gebhart/patrepeval huggingface dataset:
Monoterpene Metabolism. Cloning, Expression, and Characterization of (−)-Isopiperitenol/(−)-Carveol Dehydrogenase of Peppermint and Spearmint (2005)

The essential oils of peppermint (Mentha x piperita) and spearmint (Mentha spicata) are distinguished by the oxygenation position on the p-menthane ring of the constitutive monoterpenes that is conferred by two regiospecific cytochrome P450 limonene-3- and limonene-6-hydroxylases. Following hydroxylation of limonene, an apparently similar dehydrogenase oxidizes (-)-trans-isopiperitenol to (-)-isopiperitenone in peppermint and (-)-trans-carveol to (-)-carvone in spearmint. Random sequencing of a peppermint oil gland secretory cell cDNA library revealed a large number of clones that specified redox-type enzymes, including dehydrogenases. Full-length dehydrogenase clones were screened by functional expression in Escherichia coli using a recently developed in situ assay. A single full-length acquisition encoding (-)-trans-isopiperitenol dehydrogenase (ISPD) was isolated. The (-)-ISPD cDNA has an open reading frame of 795 bp that encodes a 265-residue enzyme with a calculated molecular mass of 27,191. Nondegenerate primers were designed based on the (-)-trans-ISPD cDNA sequence and employed to screen a spearmint oil gland secretory cell cDNA library from which a 5'-truncated cDNA encoding the spearmint homolog, (-)-trans-carveol-dehydrogenase, was isolated. Reverse transcription-PCR amplification and RACE were used to acquire the remaining 5'-sequence from RNA isolated from oil gland secretory cells of spearmint leaf. The full-length spearmint dehydrogenase shares >99% amino acid identity with its peppermint homolog and both dehydrogenases are capable of utilizing (-)-trans-isopiperitenol and (-)-trans-carveol. These isopiperitenol/carveol dehydrogenases are members of the short-chain dehydrogenase/reductase superfamily and are related to other plant short-chain dehydrogenases/reductases involved in secondary metabolism (lignan biosynthesis), stress responses, and phytosteroid biosynthesis, but they are quite dissimilar (approximately 13% identity) to the monoterpene reductases of mint involved in (-)-menthol biosynthesis. The isolation of the genes specifying redox enzymes of monoterpene biosynthesis in mint indicates that these genes arose from different ancestors and not by simple duplication and differentiation of a common progenitor, as might have been anticipated based on the common reaction chemistry and structural similarity of the substrate monoterpenes.
A Switch-Level Model and Simulator for MOS Digital Systems (1984)

The switch-level model describes the logical behavior of digital systems implemented in metal oxide semiconductor (MOS) technology. In this model a network consists of a set of nodes connected by transistor "switches" with each node having a state 0, 1, or X (for invalid or uninitialized), and each transistor having a state "open," "closed," or "indeterminate." Many characteristics of MOS circuits can be modeled accurately, including: ratioed, complementary, and precharged logic; dynamic and static storage; (bidirectional) pass transistors; buses; charge sharing; and sneak paths. In this paper we present a formal development of the switch-level model starting from a description of circuit behavior in terms of switch graphs. Then we describe an algorithm for a logic simulator based on the switch-level model which computes the new state of the network by solving a set of equations in a simple, discrete algebra. This algorithm has been implemented in the simulator MOSSIM II and operates at speeds approaching those of conventional logic gate simulators. By developing a formal theory of MOS logic circuits, we have achieved a greater degree of generality and accuracy than is found in other logic simulators for MOS.
SketchBio: a scientist’s 3D interface for molecular modeling and animation (2014)

The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.
Formation of 3-Monochloro-1,2-propanediol (3-MCPD) Di- and Monoesters from Tristearoylglycerol (TSG) and the Potential Catalytic Effect of Fe<sup>2+</sup> and Fe<sup>3+</sup> (2015)

This study investigated whether and how triacylglycerol (TAG) may serve as a precursor for 3-monochloro-1,2-propanediol (3-MCPD) fatty acid ester formation using tristearoylglycerol (TSG). TSG was reacted with inorganic chloride compounds including NaCl, KCl, FeCl2, CuCl2, ZnCl2, FeCl3 and dry HCl, or organic chlorine compound lindane at different temperatures. Only FeCl2 and FeCl3 were able to form 3-MCPD esters from TSG. Further electron spin resonance (ESR) determination of TSG, Fe2(SO4)3 and 5,5-dimethylpyrroline-N-oxide (DMPO) reactions revealed potential of Fe ion in promoting free radical generations under the experimental conditions. To further confirm the effect of Fe ion, chelating agent (EDTA-2Na) was added to the model reactions. The results showed for the first time that EDTA-2Na was able to reduce the generation of 3-MCPD esters. In addition, FT-IR examination indicated a possible involvement of a carbonyl group during the reaction. Taking all the observations together, the possible mechanisms, involving the formation of either a cyclic acyloxonium or a glycidol ester radical intermediate, were proposed for generating 3-MCPD fatty acid di- and mono- esters from TAG under a high temperature and low moisture condition, as well as the coformation of glycidol esters. The results from this study may be useful for reducing the level of 3-MCPD esters and related toxicants in the refined edible oils and food products.
Pentastarch instead of albumin as replacement fluid for therapeutic plasma exchange (1997)

BACKGROUND Human albumin is commonly used as a replacement fluid in therapeutic plasma exchange (PE). In order to determine whether Pentaspan® (PES), a synthetic low molecular weight starch solution, might be an effective substitute, we compared albumin with PES in 12 patients with myasthenia gravis or Guillain-Barré syndrome. STUDY DESIGN AND METHODS: Six patients were randomly assigned to receive PES and six to receive albumin as replacement fluid during their course of PE, which consisted of two to five treatments delivered over a maximum of 10 days. All patients were hospitalized and observed closely. Blood pressures were recorded every 4 hours and daily measurements were made of hematologic, coagulation, and immunoglobulin parameters. RESULTS: Individual exchange volumes were similar in each group (37 ml/kg—range 6–62—in patients receiving albumin vs. 41 ml/kg—range 6–41—in those receiving PES). Changes in immunoglobulin levels and coagulation parameters were similar but mild, transient thrombocytopenia was observed in three subjects given PES. Total serum protein and albumin levels decreased significantly in patients replaced with PES. Clinically, PES was well tolerated. Hypotension occurred in one patient who developed septic shock due to an infected femoral catheter; in another patient, a pre-existing pleural effusion was thought to increase slightly. CONCLUSIONS: PES appears to be a safe replacement fluid for PE, but larger clinical studies are required to confirm these findings. J. Clin. Apheresis 12:165–169, 1997. © 1997 Wiley-Liss, Inc.
Nonhematopoietic tumor cells express functional GM-CSF receptors (1989)

Human granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates the colony growth of myeloid progenitors in semisolid media, and enhances the function of mature effector cells, including neutrophils, monocytes, and eosinophils. Small cell carcinoma lines (SCCL) have properties of amine precursor uptake and decarboxylation (APUD) cells and express high levels of the enzyme, L-aromatic amino acid decarboxylase. We looked for possible expression of GM-CSF receptors on nonhematopoietic cells and found specific high-affinity binding of human GM-CSF to SCCL and to the SV40-transformed African green monkey kidney cell line, COS. The small cell carcinoma lines responded to GM-CSF with enhanced proliferation, and both small cells and COS cells were found to express authentic 84,000 dalton GM-CSF receptor protein. These findings indicate that nonhematopoietic cells can bind and respond to GM-CSF, suggesting additional biological activities as well as the possibility of tumor responses when GM-CSF is used therapeutically in humans. Since preliminary clinical trials using CSFs as adjunctive treatment in patients with solid tumors are underway, it will be important to consider the possible responsiveness of nonhematopoietic tumor cells to CSFs.
Access control by using object properties and categorized methods (2004)

We propose an access control model that is suitable for a distributed object oriented environment. Our model has two features: authentication with object properties and method categorization by a security level. The object property is meta information of a client, and the client is vested with it in advance. To use the object properties, a server can identify a huge number of clients in the environment by groups that is categorized with the object properties of the clients. And also, to use a combination of multiple object properties in authentication, an administrator of the server can determine the flexible range of target clients. The security level shows how much impact the method affects server's data. If a designer of the server categorizes the server's methods with a security level, an administrator of the server can set an authorization rule to each category instead of each server's method. The categories constitute a tree structure, since a parent category includes child categories. As a result of this, the administrator can set an authorization rule easier than authorization without categorization by the security level. Furthermore, we implemented above the access control model and we evaluated their efficiency.
Autonomic management framework for cloud-based virtual networks (2011)

Cloud computing promises to reshape the way IT service is produced and consumed by virtualizing computing resources. As if cloud providers offer virtualized CPU and storage resources via machine virtualization and distributed storage technologies respectively, the providers wish to offer to their customers' virtual networks running on the cloud. With cloud-based virtual networks (CVNs), cloud customers (often, corporate customers) can easily build new sites, effectively expanding their enterprise networks into the cloud and thus leveraging the entire benefits of cloud computing (agility, manageability, low cost, etc.). In this paper, we identify core requirements and objectives for managing CVNs. We then define a high-level autonomic CVN-management framework by demarcating between the customer and provider with CVN Management Interface (CMI). Finally we propose an open-flow based autonomic cloud data center management solution based on CVN management framework.
Indication of Anisotropy in Electromagnetic Propagation over Cosmological Distances (1997)

We report a systematic rotation of the plane of polarization of electromagnetic radiation propagating over cosmological distances. The effect is extracted independently from Faraday rotation, and found to be correlated with the angular positions and distances to the sources. Monte Carlo analysis yields probabilistic $P$ values of order ${10}^{\ensuremath{-}3}$ for this to occur as a fluctuation. A fit yields a birefringence scale of order ${10}^{25}\frac{{h}_{0}}{h}\mathrm{m}$. Dependence on redshift $z$ rules out a local effect. Barring hidden systematic bias in the data, the correlation indicates a new cosmological effect.
Wogonin, a plant flavone from <i>Scutellariae</i> radix, attenuated ovalbumin-induced airway inflammation in mouse model of asthma via the suppression of IL-4/STAT6 signaling (2015)

Bronchial asthma is a chronic inflammatory disease of the airways characterized by a marked infiltration of eosinophils at the site of inflammation. Eotaxins are potent chemoattractants for eosinophils and play important roles in pathogenesis of asthma. In the course of screening for eotaxin-3 inhibitors, we found that wogonin showed potent inhibitory activity of interleukin-4 (IL-4)-induced eotaxin-3 expression in BEAS-2B cells. In this study, we examined the effects of wogonin on IL-4/STAT6 signaling pathway and biological implication in a mouse model of asthma. Wogonin inhibited IL-4-induced activation and nuclear translocation of STAT6 which plays a key role in either the transcription of STAT6-response genes or Th2 cytokine-mediated inflammation. Oral administration of wogonin significantly reduced activation of STAT6 in the lung and the expression of eotaxin and RANTES in bronchoalveolar lavage fluids. Histological examination of lung tissue demonstrated that wogonin significantly inhibited allergen-induced eosinophilic inflammation. Administration of wogonin reduced the total IgE and ovalbumin-specific IgE levels compared with the ovalbumin-challenged group. All of these data demonstrated that wogonin could alleviate airway inflammation through inhibition of STAT6 activation induced by Th2 cytokines. Our finding implicates a potential therapeutic value of wogonin in the treatment of asthma through regulation of IL-4/STAT6 signaling pathway.
Electrolytic synthesis of aqueous aluminum nanoclusters and in situ characterization by femtosecond Raman spectroscopy and computations (2013)

The selective synthesis and in situ characterization of aqueous Al-containing clusters is a long-standing challenge. We report a newly developed integrated platform that combines (i) a selective, atom-economical, step-economical, scalable synthesis of Al-containing nanoclusters in water via precision electrolysis with strict pH control and (ii) an improved femtosecond stimulated Raman spectroscopic method covering a broad spectral range of ca. 350-1,400 cm(-1) with high sensitivity, aided by ab initio computations, to elucidate Al aqueous cluster structures and formation mechanisms in real time. Using this platform, a unique view of flat [Al13(μ3-OH)6(μ2-OH)18(H2O)24](NO3)15 nanocluster formation is observed in water, in which three distinct reaction stages are identified. The initial stage involves the formation of an [Al7(μ3-OH)6(μ2-OH)6(H2O)12](9+) cluster core as an important intermediate toward the flat Al13 aqueous cluster.
A wideband airport pseudolite architecture for the local area augmentation system (2003)

This dissertation documents the design, development, and field and flight testing of a WBAPL for integration into a prototype LAAS. One major area of risk in the LAAS CAT II/III program is the unresolved issue of sufficient system availability. One feasible, low-cost, means of augmenting the GPS constellation for LAAS to enhance availability is by the incorporation of APLs. Critical issues that seek consideration in APL design are a low-cost solution to the near-far problem, effective mitigation of APL multipath at the LGF reception sites, and a solution to the issue of measurement errors as a function of peak received signal power level. This dissertation details the development of a prototype WBAPL within the framework of LAAS requirements, with the intent of resolving the aforementioned issues. The architecture includes a simple and novel method to facilitate rapid direct-WB signal acquisition, and details a cost-effective resolution to the power-bias problem. Results from laboratory tests to verify and characterize the power-induced measurement errors are described in the dissertation. Independent solutions to the power-bias problem at the ground and airborne segments were incorporated into the prototype WBAPL architecture. The solution on the ground involves the employment of RF power-control techniques. With the aim of low-cost implementation, the solution adopted for the airborne segment relies on carrier-phase measurements as the aircraft approaches the WBAPL transmission antenna. A time-differenced carrier-phase positioning algorithm that does not require real-time resolution of the unknown carrier-phase integer ambiguities is adopted. This differential CP approach is launched from a carrier-smoothed code based solution that is maintained from the beginning of the approach until the phase handover-point. A modification to the WBAPL single difference geometry matrix is incorporated into the TDCP algorithm. The proposed architecture was successfully flight-tested to demonstrate the feasibility of its incorporation into LAAS, the results of which are presented in the dissertation. The performance of the prototype WBAPL-inclusive LAAS is gauged in terms of the accuracy of the differential positioning solution. The integration of the WBAPL into the prototype LAAS provided an additional ranging measurement, and increased system availability.
<i>In vivo</i> Contributions of BH3-Only Proteins to Neuronal Death Following Seizures, Ischemia, and Traumatic Brain Injury (2011)

The Bcl-2 homology (BH) domain 3-only proteins are a proapoptotic subgroup of the Bcl-2 gene family, which regulate cell death via effects on mitochondria. The BH3-only proteins react to various cell stressors and promote cell death by binding and inactivating antiapoptotic Bcl-2 family members and direct activation of proapoptotic multi-BH domain proteins such as Bax. Here, we review the in vivo evidence for their involvement in the pathophysiology of status epilepticus and contrast it to ischemia and traumatic brain injury. Seizures in rodents activate three potent proapoptotic BH3-only proteins: Bid, Bim, and Puma. Analysis of damage after seizures in mice singly deficient for each BH3-only protein supports a causal role for Puma and to a lesser extent Bim but, surprisingly, not Bid. In ischemia and trauma, where core aspects of the pathophysiology of cell death overlap, multiple BH3-only proteins are also activated and Bid has been shown to be required for neuronal death. The findings suggest that while each neurologic insult activates multiple BH3-only proteins, there may be specificity in their functional contribution. Future challenges include evaluating the remaining BH3-only proteins, explaining different causal contributions, and, if possible, exploring neurologic outcomes in mouse models deficient for multiple BH3-only proteins.
Arylation of Camphene with Arenediazonium Salts Catalyzed by Palladium Acetate (1991)

(E)-8-Arylcamphenes 3 were obtained in moderate to good yields by the reaction of camphene (1) with a variety of arenediazonium tetrafluoroborates 2 in the presence of palladium acetate under mild conditions. The E-configuration of the products was confirmed by 1H-NMR analyses of the reaction mixtures of photoisomerization of 3, the Nuclear Overhauser Effect (NOE) of 3a and by comparison with an authentic sample of 4j.
Effect of storage temperature on viability of Trichophyton mentagrophytes in infected guinea pig skin scales (1979)

The effect of storage temperature on the viability of Trichophyton mentagrophytes in infected guinea pig skin scales was quantitatively evaluated for 182 days. Infected skin scales were stored, while protected from light, in glass containers with desiccant at four temperatures and sampled after saline treatment at various time intervals. No decrease in viability was observed for storage at 4 degrees C, room temperature, or 30 degrees C. Storage at 37 degrees C resulted in a significant loss in viability.
Thermal energetic model of an Internal Combustion Engine for simulation of a thermal vehicle (2012)

The objective of this paper is to develop an energetic dynamical description of a model of an Internal Combustion Engine. This model is based on a simple power balance between input and output power of engine. The Energetic Macroscopic Representation (EMR) is used to organize the IC engine model. This energetic description will be coupled with the whole vehicle previously developed with EMR. The fuel consumption and the detailed power flow will be analysis for a complete drive cycle.
An analysis of neural receptive field plasticity by point process adaptive filtering (2001)

Neural receptive fields are plastic: with experience, neurons in many brain regions change their spiking responses to relevant stimuli. Analysis of receptive field plasticity from experimental measurements is crucial for understanding how neural systems adapt their representations of relevant biological information. Current analysis methods using histogram estimates of spike rate functions in nonoverlapping temporal windows do not track the evolution of receptive field plasticity on a fine time scale. Adaptive signal processing is an established engineering paradigm for estimating time-varying system parameters from experimental measurements. We present an adaptive filter algorithm for tracking neural receptive field plasticity based on point process models of spike train activity. We derive an instantaneous steepest descent algorithm by using as the criterion function the instantaneous log likelihood of a point process spike train model. We apply the point process adaptive filter algorithm in a study of spatial (place) receptive field properties of simulated and actual spike train data from rat CA1 hippocampal neurons. A stability analysis of the algorithm is sketched in the. The adaptive algorithm can update the place field parameter estimates on a millisecond time scale. It reliably tracked the migration, changes in scale, and changes in maximum firing rate characteristic of hippocampal place fields in a rat running on a linear track. Point process adaptive filtering offers an analytic method for studying the dynamics of neural receptive fields.
Natural antibodies to nucleic acids (2013)

Blood of healthy donors contains low concentrations of autoantibodies to its own components, including DNA and RNA. Increased concentrations of antibodies to DNA and RNA have been found in blood of people and animals with autoimmune diseases and viral and bacterial infections. Detection of different antibodies with catalytic activities, including abzymes with DNase and RNase activities, is the earliest indicator of the development of some autoimmune diseases. This review reveals possible mechanisms of generation of anti-DNA and anti-RNA antibodies without catalytic activities and abzymes in normal organisms and in organisms with different pathologies. A possible role of these autoantibodies and the reasons of their exceptional diversity in normal organisms and in organisms with different autoimmune diseases are discussed.
Synthesis and Investigation of [Cp*(PMe<sub>3</sub>)Rh(H)(H<sub>2</sub>)]<sup>+</sup> and Its Partially Deuterated and Tritiated Isotopomers:  Evidence for a Hydride/Dihydrogen Structure (2002)

Hydrogenolysis of [Cp(PMe(3))Rh(Me)(CH(2)Cl(2))](+)BAr'(4)(-) (4, Ar' = 3,5-C(6)H(3)(CF(3))(2)) in dichloromethane afforded the nonclassical polyhydride complex [Cp*PMe(3))Rh(H)(H(2))](+)BAr'(4)(-) (1), which exhibits a single hydride resonance at all accessible temperatures in the (1)H NMR spectrum. Exposure of solutions of 1 to D(2) or T(2) gas resulted in partial isotopic substitution in the hydride sites. Formulation of 1 as a hydride/dihydrogen complex was based upon T(1) (T(1)(min) = 23 ms at 150 K, 500 MHz), J(H-D) (ca. 10 Hz), and J(H-T) (ca. 70 Hz) measurements. The barrier (Delta G(++)) to exchange of hydride with dihydrogen sites was determined to be less than ca. 5 kcal/mol. Protonation of Cp(PMe(3))Rh(H)(2) (2) using H(OEt(2))(2)BAr'(4) resulted in binuclear species [(Cp(PMe(3))Rh(H))(2)(mu-H)](+)BAr'(4)(-) (3), which is formed in a reaction involving 1 as an intermediate. Complex 3 contains two terminal hydrides and one bridging hydride ligand which exchange with a barrier of 9.1 kcal/mol as observed by (1)H NMR spectroscopy. Additionally, the structures of 3 and 4, determined by X-ray diffraction, are reported.