gebhart/patrepeval huggingface dataset:
Differential sensitivity of vimentin and nuclear lamins from Ehrlich ascites tumor cells toward Ca2+ -activated neutral thiol proteinase. (1988)

A comparative study of the susceptibility of vimentin and nuclear lamins from cultured Ehrlich ascites tumor (EAT) cells to degradation by Ca2+ -activated neutral thiol proteinase (calpain) has been undertaken. While pure vimentin was degraded very quickly at physiological ionic strength by purified calpain, isolated lamin B was digested comparatively slowly and purified lamins A/C were fairly resistant to proteolytic degradation. Similar digestion patterns were obtained from vimentin and lamin B with intermediary breakdown products close in size to the corresponding alpha-helical rod domains. To exclude the possibility that the low susceptibility of isolated lamins to Ca2+-dependent proteolytic degradation was due to irreversible denaturation during their isolation and purification, Triton cytoskeletons were prepared and their nuclear lamina as well as vimentin filaments were exposed to relatively large quantities of purified calpain. Under these conditions, not only vimentin filaments but also lamins A and B were digested while lamin C remained intact to a high degree. The major breakdown products of vimentin and lamins were identified as polypeptides which were 35 to 45 amino acids longer than the corresponding alpha-helical rod domains. Most of the vimentin-derived material and all high molecular weight polypeptides originating from lamins remained associated with the Triton cytoskeletons as demonstrated by sodium dodecyl sulfate polyacrylamide gel electrophoresis in conjunction with immunoblotting. Indirect immunofluorescence and electron microscope analysis of the calpain-digested Triton cytoskeletons revealed that they still contained a laminalike structure around the nuclear chromatin and numerous structurally altered intermediate filaments in the cytoplasmic remnant, although all vimentin had been degraded with the formation of 40/41 kDa polypeptides as major digestion products. In untreated Triton cytoskeletons, the vimentin filaments seemed to be in direct physical contact with the nuclear lamina, whereas in digested Triton cytoskeletons there was a distinct gap between structurally altered filaments and the nuclear surface. This shows that vimentin filaments and the nuclear lamina are differentially susceptible to degradation by calpain under certain ionic conditions and suggests that both filamentous structures are intimately associated with each other.(ABSTRACT TRUNCATED AT 400 WORDS)
Magnetooptical properties of a ferromagnetic superlattice (2001)

Transmission and reflection of a normally incident wave from a magnetic superlattice consisting of 2N ferromagnetic layers with alternating orientation of the magnetization vector are considered. The characteristic matrix of a superlattice relating wave amplitudes at the entrance to the system and at the exit from it is calculated in the closed form and Jones matrices determining all the basic magnetooptical characteristics of the structure (transmission and reflection coefficients, the degree of polarization of transmitted and reflected waves, and so on) are constructed. A significant dependence of these characteristics on the number of layers is demonstrated.
Densification and Grain Growth of Large-Sized Polycrystalline Al<sub>2</sub>O<sub>3</sub> during a Two-Step Pulsed Electric Current Sintering Process (2018)

In this study, transparent polycrystalline Al2O3 with a diameter of 30 mm was fabricated by two-step pulsed electric current sintering (TS-PECS) at two different heating rates, 100 and 10°C/min. The overall TS-PECS process was divided into parts and was stopped at various positions along the timeline. The relative density and grain size of the Al2O3 samples obtained from each stop were evaluated. In general, the results show that the heating rate changed the densification rate in each sintering stage but did not strongly affect the final density. However, it dramatically influenced the grain growth of Al2O3. With the higher heating rate, the dynamic grain growth was assumed to enhance the grain growth rate because of the high concentration of defects, especially in the last stage of sintering. Especially, a grain size refinement phenomena was observed during the sintering process of polycrystalline Al2O3 for the first time.
Rational Prepayment and the Valuation of Mortgage-Backed Securities (1995)

Journal Article Rational Prepayment and the Valuation of Mortgage-Backed Securities Get access Richard Stanton Richard Stanton University of California, Berkeley Address correspondence to Richard Stanton, Haas School of Business, University of California, Berkeley, 350 Barrows Hall, Berkeley, CA 94720. Search for other works by this author on: Oxford Academic Google Scholar The Review of Financial Studies, Volume 8, Issue 3, July 1995, Pages 677–708, https://doi.org/10.1093/rfs/8.3.677 Published: 28 May 2015
Rapport d'une courte mission d'appui à la filière vanille à Mayotte (1996)

Les prix de la vanille verte et de la vanille préparée pratiqués à Mayotte sont très supérieurs aux prix actuels du marché international. Par manque de compétitivité et de professionnalisme des producteurs, la vanille mahoraise ne peut désormais être écoulée que sur des marchés très spécifiques et très restreints. La situation n'est pas encore irréversible. Des solutions techniques existent et d'énormes progrès pourraient être réalisés pour améliorer la productivité des cultures et la qualité du produit final. Pour ce faire, le conseil technique doit être affiné, dynamisé et surtout recentré sur les trop rares agriculteurs professionnels et les jeunes agriculteurs formés, dont il faut encourager l'installation. La coopérative de vanille de Mayotte doit profiter de son déménagement dans des locaux neufs pour se remettre en cause et amorcer une mutation qui lui fera jouer un rôle central dans la diffusion des bonnes pratiques culturales, la collecte et la préparation. Un effort important doit être fait pour améliorer les conditions d'hygiène lors de la préparation et du stockage. Une attention particulière doit être portée au suivi des marchés et à la recherche de nouveaux clients.
Plasma Concentrations of Cholecystokinin and Neurotensin in Patients with Cystic Fibrosis (1997)

Cystic fibrosis patients with severe pancreatic insufficiency did not have increased CCK plasma levels, suggesting that a CCK-mediated feedback mechanism of pancreatic enzyme secretion does not operate in our patients. In contrast, basal and postprandial neurotensin plasma levels were significantly increased in patients with cystic fibrosis but were independent of the severity of the pancreatic insufficiency.
Construction of Kinetic Model Library of Metabolic Networks from Dynamic Profiles (2011)

The construction of large scale kinetic metabolic models is important in the field of metabolic engineering, but challenging due to the large number of unknown kinetic parameters. Unfortunately, estimating these parameters from data is difficult as the problem typically becomes under-determined. In this work, an incremental approach is proposed by dividing the model identification task into two steps— dynamic flux estimation (DFE) from con- centration time series data and kinetic parameter regres- sions. The proposed approach decouples the estimation task into smaller, easy to solve sub-problems and cir- cumvents the lack of complete parameter identifiability problem by generating a family of models. In particular, a kinetic model library is constructed through random samplings or combinatorial combinations of a subset of parameters and the screening of the final models, accord- ing to some parametric bounds. The performance of this method has been demonstrated in a case study involving the glycolytic pathway in L. lactis.
Deep learning methods for protein torsion angle prediction (2017)

Our experiment demonstrates that deep learning is a valuable method for predicting protein torsion angles. The deep recurrent network architecture performs slightly better than deep feed-forward architecture, and the predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments are useful features for improving prediction accuracy.
Adenylate kinase-4 modulates oxidative stress and stabilizes HIF-1α to drive lung cancer metastasis (2017)

Abstract Disrupting signaling axes that are essential for tumor metastasis may provide therapeutic opportunity to cure cancer. We previously identified adenylate kinase 4 (AK4) as a biomarker of metastasis in lung cancer. Here we analyze AK4-associated metabolic gene signature and reveal HIF-1α is transcriptionally activated and associated with poor prognosis in lung adenocarcinoma patients. Overexpression of AK4 shifts metabolism towards aerobic glycolysis and elevates intracellular reactive oxygen species (ROS), which stabilizes and exaggerates HIF1-α protein expression and concurrently drives epithelial-to-mesenchymal transition (EMT) in hypoxia. Furthermore, overexpression of AK4 reduces hypoxic necrosis in tumors and promotes liver metastasis in vivo . Connectivity map analysis of AK4 gene signature identifies Withaferin-A as a potential compound to inhibit AK4-HIF-1α signaling axis, which then shows promising anti-metastatic potency in an orthotopic xenograft model of lung cancer. Our findings offer an alternative strategy to impair lung cancer metastasis via targeting AK4-HIF-1α axis.
Dust deposition on the Mars Exploration Rover Panoramic Camera (Pancam) calibration targets (2007)

The Panoramic Camera (Pancam) on the Mars Exploration Rover mission has acquired in excess of 20,000 images of the Pancam calibration targets on the rovers. Analysis of this data set allows estimates of the rate of deposition and removal of aeolian dust on both rovers. During the first 150–170 sols there was gradual dust accumulation on the rovers but no evidence for dust removal. After that time there is ample evidence for both dust removal and dust deposition on both rover decks. We analyze data from early in both rover missions using a diffusive reflectance mixing model. Assuming a dust settling rate proportional to the atmospheric optical depth, we derive spectra of optically thick layers of airfall dust that are consistent with spectra from dusty regions on the Martian surface. Airfall dust reflectance at the Opportunity site appears greater than at the Spirit site, consistent with other observations. We estimate the optical depth of dust deposited on the Spirit calibration target by sol 150 to be 0.44 ± 0.13. For Opportunity the value was 0.39 ± 0.12. Assuming 80% pore space, we estimate that the dust layer grew at a rate of one grain diameter per ∼100 sols on the Spirit calibration target. On Opportunity the rate was one grain diameter per ∼125 sols. These numbers are consistent with dust deposition rates observed by Mars Pathfinder taking into account the lower atmospheric dust optical depth during the Mars Pathfinder mission.
Protein burden in Zymomonas mobilis: negative flux and growth control due to overproduction of glycolytic enzymes (1995)

Increasing the expression of various glycolytic operons in Zymomonas mobilis caused a significant decrease rather than increase in the glycolytic flux and growth rate. Because the relative decrease depended on the amount of overexpressed protein, and was independent of which enzyme was overexpressed, we attributed it to a protein burden effect. More specifically, we examined if the decrease in glycolytic flux could be explained by a decreased concentration of other glycolytic enzymes (for which glucokinase was used as a marker enzyme). Using the summation theorem of metabolic control theory we predicted the extent of this protein burden effect. The predictions were in good agreement with the experimental observations. This suggests that the negative flux control is caused either by a simple competition of the overexpressed gene with the expression of all other genes or by simple dilution. Furthermore, we determined the implications of protein burden for the determination of the extent to which an enzyme limits a flux. We conclude that a protein burden can cause a significant underestimation of the flux control coefficient, especially if the enzyme under investigation is a highly expressed enzyme.
Aromatic radiofluorination with (/sup 18/F)fluorine gas: 6-(/sup 18/F)fluoro-L-dopa (1984)

A new synthesis is described for the routine production of 3,4-dihydroxy-6-(/sup 18/F)fluoro-phenyl-L-alanine (6-(/sup 18/F)fluoro-L-dopa). The reaction between (/sup 18/F)fluorine gas and 3,4-dihydroxyphenyl-L-alanine (L-dopa) in liquid hydrogen fluoride gave 2-, 5-, and 6-(/sup 18/F)fluoro-L-dopa. 6-(/sup 18/F)Fluoro-L-dopa was isolated by reverse-phase high-pressure liquid chromatography. From 100 mCi (/sup 18/F)F/sub 2/, the method produces 3 mCi of 6-(/sup 18/F)fluoro-L-dopa at the end of synthesis.
Investigation of the Mode Characteristics of Quasi-Waveguide Lasers (2006)

Based on the theory of ordinary open cavity emersion mode and waveguide mode,a new kind of mode lying between the liberty room mode and waveguide mode was studied,and the method of diffraction integral of Fox-Li in the area between the cavity mirror and the waveguide was used,the electric field was dispersed into every waveguide mode in the waveguide,by time after time alternating,the stabilization electric field in the space between the waveguide dimension and non-waveguide dimension was analied.Having the difference between the new mode,waveguide mode and Gauss mode,it is yalidated that the new electric distribution is similar to them,but a new electric field.
Synthesis and antiviral activity of 9-alkoxypurines. 2. 9-(2,3-Dihydroxypropoxy)-, 9-(3,4-dihydroxybutoxy)-, and 9-(1,4-dihydroxybut-2-oxy)purines (1991)

Reaction of alkenoxyamines (3,5) or (R,S)-, (R)-, and (S)-hydroxy-protected derivatives of hydroxyalkoxyamines (20a,b, 37a-c) with 4,6-dichloro-2,5-diformamidopyrimidine (4) and cyclization of the resultant 6-[(alkenoxy)amino]-and 6-(alkoxyamino)pyrimidines (6,7,21a,b, 38a,b,c) by heating with diethoxymethyl acetate afforded 9-alkenoxy- and 9-alkoxy-6-chloropurines (9,10,22a,b, 39a-c, 40a). These were subsequently converted to 9-(2,3-dihydroxypropoxy), 9-(3,4-dihydroxybutoxy), and 9-(1,4-dihydroxybut-2-oxy) derivatives of guanine and 2-aminopurine (13-16, 25-28, 41a-c, 42a). A 2-amino-6-methoxypurine derivative (17) was also prepared. The racemic guanine derivative 13 showed potent and selective activity against herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), but was less active against varicella zoster virus (VZV). Its antiviral activity is attributable to the S isomer (28), which was found to be more active than acyclovir against HSV-1 and HSV-2 and about 4 times less active than acyclovir against VZV. The S enantiomer of 9-(1,4-dihydroxybut-2-oxy)guanine (41c) also showed noteworthy antiviral activity in cell culture. Although this acyclonucleoside (41c) is only weakly active against HSV-1 and inactive against HSV-2, it is about twice as active as acyclovir against VZV.
Optimization of an Osmotic Shock Procedure for Isolation of a Protein Product Expressed in E. coli (2003)

Small-scale experiments were performed to evaluate the impact of several processing variables on recovery by osmotic shock of a protein product expressed in E. coli utilizing feed material manufactured at large scale. Equilibration time, type and concentration of osmotic supplements, and pH of the osmotic shock buffer were found to have significant impact on the osmotic shock recovery. Improved recovery was documented under conditions of increased equilibration time before the osmotic shock and increased Tris-HCl concentration in the osmotic shock buffer, as well as initial dispersal of cells into the osmotic shock buffer. Recovery of up to 65% was achieved under the optimized conditions.
Cover Picture: Chromophore‐Linked Substrate (CLS405): Probing Metallo‐β‐Lactamase Activity and Inhibition (ChemMedChem 12/2013) (2013)

The front cover picture shows the hydrolysis of chromogenic substrate CLS405 (green) by NDM-1 (blue protein structure), a metallo-beta-lactamase (MBL), generating the detectable para-nitrophenolate product (yellow). Upon binding of an inhibitor (N-hydroxythiazole shown in gray), hydrolysis of the substrate is hampered, thus facilitating rapid residual activity determination. Monitoring inhibition in a concentration-dependent manner allows for straightforward IC50 value determination using chromogenic substrate CLS405. Given the threat posed by MBLs to the clinical use of beta-lactam antibiotics, the identification of MBL inhibitors is an important research goal. CLS405 represents a useful tool compound to facilitate the identification of improved MBL inhibitors with therapeutic potential against resistant strains of bacteria. For more details, see the Full Paper by Jürgen Brem, Christopher J. Schofield et al. on p. 1923 ff.
Exploration of the Correlation between Solvation Dynamics and Internal Dynamics of a Protein (2010)

Protein function is intimately related to the dynamics of the protein as well as to the dynamics of the solvent shell around the protein. Although it has been argued extensively that protein dynamics is slaved to solvent dynamics, experimental support for this hypothesis is scanty. In this study, measurements of fluorescence anisotropy decay kinetics have been used to determine the motional dynamics of the fluorophore acrylodan linked to several locations in a small protein barstar in its various structural forms, including the native and unfolded states as well as the acid and protofibril forms. Fluorescence upconversion and streak camera measurements have been used to determine the solvation dynamics around the fluorophore. Both the motional dynamics and solvent dynamics were found to be dependent upon the location of the probe as well as on the structural form of the protein. While the (internal) motional dynamics of the fluorophore occur in the 0.1-3 ns time domain, the observed mean solvent relaxation times are in the range of 20-300 ps. A strong positive correlation between these two dynamical modes was found in spite of the significant difference in their time scales. This observed correlation is a strong indicator of the coupling between solvent dynamics and the dynamics in the protein.
Capillary Electrokinetic Chromatography (CEC): An Introduction to a High-Efficiency Microanalytical Technique (1997)

Capillary electrokinetic chromatography (CEC, also called “capillary electrochromatography”) is a relatively new separation technique based on a combination of liquid chromatographic and electrophoretic separation methods. CEC offers both the efficiency of capillary electrophoresis (CE) and the selectivity and sample capacity of packed capillary high performance liquid chromatography (HPLC). These advantages are provided in part because of the favorable flow characteristics of electroosmosis, a method of pumping a liquid by applying a high potential axially to a thin, fluid-filled tube. The speed at which analytes move through the separation conduit under the influence of electroosmosis is quite uniform, regardless of the position of the analyte with respect to adjacent surfaces (within certain limits). This results in very little spreading of zones of analyte; narrow, compact bands of analytes are therefore maintained, which results in high efficiency. Because the capillaries used in CEC are packed with HPLC packing materials, the wealth of selectivities available in HPLC are also available in CEC. The high surface area of these packing materials enables CEC capillaries to accommodate relatively large amounts of sample, making detection a simpler task than it is in capillary electrophoresis (CE). This paper will briefly visit the theory and practice of CEC, and will provide examples of how CEC can be applied in sample analysis.
Model Based System Testing: Bringing Testing and Simulation Close Together (2016)

Experimental modal analysis is commonly associated with the use of simulation models for validation, correlation and model updating. However, this interaction between simulation and test is constantly evolving, not in the least because it can be applied to model-based design engineering in the broad sense. Over time, new simulation methods have emerged and consequently, new approaches combining experimental and numerical methodologies are needed and possible. Model Based System Testing (MBST) is an innovative paradigm that allows to structure this process and, in particular, to investigate how the well-established modal testing and analysis procedures and ways of working can be adopted to the multiphysical nature of mechatronic systems. As a result, many possibilities arise: test data can be used to validate multiphysical models, models help gaining insights into test conditions, hybrid approaches allow combining testing and simulation on hardware-in-the-loop and system-in-the-loop test benches, where physical systems can be combined with simulation models to apply loads and more realistic test conditions, as well as the use of data coming from feedback control system information for testing purposes. In this paper, the context and concepts of MBST will be introduced, and application examples will be shown, highlighting the advantages of such a methodology.
Hindu Eschatology (2009)

Abstract In a survey of the extensive, complex, and cumulative history of Hinduism, it might be opportune to divide personal and cosmic eschatologies. Similarly, it could be convenient to separate the early from the classical history of Hinduism and concentrate solely on the latter. The early history, framed by a sacrificial world view and veering toward an almost mechanistic understanding of gods and the cosmos, is entirely dependent upon the eternal Vedas. With certain sectarian and modernizing exceptions, a generally acknowledged set of contemporary Hindu beliefs and practices would include the following: acceptance of the Vedas as basic authority, belief in transmigration and the effects of human action (karma) on rebirths, devoted recognition of certain divine beings (gods, goddesses, living and departed saints), acknowledgment of a class and caste social hierarchy, ritual attention to ancestors, and a general understanding of life as moral progress toward an eventual liberation from rebirths. This article examines Hindu eschatology, focusing on Hindu beliefs such as immortality, metaphors of regeneration, brahman, Aranyakas, Upanishads, classical Sanskrit texts, preta, and world dissolution.