIOL. One month after the exchange, the uncorrected visual acuity was 20/20 and the patient's glare complaints had disappeared. Slitlamp examination showed no signs of inflammation in the anterior segment or cell deposits on the PMMA Artisan pIOL. Scanning electron microscopy demonstrated multiple cell deposits on the explanted Artiflex pIOL.
REDUCING ANTIBLOCK AND POLYMER PROCESSING ADDITIVE INTERACTIONS FOR IMPROVED BLOWN FILM MELT FRACTURE ELIMINATION (2000)

Combinations of antiblock and polymer processing additives (PPA) can result in interactions that reduce the PPA effectiveness. This is typically characterized by the need for higher concentrations of PPA to eliminate melt fracture compared to formulations not containing antiblock. Our experiments demonstrated that a new high-clarity antiblock interacts less with different PPAs in terms of melt fracture elimination and extruder pressure drop. Also, a new experimental antiblock showed almost no interaction with PPA, even when added via a combined masterbatch. New technology also results in improved optical properties for linear low density polyethylene (LLDPE) film.
Homogeneous Hydrogenation of Tri‐ and Tetrasubstituted Olefins: Comparison of Iridium‐Phospinooxazoline [Ir‐PHOX] Complexes and Crabtree Catalysts with Hexafluorophosphate (PF<sub>6</sub>) and Tetrakis[3,5‐bis(trifluoromethyl)phenyl]borate (BAr<sub>F</sub>) as Counterions (2007)

Abstract Four iridium complexes with achiral phosphino‐oxazoline (PHOX) ligands were readily prepared in two steps starting from commercially available phenyloxazolines. The air‐stable complexes with tetrakis[3,5‐bis(trifluoromethyl)phenyl]borate (BAr F ) as counterion showed high reactivity in the hydrogenation of a range of tri‐ and tetrasubstituted olefins. The best results were obtained with an iridium complex ( 11 ) derived from a dicyclohexylphosphino‐oxazoline ligand bearing no additional substituents in the oxazoline ring. With several substrates, which gave only low conversion with the Crabtree catalyst, [Ir(Py)(PCy 3 )(COD)]PF 6 , full conversion was observed. The productivity of the Crabtree catalyst could be strongly increased by replacing the hexafluorophosphate anion with tetrakis[3,5‐bis(trifluoromethyl)phenyl]borate. In one case, in the hydrogenation of a tetraalkyl‐substituted CC bond, [Ir(Py)(PCy 3 )(COD)]BAr F gave higher conversion than catalyst 11 . However, with several other substrates complex 11 proved to be superior.
Tandem mass spectrometry: From infancy to maturity in twenty‐five years (1993)

Abstract When this journal was initiated in 1968, there were only hints of the important applications of tandem mass spectrometry that are so well recognized today. It appears particularly appropriate to review briefly this development when celebrating the silver anniversary of the first mass spectrometry journal.
Interactions among components of the <i>Salmonella</i> flagellar export apparatus and its substrates (2000)

We have examined the cytoplasmic components (FliH, FliI and FliJ) of the type III flagellar protein export apparatus, plus the cytoplasmic domains (FlhAC and FlhBC) of two of its six membrane components. FliH, FlhAC and FliJ, when overproduced, caused inhibition of motility of wild-type cells and inhibition of the export of substrates such as the hook protein FlgE. Co-overproduction of FliH and FliI substantially relieved the inhibition caused by FliH, suggesting that it is excess free FliH that is inhibitory and that FliH and FliI form a complex. We purified His-FLAG-tagged versions of: (i) export components FliH, FliI, FliJ, FlhAC and FlhBC; (ii) rod/hook-type export substrates FlgB (rod protein), FlgE (hook protein), FlgD (hook capping protein) and FliE (basal body protein); and (iii) filament-type export substrates FlgK and FlgL (hook-filament junction proteins) and FliC (flagellin). We tested for protein-protein interactions by affinity blotting. In many cases, a given protein interacted with more than one other component, indicating that there are likely to be multiple dynamic interactions or interactions that involve more than two components. Interactions of FlhBC with rod/hook-type substrates were strong, whereas those with filament-type substrates were very weak; this may reflect the role of FlhB in substrate specificity switching. We propose a model for the flagellar export apparatus in which FlhA and FlhB and the other four integral membrane proteins of the apparatus form a complex at the base of the flagellar motor. A soluble complex of at least three proteins (FliH, FliI and FliJ) bind the protein to be exported and then interact with the complex at the motor to deliver the protein, which is then exported in an ATP-dependent process mediated by FliI.
Bidding to lose? Auctions with resale (2007)

A losing bidder can still purchase the prize from the winner after the auction. We show why a strong bidder may prefer to drop out of the auction before the price has reached her valuation and acquire the prize in the aftermarket: a strong bidder may be in a better bargaining position in the aftermarket if her rival won at a relatively low price. So it can be common knowledge that, in equilibrium, a weak bidder will win the auction and, even without uncertainty about relative valuations, resale will take place. The possibility of reselling to a strong bidder attracts weak bidders to participate in the auction and raises the seller's revenue.
Random fields, analysis and synthesis (1983)

Random variation over space and time is one of the few attributes that might safely be predicted as characterizing almost any given complex system. Random fields or distributed disorder systems confront astronomers, physicists, geologists, meteorologists, biologists, and other natural scientists. They appear in the artifacts developed by electrical, mechanical, civil, and other engineers. They even underlie the processes of social and economic change. The purpose of this book is to bring together existing and new methodologies of random field theory and indicate how they can be applied to these diverse areas where a deterministic treatment is inefficient and conventional statistics insufficient. Many new results and methods are included.After outlining the extent and characteristics of the random field approach, the book reviews the classical theory of multidimensional random processes and introduces basic probability concepts and methods in the random field context. It next gives a concise amount of the second-order analysis of homogeneous random fields, in both the space-time domain and the wave number-frequency domain. This is followed by a chapter on spectral moments and related measures of disorder and on level excursions and extremes of Gaussian and related random fields.After developing a new framework of analysis based on local averages of one-, two-, and n-dimensional processes, the book concludes with a chapter discussing ramifications in the important areas of estimation, prediction, and control. The mathematical prerequisite has been held to basic college-level calculus.
CO<sub>2</sub>decomposition using electrochemical process in molten salts (2012)

The electrochemical decomposition of CO2 gas to carbon and oxygen gas in LiCl-Li2O and CaCl2-CaO molten salts was studied. This process consists of electrochemical reduction of Li2O and CaO, as well as the thermal reduction of CO2 gas by the respective metallic Li and Ca. Two kinds of ZrO2 solid electrolytes were tested as an oxygen ion conductor, and the electrolytes removed oxygen ions from the molten salts to the outside of the reactor. After electrolysis in both salts, the aggregations of nanometer-scale amorphous carbon and rod-like graphite crystals were observed by transmission electron microscopy. When 9.7 %CO2-Ar mixed gas was blown into LiCl-Li2O and CaCl2-CaO molten salts, the current efficiency was evaluated to be 89.7 % and 78.5 %, respectively, by the exhaust gas analysis and the supplied charge. When a solid electrolyte with higher ionic conductivity was used, the current and carbon production became larger. It was found that the rate determining step is the diffusion of oxygen ions into the ZrO2 solid electrolyte.
The 26th Congress of the Scandinavian Society of Anaesthesiology and Intensive Care Medicine, Tromso, Norway, 13-17 June 2001. (2001)

The 26th Congress of the Scandinavian Society of Anaesthesiology and Intensive Care Medicine took place in the state-of-the art Tromso University Hospital. There were over 500 participants, and approximately 300 oral and poster presentations highlighted the latest progress in diverse areas. Much interest focused on activated protein C (APC) and other ways forward in sepsis treatment, pain management, novel markers of neurotrauma and antioxidants in bypass surgery. The meeting continues to be the leading anaesthesiology and intensive care conference in the region.