gebhart/patrepeval huggingface dataset:
Petri nets: Properties, analysis and applications (1989)

Starts with a brief review of the history and the application areas considered in the literature. The author then proceeds with introductory modeling examples, behavioral and structural properties, three methods of analysis, subclasses of Petri nets and their analysis. In particular, one section is devoted to marked graphs, the concurrent system model most amenable to analysis. Introductory discussions on stochastic nets with their application to performance modeling, and on high-level nets with their application to logic programming, are provided. Also included are recent results on reachability criteria. Suggestions are provided for further reading on many subject areas of Petri nets.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An incremental fitness function for partitioning parallel tasks (2001)

We describe a novel GA approach to partition programs to be executed on a parallel system. Two unique features distinguish this GA from traditional GA programs. First, this GA uses a dynamically incremental fitness function which starts out rewarding for simpler goals, gradually increasing the difficulty of the desired fitness values or goals until a full solution is found. Second, this GA uses a flexible representation style which allows the GA itself more control over both the structure and the value of the evolved solutions.
Identification of T- and B-cell epitopes of the S2 and S3 subunits of pertussis toxin by use of synthetic peptides (1992)

To design an optimized synthetic vaccine against whooping cough, we have studied the biological and immunological properties of three peptides of the S2 subunit and nine overlapping synthetic peptides covering the entire sequence of the S3 subunit of pertussis toxin (PT). Synthetic peptides corresponding to sequences 18 to 41, 78 to 108, 134 to 154, and 149 to 176 of S3 were found to be consistently capable of stimulating the proliferation of PT-specific T-cell lines primed with pertussis toxoid in both BALB/c and A/J strains of mice. All synthetic peptides were recognized by rabbit antisera raised against PT or pertussis toxoid. Both S2 and S3 peptide-keyhole limpet hemocyanin (KLH) conjugates in the presence of complete Freund's adjuvant induced peptide-specific antibody responses in rabbits, and the antisera raised against S2(1-23), S3(18-41), S3(37-64), and S3(149-176) peptide-KLH conjugates cross-reacted with both subunits in the immunoblots. All antisera except those against S2(123-154) and S3(103-127) reacted with native PT in an enzyme-linked immunosorbent assay (ELISA) with PT directly coated onto microtiter wells. In contrast, antisera raised against S2(123-154), S3(1-23), S3(18-41), S3(37-64), S3(60-87), and S3(103-127) peptide-KLH conjugates recognized native PT in a fetuin-PT capture ELISA. S2(78-98), S3(1-23), and S3(149-176) peptide-KLH conjugates elicited good PT-neutralizing antibody responses as judged by the antitoxin CHO cell assay. Identification of these B-cell neutralization epitopes and T-cell immunodominant determinants represents a first step towards the rational design of a synthetic vaccine against whooping cough.
Formation of the neuromuscular junction (1999)

Synapses are essential relay stations for the transmission of information between neurones and other cells. An ordered and tightly regulated formation of these structures is crucial for the functioning of the nervous system. The induction of the intensively studied synapse between nerve and muscle is initiated by the binding of neurone-specific isoforms of the basal membrane protein agrin to receptors on the surface of myotubes. Agrin activates a receptor complex that includes the muscle-specific kinase and most likely additional, yet to be identified, components. Receptor activation leads to the aggregation of acetylcholine receptors (AChR) and other proteins of the postsynaptic apparatus. This activation process has unique features which distinguish it from other receptor tyrosine kinases. In particular, the autophosphorylation of the kinase domain, which usually induces the recruitment of adaptor and signalling molecules, is not sufficient for AChR aggregation. Apparently, interactions of the extracellular domain with unknown components are also required for this process. Agrin binds to a second protein complex on the muscle surface known as the dystrophin-associated glycoprotein complex. This binding forms one end of a molecular link between the extracellular matrix and the cytoskeleton. While many components of the machinery triggering postsynaptic differentiation have now been identified, our picture of the molecular pathway causing the redistribution of synaptic proteins is still incomplete.
Trans Influence on the Rate of Reductive Elimination. Reductive Elimination of Amines from Isomeric Arylpalladium Amides with Unsymmetrical Coordination Spheres (2003)

To determine the trans effect on the rates of reductive eliminations from arylpalladium(II) amido complexes, the reactions of arylpalladium amido complexes bearing symmetrical and unsymmetrical DPPF (DPPF = bis(diphenylphosphino)ferrocene) derivatives were studied. THF solutions of LPd(Ar)(NMeAr') (L = DPPF, DPPF-OMe, DPPF-CF3, DPPF-OMe,Ph, DPPF-Ph,CF3, and DPPF-OMe,CF3; Ar = C6H4-4-CF3; Ar' = C6H4-4-CH3, Ph, and C6H4-4-OMe) underwent C-N bond forming reductive elimination at -15 C to form the corresponding N-methyldiarylamine in high yield. Complexes ligated by symmetrical DPPF derivatives with electron-withdrawing substituents on the DPPF aryl groups underwent reductive elimination faster than complexes ligated by symmetrical DPPF derivatives with electron-donating substituents on the ligand aryl groups. Studies of arylpalladium amido complexes containing unsymmetrical DPPF ligands revealed several trends. First, the complex with the weaker donor trans to nitrogen and the stronger donor trans to the palladium-bound aryl group underwent reductive elimination faster than the regioisomeric complex with the stronger donor trans to nitrogen and the weaker donor trans to the palladium-bound aryl group. Second, the effect of varying the substituents on the phosphorus donor trans to the nitrogen was larger than the effect of varying the substituents on the phosphorus donor trans to the palladium-bound aryl group. Third, the difference in rate between the isomeric arylpalladium amido complexes was similar in magnitude to the differences in rates resulting from conventional variation of substituents on the symmetric phosphine ligands. This result suggests that the geometry of the complex is equal in importance to the donating ability of the dative ligands. The ratio of the differences in rates of reaction of the isomeric complexes was similar to the relative populations of the two geometric isomers. This result and consideration of transition state geometries suggest that the reaction rates are controlled more by substituent effects on ground state stability than on transition state energies. In addition, variation of the aryl group at the amido nitrogen showed systematically that complexes with more electron-donating groups at nitrogen undergo faster reductive elimination than those with less electron-donating groups at nitrogen.
Characterization of acetyl‐CoA/propionyl‐CoA carboxylase in Metallosphaera sedula (2003)

Autotrophic Archaea of the family Sulfolobaceae (Crenarchaeota) use a modified 3-hydroxypropionate cycle for carbon dioxide assimilation. In this cycle the ATP-dependent carboxylations of acetyl-CoA and propionyl-CoA to malonyl-CoA and methylmalonyl-CoA, respectively, represent the key CO2 fixation reactions. These reactions were studied in the thermophilic and acidophilic Metallosphaera sedula and are shown to be catalyzed by one single large enzyme, which acts equally well on acetyl-CoA and propionyl-CoA. The carboxylase was purified and characterized and the genes were cloned and sequenced. In contrast to the carboxylase of most other organisms, acetyl-CoA/propionyl-CoA carboxylase from M. sedula is active at 75 degrees C and is isolated as a stabile functional protein complex of 560 +/- 50 kDa. The enzyme consists of two large subunits of 57 kDa each representing biotin carboxylase (alpha) and carboxytransferase (gamma), respectively, and a small 18.6 kDa biotin carrier protein (beta). These subunits probably form an (alpha beta gamma)4 holoenzyme. It has a catalytic number of 28 s-1 at 65 degrees C and at the optimal pH of 7.5. The apparent Km values were 0.06 mm for acetyl-CoA, 0.07 mm for propionyl-CoA, 0.04 mm for ATP and 0.3 mm for bicarbonate. Acetyl-CoA/propionyl-CoA carboxylase is considered the main CO2 fixation enzyme of autotrophic members of Sulfolobaceae and the sequenced genomes of these Archaea contain the respective genes. Due to its stability the archaeal carboxylase may prove an ideal subject for further structural studies.
Femtosecond-pulse distortion in quantum wells (1993)

We show that a low-intensity femtosecond pulse is severely distorted while propagating through a relatively thin (7000 \AA{}) GaAs multiple-quantum-well sample and that this pulse distortion depends critically on the dephasing time ${\mathit{T}}_{2}$ and the total thickness l. An interferometric measurement reveals the existence of well-defined nodes at which the envelope function changes its sign. This pulse distortion significantly affects femtosecond experiments such as pump-probe or four-wave-mixing experiments.
The natural cross‐pollination of crop plants with particular reference to the radish (1943)

Experiments were carried out to determine what degree of intervarietal cross‐pollination occurs when two radish varieties are grown at varying distances apart. The varieties chosen were Icicle and Scarlet Globe. Hybrids are distinctive; thus crossing is readily determined. In closely planted experiments, where one half of the plot was Icicle and the other half Scarlet Globe, the amount of intercrossing ranged from 30 to 40 % at a distance of 9 in. to an average of about 1 % at 15 ft. Intercrossing decreased fairly regularly and rapidly with distance. Single plants of Icicle were run out from plots of Scarlet Globe; in 1941 at distances from 9 in. to 95 ft. and in 1942 from 9 in. to 408 ft. In the plants near the red plots crossing was approximately 100 %. In 1941 there was a regular and rapid fall with distance and intervarietal crossing stopped at 95 ft. In 1942 the plots were closer to beehives; intercrossing was less regular and extended farther than in 1941, but beyond 240 ft. it was only 0.1%, and in an all‐white plot 360 ft. from a red plot with no intervening stringer plants it was nil. Given a mass of plants and a profusion of flowers, bees confine their flower visiting to a small area. When radishes are grown in quantity 300 ft. guards against contamination of stock due to intervarietal crossing. If only small numbers are grown intercrossing is likely to occur over a greater distance.
A novel helper phage that improves phage display selection efficiency by preventing the amplification of phages without recombinant protein (2003)

Phage display is a widely used technology for the isolation of peptides and proteins with specific binding properties from large libraries of these molecules. A drawback of the common phagemid/helper phage systems is the high infective background of phages that do not display the protein of interest, but are propagated due to non-specific binding to selection targets. This and the enhanced growth rates of bacteria harboring aberrant phagemids not expressing recombinant proteins leads to a serious decrease in selection efficiency. Here we describe a VCSM13-derived helper phage that circumvents this problem, because it lacks the genetic information for the infectivity domains of phage coat protein pIII. Rescue of a library with this novel CT helper phage yields phages that are only infectious when they contain a phagemid-encoded pIII-fusion protein, since phages without a displayed protein carry truncated pIII only and are lost upon re-infection. Importantly, the CT helper phage can be produced in quantities similar to the VCSM13 helper phage. The superiority of CT over VCSM13 during selection was demonstrated by a higher percentage of positive clones isolated from an antibody library after two selection rounds on a complex cellular target. We conclude that the CT helper phage considerably improves the efficiency of selections using phagemid-based protein libraries.
Adaptive active appearance models (2005)

The active appearance model (AAM) is a powerful tool for modeling images of deformable objects and has been successfully used in a variety of alignment, tracking, and recognition applications. AAM uses subspace-based deformable models to represent the images of a certain object class. In general, fitting such complicated models to previously unseen images using standard optimization techniques is a computationally complex task because the gradient matrix has to be numerically computed at every iteration. The critical feature of AAM is a fast convergence scheme which assumes that the gradient matrix is fixed around the optimal coefficients for all images. Our work in this paper starts with the observation that such a fixed gradient matrix inevitably specializes to a certain region in the texture space, and the fixed gradient matrix is not a good estimate of the actual gradient as the target texture moves away from this region. Hence, we propose an adaptive AAM algorithm that linearly adapts the gradient matrix according to the composition of the target image's texture to obtain a better estimate for the actual gradient. We show that the adaptive AAM significantly outperforms the basic AAM, especially in images that are particularly challenging for the basic algorithm. In terms of speed and accuracy, the idea of a linearly adaptive gradient matrix presented in this paper provides an interesting compromise between a standard optimization technique that recomputes the gradient at every iteration and the fixed gradient matrix approach of the basic AAM.
Short‐chain dehydrogenase/reductase catalyzing the final step of noscapine biosynthesis is localized to laticifers in opium poppy (2013)

The final step in the biosynthesis of the phthalideisoquinoline alkaloid noscapine involves a purported dehydrogenation of the narcotinehemiacetal keto moiety. A short-chain dehydrogenase/reductase (SDR), designated noscapine synthase (NOS), that catalyzes dehydrogenation of narcotinehemiacetal to noscapine was identified in opium poppy and functionally characterized. The NOS gene was isolated using an integrated transcript and metabolite profiling strategy and subsequently expressed in Escherichia coli. Noscapine synthase is highly divergent from other characterized members of the NADPH-dependent SDR superfamily involved in benzylisoquinoline alkaloid metabolism, and it exhibits exclusive substrate specificity for narcotinehemiacetal. Kinetic analyses showed that NOS exhibits higher catalytic efficiency with NAD+ as the cofactor compared with NADP+. Suppression of NOS transcript levels in opium poppy plants subjected to virus-induced gene silencing resulted in a corresponding reduction in the accumulation of noscapine and an increase in narcotinehemiacetal levels in the latex. Noscapine and NOS transcripts were detected in all opium poppy organs, but both were most abundant in stems. Unlike other putative biosynthetic genes clustered in the opium poppy genome, and their corresponding proteins, NOS transcripts and the cognate enzyme were abundant in latex, indicating that noscapine metabolism is completed in a distinct cell type compared with the rest of the pathway.
Wafer-Scale Synthesis of Single-Crystal Zigzag Silicon Nanowire Arrays with Controlled Turning Angles (2010)

Silicon nanowires (SiNWs) having curved structures may have unique advantages in device fabrication. However, no methods are available to prepare curved SiNWs controllably. In this work, we report the preparation of three types of single-crystal SiNWs with various turning angles via metal-assisted chemical etching using (111)-oriented silicon wafers near room temperature. The zigzag SiNWs are single crystals and can be p- or n-doped using corresponding Si wafer as substrate. The controlled growth direction is attributed to the preferred movement of Ag nanoparticles along 001 and other directions in Si wafer. Our results demonstrate that metal-assisted chemical etching may be a viable approach to fabricate SiNWs with desired turning angles by utilizing the various crystalline directions in a Si wafer.
Amino Acid Control of Neurotransmitter Synthesis and Release: Physiological and Clinical Implications (1993)

Brain catecholamine and serotonin neurons are intimately involved in a number of physiological functions such as cardiovascular regulation, neuroendocrine secretion, regulation of behavior, mood and appetite control. The synthesis and release of these neurotransmitters appear to be remarkably correlated with the subsequent physiological changes observed. While there are numerous pharmacological approaches that affect the neurotransmitters involved (i.e., the catecholamines dopamine, noradrenaline and adrenaline as well as the indoleamine serotonin), one particularly attractive (while specific) approach involves the administration of a precursor amino acid. It is thus a prerequisite for the physiological and possibly therapeutic properties of the precursor amino acids l-tyrosine and l-tryptophan that they affect synthesis and release of their transmitter product. We will describe in detail the nature of the different neurochemical mechanisms guiding transmitter synthesis and their dependent physiological responses, in particular appetite control and neuroendocrine regulation.
The Locator/ID Separation Protocol (LISP) for Multicast Environments (2013)

This document describes how inter-domain multicast routing will function in an environment where Locator/ID Separation is deployed using the Locator/ID Separation Protocol (LISP) architecture.
Betaine can eliminate the base pair composition dependence of DNA melting (1993)

We show that the amino acid analogue betaine shares with small tetraalkylammonium ions [Melchior, W. B., Jr., & von Hippel, P. H. (1973) Proc. Natl. Acad. Sci. U.S.A. 70, 298-302] the ability to reduce or even eliminate the base pair composition dependence of DNA thermal melting transitions. The "isostabilizing" concentration of betaine (at which AT and GC base pairs are equally stable) is approximately 5.2 M. Betaine exerts its isostabilizing effect without appreciably altering the conformation of double-stranded DNA from the B form. The presence of > 5 M betaine also does not greatly change the behavior of DNA as a polyelectrolyte; this lack of effect on electrostatic interactions is expected because betaine exists as a zwitterion near neutral pH. Study of DNA melting transitions in high concentrations of betaine thus allows the experimental separation of compositional and polyelectrolyte effects on DNA melting. As a consequence, betaine solutions can also be used to investigate DNA-protein interactions under isostabilizing (or close to isostabilizing) conditions, which has not been possible using isostabilizing salts. This potential is illustrated by examining the highly salt concentration-dependent interaction of ribonuclease A with DNA in concentrated betaine solutions.
Effects of Extraction Conditions on Improving the Yield and Quality of an Anthocyanin‐Rich Purple Corn ( Zea mays L.) Color Extract (2007)

Purple corn (Zea mays L.) is a rich and economic source of anthocyanin colorants and functional ingredients. However, high levels of anthocyanin-rich waste are generated during processing, reducing the yields and increasing the costs of the final product. This waste has been associated with anthocyanin complexation with tannins and proteins. Our objective was to evaluate anthocyanin extraction methods to reduce purple corn waste. Different solvents (water, 0.01%-HCl-acidified water, and 0.01%-HCl-acidified ethanol), temperatures (room temperature, 50, 75, and 100 degrees C), and times of exposure to the solvents were investigated. Acetone (70% acetone in water) extraction was used as control. Anthocyanins, total phenolics, tannins, and proteins in extracts were measured by the pH differential, Folin-Ciocalteu, protein precipitation, and BCA assay methods. Qualitative analyses were done by HPLC coupled to a PDA detector and SDS-PAGE analysis. Water at 50 degrees C achieved the highest yield of anthocyanins (0.94 +/- 0.03 g per 100 g dry corncob) with relatively low tannins and proteins, comparable to the anthocyanin yield obtained by 70% acetone (0.98 +/- 0.08 g per 100 g dry corncob). Extending the extraction time from 20 to 60 min and using consecutive reextraction procedures reduced anthocyanin purity, increasing the yields of other phenolics. A neutral protease was applied to the extracts and effectively decomposed the major protein that was believed to contribute to the development of anthocyanin complexation and waste generation. Extraction time, consecutive reextraction procedures, and enzyme hydrolysis should be considered for high yield of anthocyanins and waste reduction.
Carbon monoxide provides protection against hyperoxic lung injury (1999)

Findings in recent years strongly suggest that the stress-inducible gene heme oxygenase (HO)-1 plays an important role in protection against oxidative stress. Although the mechanism(s) by which this protection occurs is poorly understood, we hypothesized that the gaseous molecule carbon monoxide (CO), a major by-product of heme catalysis by HO-1, may provide protection against oxidative stress. We demonstrate here that animals exposed to a low concentration of CO exhibit a marked tolerance to lethal concentrations of hyperoxia in vivo. This increased survival was associated with highly significant attenuation of hyperoxia-induced lung injury as assessed by the volume of pleural effusion, protein accumulation in the airways, and histological analysis. The lungs were completely devoid of lung airway and parenchymal inflammation, fibrin deposition, and pulmonary edema in rats exposed to hyperoxia in the presence of a low concentration of CO. Furthermore, exogenous CO completely protected against hyperoxia-induced lung injury in rats in which endogenous HO enzyme activity was inhibited with tin protoporphyrin, a selective inhibitor of HO. Rats exposed to CO also exhibited a marked attenuation of hyperoxia-induced neutrophil infiltration into the airways and total lung apoptotic index. Taken together, our data demonstrate, for the first time, that CO can be therapeutic against oxidative stress such as hyperoxia and highlight possible mechanism(s) by which CO may mediate these protective effects.
ChemInform Abstract: PHENETHYLAMINE IN A SEMI‐RIGID FRAMEWORK: SYNTHESIS AND BIOLOGICAL ACTIVITY OF N‐SUBSTITUTED 1‐AMINOMETHYL‐5,6‐ AND 6,7‐DIMETHOXYISOCHROMANS (1979)

Abstract Die durch Cyclokondensation der Alkohole (I) mit Amino‐ bzw. Brom‐acetaldehyddiethylacetal erhältlichen Isochromane (IIa) und (IIb) werden durch N‐Acylierung bzw. durch Amino‐Substitution des Br‐Atoms in 1‐Aminomethylisochromane, wie z.B. (III), (IV) und (Va), übergeführt.