gebhart/patrepeval huggingface dataset:
Influence of Human Immunodeficiency Virus Nucleocapsid Protein on Synthesis and Strand Transfer by the Reverse Transcriptase in Vitro (1995)

Human immunodeficiency virus (HIV) nucleocapsid protein (NC) influences HIV reverse transcriptase (RT) catalyzed strand transfer synthesis from internal regions of natural sequence RNA. In the strand transfer assay reaction in vitro, primer synthesis initiated on a donor template can transfer and be completed on an acceptor template. NC was added at concentrations up to twice that needed for 100% template coating. As the concentration of NC was increased, primer extension was stimulated until NC coated approximately 50% of the template. Stimulation was caused in part by an increase in the number of primers that sustained synthesis. Subsequent increments of NC decreased synthesis. The presence of NC also increased the efficiency of the strand transfer reaction, allowing a greater proportion of extended primers to transfer from donor to acceptor templates. Processivity of the RT on the donor template was measured using both challenged and enzyme dilution assays. NC did not alter the proportion of synthesis products that reached the end of the template, indicating little effect on processivity. This result suggests that the increase in full-length product synthesis, observed in reactions where the RT repeatedly bound the primer-template, resulted from promotion of RT reassociation by NC. Consequently, since the RT could not reassociate with the template in the processivity assay, NC could not stimulate the amount of full-length synthesis. No strand transfer was observed in dilution processivity assays, suggesting that the RT must dissociate and rebind during the transfer reaction. Stimulation of synthesis, e.g. by increased dNTP concentration, normally inhibits strand transfer. Stimulation of both synthesis and transfer by NC indicates that properties of NC that improve the transfer event prevail over the negative effects of rapid synthesis on transfer efficiency.
Overexpression of (<i>At</i>)<i>NPR1</i> in Rice Leads to a BTH- and Environment-Induced Lesion-Mimic/Cell Death Phenotype (2004)

Systemic acquired resistance (SAR) is an inducible defense response that protects plants against a broad spectrum of pathogens. A central regulator of SAR in Arabidopsis is NPR1 (nonexpresser of pathogenesis-related genes). In rice, overexpression of Arabidopsis NPR1 enhances plant resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae. This report demonstrates that overexpression of (At)NPR1 in rice also triggers a lesion-mimic/cell death (LMD) phenotype. The LMD phenotype is environmentally regulated and heritable. In addition, the development of lesions and death correlates with the expression of rice defense genes and the accumulation of hydrogen peroxide. Application of the salicylic acid (SA) analog, benzo(1,2,3) thiadiazole-7-carbothioc acid S-methyl ester (BTH), potentiates this phenotype Endogenous SA levels are reduced in rice overexpressing (At)NPR1 when compared with wildtype plants, supporting the idea that (At)NPR1 may perceive and modulate the accumulation of SA. The association of (At)NPR1 expression in rice with the development of an LMD phenotype suggests that (At)NPR1 has multiple roles in plant stress responses that may affect its efficacy as a transgenic tool for engineering broad-spectrum resistance.
Current related relaying algorithms immune to saturation of current transformers (1997)

Current transformers (CTs) supplying protective relays may suffer permanent or transient saturation under severe faults. The majority of protective relays are more or less sensitive to CT saturation. On the other hand, contemporary microprocessor-based relays open the window of opportunity for performing sophisticated checking in order to either reconstruct the secondary current waveform or compensate the measuring algorithms for saturation of CTs. This paper describes algorithms for amplitude and impedance components, resistive to transient saturation of CTs. The presented algorithms combine two procedures: (1) recognition of periods of saturated/linear operation of an observed CT; and (2) variable-length data window measuring algorithms that use unsaturated samples of the secondary current.
Cloning and Complete Primary Structure of the Mouse Laminin α3 Chain (1995)

We have isolated and characterized overlapping cDNA clones encoding the alpha 3A and alpha 3B chains of mouse laminin 5. Sequence analysis of the cDNA for the alpha 3B predicts a polypeptide of 2541 amino acids (279,510 Da) comprising a truncated short arm and a carboxyl-terminal long arm common to the laminin alpha chains identified thus far. The short arm of the alpha 3B chain harbors two alternating epidermal growth factor-like domains and two globular domains. The amino-terminal globular domain, thought to mediate interactions with molecules of the extracellular matrix, shows no significant homology to any globular domain at the tips of the known laminin isoforms. The alpha 3A cDNA predicts a polypeptide of 1711 amino acids (186,230 Da) that substitutes a short sequence of 43 amino acids for the short arm seen in the alpha 3B isoform and displays 77% conservative homology to the alpha 3Ep chains of the adhesion ligand epiligrin. Northern and Western blot analyses of skin and lung epithelial cells demonstrated the tissue-specific expression of the laminin alpha 3A and alpha 3B isoforms, and in situ hybridization on mouse embryos revealed a focal localization of alpha 3B in areas of the central nervous system.
Lineage‐specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales (2015)

Betalain pigments are unique to the Caryophyllales and structurally and biosynthetically distinct from anthocyanins. Two key enzymes within the betalain synthesis pathway have been identified: 4,5-dioxygenase (DODA) that catalyzes the formation of betalamic acid and CYP76AD1, a cytochrome P450 gene that catalyzes the formation of cyclo-DOPA. We performed phylogenetic analyses to reveal the evolutionary history of the DODA and CYP76AD1 lineages and in the context of an ancestral reconstruction of pigment states we explored the evolution of these genes in relation to the complex evolution of pigments in Caryophylalles. Duplications within the CYP76AD1 and DODA lineages arose just before the origin of betalain pigmentation in the core Caryophyllales. The duplications gave rise to DODA-α and CYP76AD1-α isoforms that appear specific to betalain synthesis. Both betalain-specific isoforms were then lost or downregulated in the anthocyanic Molluginaceae and Caryophyllaceae. Our findings suggest a single origin of the betalain synthesis pathway, with neofunctionalization following gene duplications in the CYP76AD1 and DODA lineages. Loss of DODA-α and CYP76AD1-α in anthocyanic taxa suggests that betalain pigmentation has been lost twice in Caryophyllales, and exclusion of betalain pigments from anthocyanic taxa is mediated through gene loss or downregulation. [Correction added after online publication 13 May 2015: in the last two paragraphs of the Summary the gene name CYP761A was changed to CYP76AD1.].
Electromagnetic scattering by surfaces of arbitrary shape (1982)

The electric field integral equation (EFIE) is used with the moment method to develop a simple and efficient numerical procedure for treating problems of scattering by arbitrarily shaped objects. For numerical purposes, the objects are modeled using planar triangular surfaces patches. Because the EFIE formulation is used, the procedure is applicable to both open and closed surfaces. Crucial to the numerical formulation is the development of a set of special subdomain-type basis functions which are defined on pairs of adjacent triangular patches and yield a current representation free of line or point charges at subdomain boundaries. The method is applied to the scattering problems of a plane wave illuminated flat square plate, bent square plate, circular disk, and sphere. Excellent correspondence between the surface current computed via the present method and that obtained via earlier approaches or exact formulations is demonstrated in each case.
Development of high frequency ferrite phase-shifter (2001)

A phase-shifter was fabricated on a c-texture Zn/sub 2/Y (Zn/sub 2/Ba/sub 2/Fe/sub 12/O/sub 22/) single crystal substrate, and tested over microwave frequencies from 2 to 35 GHz and for biasing magnetic fields from 0.2 to 5 kOe. The differential phase-shift rate was 90/spl deg//kOe.mm at a microwave frequency of 20 GHz and a magnetic bias-field of 1.3 kOe. This device showed that it is possible to reduce the bias-field requirement efficiently and simply by utilizing the large in-plane anisotropy in Y-type hexaferrites and magnetostatic modes. A simple model based on the conjugate method for a TEM wave gave a reasonable match with the measured performance of the device, when the uniaxial magnetic anisotropy and magnetostatic modes were included.
Coherent Transfer of Spin through a Semiconductor Heterointerface (2000)

Spin transport between two semiconductors of widely different band gaps is time resolved by two-color pump-probe optical spectroscopy. Electron spin coherence is created in a GaAs substrate and subsequently appears in an adjacent ZnSe epilayer at temperatures ranging from 5 to 300 K. The data show that spin information can be protected by transport to regions of low spin decoherence, and regional boundaries used to control the resulting spin coherent phase.
Leukotriene C promotes prostacyclin synthesis by human endothelial cells. (1983)

Cultured endothelial cells from human umbilical vein were labelled with [3H]arachidonic acid for 16 hr. The radiolabel was localized primarily in phospholipids (93%) and 73% was distributed equally between phosphatidylcholine and phosphatidylethanolamine. Leukotriene C (10-1,000 nM) promoted a dose-dependent release of radiolabel into the culture medium. This response was 3.3 times control values at 100 nM. The major arachidonic acid metabolite synthesized was prostacyclin, which was 33% of the total released radiolabel. Endothelial cells also released small amounts of prostaglandin F2 alpha (6.1%), unidentified lipoxygenase products (14.8%), and unreacted arachidonic acid (33%). The 30-min time course of release was independent of the leukotriene C concentration used. Leukotriene D at similar concentrations also promoted endothelial cells to release primarily prostacyclin and unreacted arachidonic acid. The release of prostacyclin, a potent vasodilator agent, may be an important mediator in slow reacting substance effects on the vasculature.
Self-sensing of temperature rises on light emitting diode based optrodes (2018)

This paper, therefore, presents a method to utilize the light emitting diode as its own temperature sensor.
FLAVONOID GLYCOSIDES FROM LEDUMPALUSTRE L. SUBSP. DECUMBENS (AIT) HULTON (1999)

From the leaves of Ledum palustre L. subsp. decumbens (Ait.) Hulton a novel flavonoid glyco&amp;not;&quot;nside, quercetin 3-p-D-(6-^-coumaroyI) galactoside, and quercetin 3-p-D-(6-/?-hydroxy-benzoyI)&quot;ngalactoside, were isolated. Their structures were elucidated by spectroscopic methods. Both&quot;ncompounds showed in vitro antifungal activity against Cryptococcus moformcms, Saccharomyces&quot;ncerevisiae, Aspergillus niger and Candida albicans, as well as cytotoxicity against KB cells.
Repair of Oxidized Calmodulin by Methionine Sulfoxide Reductase Restores Ability To Activate the Plasma Membrane Ca-ATPase (1998)

We have investigated the ability of methionine sulfoxide reductase (MsrA) to maintain optimal calmodulin (CaM) function through the repair of oxidized methionines, which have been shown to accumulate within CaM in senescent brain [Gao, J., Yin, D. H., Yao, Y., Williams, T. D., and Squier, T. C. (1998) Biochemistry 37, 9536-9548]. Oxidatively modified calmodulin (CaMox) isolated from senescent brain or obtained by in vitro oxidation was incubated with MsrA. This treatment restores the functional ability of CaMox to activate the plasma membrane (PM) Ca-ATPase, confirming that (i) the decreased ability of CaM isolated from senescent animals to activate the PM Ca-ATPase results solely from methionine sulfoxide formation and (ii) MsrA can repair methionine sulfoxides within cytosolic proteins. We have used electrospray ionization mass spectrometry to investigate the extent and rates of methionine sulfoxide repair within CaMox. Upon exhaustive repair by MsrA, there remains a distribution of methionine sulfoxides within functionally reactivated CaMox, which varies from three to eight methionine sulfoxides. The rates of repair of methionine sulfoxides within individual tryptic fragments of CaMox vary by a factor of 2, where methionine sulfoxides located within hydrophobic sequences are repaired in preference to methionines that are more solvent accessible within the native structure. However, no single methionine sulfoxide is completely repaired in all CaM oxiforms. Decreases in the alpha-helical content and a disruption of the tertiary structure of CaM have previously been shown to result from methionine oxidation. Repair of selected methionine sulfoxides in CaMox by MsrA results in a partial refolding of the secondary structure, suggesting that MsrA repairs methionine sulfoxides within unfolded sequences until native-like structure and function are re-attained. The ability of CaMox isolated from senescent brain to fully activate the PM Ca-ATPase following repair by MsrA suggests the specific activity of MsrA is insufficient to maintain CaM function in aging brain. These results are discussed in terms of the possible regulatory role MsrA may play in the modulation of CaM function and calcium homeostasis under conditions of oxidative stress.
Preparation of Analytically Pure Monobasic Copper Salicylate (1971)

Abstract : Preparation of analytically pure monobasic copper salicylate by two distinct synthetic routes and characterization of the products by infrared spectroscopy, X-ray diffraction and thermogravimetric analysis is described. Analytically pure monobasic copper salicylate can be synthesized in excellent yield by reacting basic copper carbonate and salicylic acid in a 1 to 2.2 molar ratio. The pure monobasic salt can also be prepared by reacting copper hydroxide and salicylic acid in a 1 to 1 molar ratio. However, the yield, in this case, is comparatively low, Characterization of the product can be accomplished by infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, and elemental analysis for copper, carbon and hydrogen.
Lung Endoderm Morphogenesis: Gasping for Form and Function (2015)

The respiratory endoderm develops from a small cluster of cells located on the ventral anterior foregut. This population of progenitors generates the myriad epithelial lineages required for proper lung function in adults through a complex and delicately balanced series of developmental events controlled by many critical signaling and transcription factor pathways. In the past decade, understanding of this process has grown enormously, helped in part by cell lineage fate analysis and deep sequencing of the transcriptomes of various progenitors and differentiated cell types. This review explores how these new techniques, coupled with more traditional approaches, have provided a detailed picture of development of the epithelial lineages in the lung and insight into how aberrant development can lead to lung disease.
Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions (2015)

We extracted collagen from moon jellyfish under neutral pH conditions and analyzed its amino acid composition, secondary structure, and thermal stability. The content of hydroxyproline was 4.3%, which is lower than that of other collagens. Secondary structure analysis using circular dichroism (CD) showed a typical collagen helix. The thermal stability of this collagen at pH 3.0 was lower than those from fish scale and pig skin, which also correlates closely with jellyfish collagen having lower hydroxyproline content. Because the solubility of jellyfish collagen used in this study at neutral pH was quite high, it was possible to analyze its structural and physical properties under physiological conditions. Thermodynamic analysis using CD and differential scanning calorimetry showed that the thermal stability at pH 7.5 was higher than at pH 3.0, possibly due to electrostatic interactions. During the process of unfolding, fibrillation would occur only at neutral pH.
Phase-Matched Raman-Resonant Four-Wave Mixing in a Dispersion-Compensated High-Finesse Optical Cavity (2008)

A highly efficient intracavity four-wave mixing in a Raman-active medium pumped by a continuous-wave laser is first demonstrated. Managing the intracavity dispersion to satisfy the phase matching in a high-finesse cavity substantially enhances the anti-Stokes emission. This process is observed in a region far beyond small signal approximation, indicating the generation of phase-locked sidebands arising from molecular modulation. This points to a novel approach of an optical modulator and mode-locked laser operating at a frequency of more than 10 THz.
Dual Spatial Folds and Different Local Structures of the HIV-1 Immunogenic Crown in Various Virus Isolates (2004)

Local and global structural properties of the HIV-1 principal neutralizing epitope were studied in terms of NMR spectroscopy data reported in literature for the HIV-Haiti and HIV-RF isolates. To this effect, the NMR-based method comprising a probabilistic model of protein conformation in conjunction with the molecular mechanics and quantum chemical computations was used for determining the ensembles of conformers matching the NMR requirements and energy criteria. As a matter of record, the high resolution 3D structure models were constructed for the HIV-Haiti and HIV-RF immunogenic crowns, and their geometric parameters were collated with the ones of conformers derived previously for describing the conformational features of immunogenic tip of gp120 from Thailand and MN HIV-1 strains. The HIV-1 neutralization site was demonstrated to constitute in water solution highly flexible system sensitive to its environment. This inference is completely valid for the geometric space of dihedral angles where statistically significant differences in local structures of simulated conformers have been found for all virus isolates of interest. In spite of this fact, the stretch analyzed was shown to manifest a certain conservatism in the space of atomic coordinates, building up in four HIV-1 isolates two spatial folds similar to those observed in crystal for the V3 loop peptides bound to different neutralizing Fabs. The results are discussed in the light of literature data on HIV-1 neutralizing epitope structure.
Mechanism of free fatty acid re-esterification in human adipocytes in vitro. (1990)

Within adipose tissue, free fatty acids liberated by lipolysis may be re-esterified into newly synthesized triacylglycerol. We hypothesized that re-esterification may occur via an extracellular route, such that free fatty acids arising from lipolysis must leave the adipocyte and be taken up again before they can be re-esterified. We simultaneously measured rates of lipolysis, acylglycerol synthesis, and free fatty acid re-esterification in human adipose tissue and isolated adipocytes in vitro, utilizing a dual-isotopic technique. We manipulated incubations to increase mixing of released free fatty acids with the incubation medium. Such manipulations should decrease the probability that released free fatty acids would be taken up and re-esterified. We found that re-esterification was decreased in isolated adipocytes compared to fragments of tissue, in shaken compared to unshaken incubations, and in low adipocyte concentrations compared to high adipocyte concentrations. Rates of acylglycerol synthesis and lipolysis were unaltered by these manipulations, indicating that changes in free fatty acid re-esterification are not secondary to effects on these processes. The results are consistent with an extracellular route for free fatty acid re-esterification. Such a mechanism suggests that adipose tissue blood flow may play an important role in the regulation of free fatty acid release from adipose tissue.
Exploit failure prediction for adaptive fault-tolerance in cluster computing (2006)

As the scale of cluster computing grows, it is becoming hard for long-running applications to complete without facing failures on large-scale clusters. To address this issue, checkpointing/restart is widely used to provide the basic fault-tolerant functionality, yet it suffers from high overhead and its reactive characteristic. In this work, we propose FT-Pro, an adaptive fault management mechanism that optimally chooses migration, checkpointing or no action to reduce the application execution time in the presence of failures based on the failure prediction. A cost-based evaluation model is presented for dynamic decision at run-time. Using the actual failure log from a production cluster at NCSA, we demonstrate that even with modest failure prediction accuracy, FT-Pro outperforms the traditional checkpointing/restart strategy by 13%-30% in terms of reducing the application execution time despite failures, which is a significant performance improvement for long-running applications.
A prospective, controlled, double-blind, cross-over study of tripterygium wilfodii hook F in treatment of rheumatoid arthritis. (1989)

A polyglycosides of Tripterygium wilfodii hook F (TWH) preparation with a code name of T2 is used in the present double-blind, controlled, cross-over study on the treatment of 70 cases of rheumatoid arthritis (RA). An impressive curative effect of T2 is confirmed much more convincingly by the present study than that by the previously reported clinical open trials. The adverse reactions and the probable pharmacological mechanism of T2 are also discussed.
Smart engine speed control system with ECU system interface (2018)

Despite decades of reformative legislation regarding the safety of motorists and immense efforts by manufacturers to improve vehicle safety features, motor vehicle accidents related to speeding claim the lives of approximately 3000 teenagers (aged 16-19) each year. This study proposes an embedded smart control system to limit the vehicle speed to the maximum allowable road speed. This can be achieved by establishing a live communication between the cruise control system and the onboard GPS module. Using the Engine Control Unit (ECU) to control the electronic throttle and air valve, the maximum rotational velocity of the engine can be limited so that the vehicle's speed does not surpass a road speed limit. By implementing this embedded system to control the speed of the motor vehicle, this system has the potential to reduce the number of speeding-related accidents. This study evaluates the practicability of the proposed embedded system and discusses alternative controlling methods. For this purpose, a graphical user interface (GUI) module is also developed to make the system more user-friendly. The data used to test the system was collected through a GPS service from the streets around the campus of the University of Central Oklahoma.