gebhart/patrepeval huggingface dataset:
1D Simulation of Polymer Flooding Including the Viscoelastic Effect of Polymer Solution (1992)

Summary Simple simulation models are constructed to predict the performance of 1D polymer flooding. In the models, two phases of oil and polymer solution were assumed to be immiscible with each other. Because the displacing fluid was non-Newtonian, the BucldeyLeverett equation could be modified and a new approach developed to calculate fractional-flow curves. The rheological behavior of polymer solution was modeled with an Ellis type model and a viscoelastic model. To verify the models, two 1D flooding experiments were carried out on 2.8-cm-diameter, 47-cm-long, unconsolidated cores packed with glass beads (70/100 mesh). Porosities of the cores are about 37% and permeabilities are around 26 μm2. Two white mineral oils of viscosities 25 and 60 mPa·s and a 200-ppm polyacrylamide solution were used. In each experiment, polymer flooding was done after waterflooding. Initial water saturation was controlled to be almost the same at the start of each flood. The calculated polymer-flooding performances were compared with experimental data. The Ellis model predicted earlier breakthrough of polymer solution and lower oil recoveries than the experimental data. On the other hand, the viscoelastic model predicted fractional-flow curves, oil recovery performances, and breakthrough times of the experiments very well. The viscoelastic effect of polymer solution is thought to play an important role in the improvement of oil recovery.
Prospects for inferring pairwise relationships with single nucleotide polymorphisms (2003)

An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full-sibs from half-sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al. (1996). We have explored a 'best case scenario' in which 100 independently segregating SNPs are available. For discrimination among single-generation relationships or for the identification of parent-offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16-20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future.
Mutational analysis of phenylalanine ammonia lyase to improve reactions rates for various substrates (2010)

Phenylalanine ammonia lyases (PAL) catalyze the reversible, non-reductive amination of trans-cinnamic acid to l-phenylalanine in the presence of high ammonia concentrations. Since neither cofactor recycling nor other additives are needed and by this asymmetric synthesis theoretical yields of 100% can be reached, it is an interesting reaction for industrial processes. In this study we demonstrate the superior properties of p-nitro-cinnamic acid (p-n-CA) in the amination reaction using the PAL from Petroselinum crispum (pcPAL). By focused-directed evolution, three mutants were identified showing increased reaction rates and decreased substrate inhibition. Together, the F137V mutant with p-n-CA showed a 15-fold increased reaction rate compared with the pcPAL WT with the natural cinnamic acid. The high reaction rates were also proven in preparative scale experiments. Activities towards other p-substituted cinnamic acids showing different electronic effects of the substituent were analyzed. Focused-directed evolution around the carboxylic acid- and amine-binding site always decreased PAL activity, due to a sensitive H-bond network.
Interactive 3D distance field computation using linear factorization (2006)

We present an interactive algorithm to compute discretized 3D Euclidean distance fields. Given a set of piecewise linear geometric primitives, our algorithm computes the distance field for each slice of a uniform spatial grid. We express the non-linear distance function of each primitive as a dot product of linear factors. The linear terms are efficiently computed using texture mapping hardware. We also improve the performance by using culling techniques that reduce the number of distance function evaluations using bounds on Voronoi regions of the primitives. Our algorithm involves no preprocessing and is able to handle complex deforming models at interactive rates. We have implemented our algorithm on a PC with NVIDIA GeForce 7800 GPU and applied it to models composed of thousands of triangles. We demonstrate its application to medial axis approximation and proximity computations between rigid and deformable models. In practice, our algorithm is more accurate and almost one order of magnitude faster as compared to previous distance computation algorithms that use graphics hardware.
Novel Aromatic Azopolymers with Regularly Interposed Tellurium Atoms in the Backbone (1995)

Abstract Previously unknown alt ‐copoly(telluro‐1,4‐phenylene/azo‐1,4‐phenylene) and related polymers were synthesized by several different approaches, which include a) reductive polymerization of bis(4‐nitrophenyl) tellurides with zinc; b) oxidative polymerization of bis(4‐aminophenyl) telluride using a Cu I /Cu II redox system as catalyst under oxygen; c) electrochemical polymerization of bis(4‐amino‐3,5‐dimethylphenyl) telluride; d) condensation polymerization of 1,4‐dinitrosobenzene with bis(4‐aminophenyl) telluride Te, Te ‐dichloride, and e) condensation polymerization of bis(4‐nitrophenyl) telluride with bis(4‐aminophenyl) telluride in the presence of sodium hydroxide. The polymers obtained were characterized by elemental analysis, 13 C‐CPMAS NMR, IR and UV‐vis spectroscopy, GPC, and inherent viscosity measurements, and their properties were examined, particularly their electrical conductivity. The electrical conductivities of the new polymers 9b c , and 10 were shown to increase from below 10 −7 up to 10 −5 ∽ 10 −2 S cm −1 upon bromine doping in spite of their formally interrupted conjugation structure.
Morphology and modulus–temperature behavior of semicrystalline poly(ethylene terephthalate) (PET) (1976)

Abstract The influence of the thermal history on the morphology and mechanical behavior of PET was studied. The degree of crystallinity (density measurements) and the morphological structure (electron microscopy and small‐angle x‐ray diffraction) depend on the crystallization temperature. The viscoelastic parameters obtained from the modulus–temperature curves are mainly determined by the morphology of the samples. The glass‐transition temperature, T i , is a function of the crystallinity and the crystallization temperature. It is maximum for a crystallinity between 0.34 and 0.39 for a sample crystallized isothermally between 120 and 150°C. This dependence on crystallization conditions is ascribed to the conformation of the amorphous chain segments between the crystalline lamellae as well as the concentration and the molecular weight of the polymer material rejected during isothermal crystallization. Both factors are supposed to be temperature‐dependent. The value of the rubbery modulus is a function of both the volume concentration of the crystalline lamellae and the structure of the interlamellar amorphous regions (chain folds, tie molecules, chain ends, and segregated low molecular weight material). Annealing above the crystallization temperature of isothermally crystallized samples has a marked influence on their morphology and mechanical behavior. The morphological structure and the viscoelastic properties of annealed PET samples are completely different from those obtained with samples isothermally crystallized at the same temperature.
Automatic metaphase finding by inter-chromosome extrema profile analysis (2005)

In this paper we report our experiences with a new texture coarseness measure, as a step towards automation of metaphase finding in cell proliferation studies. This measure is highly specific to grey-level inter-chromosome coarseness features in microscopic images of metaphase spreads, and allows to quantify the texture of the cytological objects analysing the intensity profile between chromosome-extrema samples. Chromosome fragments produce patterns of pixels at low-resolution, and the local neighbourhood of their individual extrema presents a characteristic coarseness, along intensity profiles on random-oriented test lines. Results of its use on images of fields of metaphases and artefacts are compared with some representative texture measures, outperforming metaphase detection and artefacts elimination. This coarseness feature provides a specific metaphase signature that can be used in conjunction with other morphological and textural parameters for automated metaphase discrimination.
Asymptomatic bacteriuria Escherichia coli strain 83972 carries mutations in the foc locus and is unable to express F1C fimbriae (2006)

Escherichia coli is the most common organism associated with asymptomatic bacteriuria (ABU). In contrast to uropathogenic E. coli (UPEC), which causes symptomatic urinary tract infection (UTI), very little is known about the mechanisms by which these strains colonize the urinary tract. Bacterial adhesion conferred by specific surface-associated adhesins is normally considered as a prerequisite for colonization of the urinary tract. The prototype ABU E. coli strain 83972 was originally isolated from a girl who had carried it asymptomatically for 3 years. This study characterized the molecular status of one of the primary adhesion factors known to be associated with UTI, namely F1C fimbriae, encoded by the foc gene cluster. F1C fimbriae recognize receptors present in the human kidney and bladder. Expression of the foc genes was found to be up-regulated in human urine. It was also shown that although strain 83972 contains a seemingly intact foc gene cluster, F1C fimbriae are not expressed. Sequencing and genetic complementation revealed that the focD gene, encoding a component of the F1C transport and assembly system, was non-functional, explaining the inability of strain 83972 to express this adhesin. The data imply that E. coli 83972 has lost its ability to express this important colonization factor as a result of host-driven evolution. The ancestor of the strain seems to have been a pyelonephritis strain of phylogenetic group B2. Strain 83972 therefore represents an example of bacterial adaptation from pathogenicity to commensalism through virulence factor loss.
Receptor Activator of Nuclear Factor-κB Ligand Activates Nuclear Factor-κB in Osteoclast Precursors* (2001)

Receptor activator of nuclear factor-kappa B ligand [RANK ligand (RANK-L)] stimulates mature osteoclasts to resorb bone, a process associated with NF-kappa B activation. RANK-L also prompts macrophages to develop the osteoclast phenotype. Although NF-kappa B is essential for osteoclast differentiation, it is not known whether RANK-L activates this transcription complex in osteoclast precursors. We report that RANK-L rapidly induces NF-kappa B activation in both authentic osteoclast precursors, namely bone marrow macrophages, and RAW 264.7 cells, a murine macrophage line also capable of RANK-L-mediated osteoclastogenesis. Supershift studies reveal the RANK-L-induced DNA binding moiety contains p50/p65, the most common NF-kappa B complex. Subcellular translocation of p50 and p65 subunits is confirmed by Western blots and immunofluorescence analysis. RANK-L activates NF-kappa B in both bone marrow macrophages and RAW 264.7 cells by serine phosphorylation of I kappa B alpha within 5 min, resulting in rapid I kappa B alpha degradation and resynthesis. Attesting to function, RANK-L treatment of RAW 264.7 cells transiently transfected with a plasmid containing NF-kappa B consensus elements linked to luciferase greatly enhances reporter activity. Our data suggest that activation of the NF-kappa B pathway is an integral component of RANK-L-induced osteoclast differentiation.
Results of field trials for the PELAN system (2002)

PELAN (Pulsed ELemental Analsys with Neutrons) is a man-portable system for the detection of explosives and chemical warfare agents, weighing 40 kg. It is based on the principle that explosives and other contraband contain various chemical elements such as H, C, N, O, etc. in quantities and ratios that differentiate them from ot her innocuous substances. The pulsed neutrons are produced with a pulsed 14 MeV (d-T) neutron generator. Separate gamma-ray spectra from fast neutron, thermal neutron and activation reactions are accumulated and analyzed to determine elemental content. Data analysis is performed in an automatic manner and a final result of whether a threat is present is returned to the operator. Since 1999, PELAN has undergone several field trials and demonstrations, including in 2001, demonstrations in Belgium andin the US of its ability to identify chemical warfare agents. We will review the results of these tests and also discuss the modifications made to the system.
Studies of Amino-acyl Insertion (1964)

Amino-acyl insertion reactions have been carried out with \(\beta\)-amino.acid ester of \(\alpha\) <em>, \(\beta\), </em>and \(\gamma\)-hydroxy acid amides.
High-Energy 2-Micrometers Doppler Lidar for Wind Measurements (2006)

High-energy 2-micrometer wavelength lasers have been incorporated in a prototype coherent Doppler lidar to test component technologies and explore applications for remote sensing of the atmosphere. Design of the lidar is presented including aspects in the laser transmitter, receiver, photodetector, and signal processing. Calibration tests and sample atmospheric data are presented on wind and aerosol profiling.
Architecture for a Non-Copyable Disk (NCdisk) Using a Secret-Protection (SP) SoC Solution (2007)

Piracy of copyrighted digital contents, such as movies and music is rampant in cyberspace. A piece of digital material may be repeatedly copied and proliferated throughout the Internet with ease. We examined both software and hardware vulnerabilities in existing digital copy-protection methods. As a result, we propose a non-copyable disk (NCdisk) that makes it significantly harder for digital contents to be copied. Any digital content written onto the NCdisk can only be read through a predefined set of outputs of the NCdisk, and the original plaintext digital form may never be read out of the NCdisk. We add a minimal set of components based on the secret-protection (SP) architecture to the existing disk's SoC chipset to attribute the disk with the non-copyable property. We further present the security protocol to be used along with the NCdisk to provide a copy-protected digital movie download scenario.
Enhanced percutaneous absorption of ionizable water-soluble drugs. (1987)

The percutaneous absorption of diltiazem hydrochloride (DIL) and disodium cromoglycate (DSCG) [representative, respectively, of cationic and anionic water-soluble drugs] was studied in rabbits, using films prepared from water-soluble components. When corresponding fat-soluble counter-ions were added to films prepared using the electrically neutral components polyvinylalcohol and glycerol, the percutaneous absorption of the drugs was enhanced. Furthermore, when non-electrolytes such as BL-9EX or urea were added to the films together with the counter-ions, the bioavailability of the drugs increased. Consequently, it is postulated that ionizable water-soluble drugs are absorbed through skin by forming fat-soluble ion-pairs and additionally that the barrier function against absorption is reduced by non-electrolytes such as BL-9EX or urea. Such non-electrolytes must not hinder the formation of ion-pairs between the drugs and corresponding counter-ions.
Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency (2014)

The WDR5 subunit of the MLL complex enforces active chromatin and can bind RNA; the relationship between these two activities is unclear. Here we identify a RNA binding pocket on WDR5, and discover a WDR5 mutant (F266A) that selectively abrogates RNA binding without affecting MLL complex assembly or catalytic activity. Complementation in ESCs shows that WDR5 F266A mutant is unable to accumulate on chromatin, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and ESC self renewal. We identify a family of ESC messenger and lncRNAs that interact with wild type WDR5 but not F266A mutant, including several lncRNAs known to be important for ESC gene expression. These results suggest that specific RNAs are integral inputs into the WDR5-MLL complex for maintenance of the active chromatin state and embryonic stem cell fates. DOI: http://dx.doi.org/10.7554/eLife.02046.001.
Titration and Conditional Knockdown of the <i>prfB</i> Gene in <i>Escherichia coli</i> : Effects on Growth and Overproduction of the Recombinant Mammalian Selenoprotein Thioredoxin Reductase (2007)

Release factor 2 (RF2), encoded by the prfB gene in Escherichia coli, catalyzes translational termination at UGA and UAA codons. Termination at UGA competes with selenocysteine (Sec) incorporation at Sec-dedicated UGA codons, and RF2 thereby counteracts expression of selenoproteins. prfB is an essential gene in E. coli and can therefore not be removed in order to increase yield of recombinant selenoproteins. We therefore constructed an E. coli strain with the endogenous chromosomal promoter of prfB replaced with the titratable P(BAD) promoter. Knockdown of prfB expression gave a bacteriostatic effect, while two- to sevenfold overexpression of RF2 resulted in a slightly lowered growth rate in late exponential phase. In a turbidostatic fermentor system the simultaneous impact of prfB knockdown on growth and recombinant selenoprotein expression was subsequently studied, using production of mammalian thioredoxin reductase as model system. This showed that lowering the levels of RF2 correlated directly with increasing Sec incorporation specificity, while also affecting total selenoprotein yield concomitant with a lower growth rate. This study thus demonstrates that expression of prfB can be titrated through targeted exchange of the native promoter with a P(BAD)-promoter and that knockdown of RF2 can result in almost full efficiency of Sec incorporation at the cost of lower total selenoprotein yield.
Measuring Amide Nitrogen Quadrupolar Coupling by High-Resolution <sup>14</sup>N/<sup>13</sup>C NMR Correlation under Magic-Angle Spinning (2006)

The measurement of amide nitrogen 14N quadrupolar coupling by two-dimensional 14N/13C correlation experiment is presented with a natural abundant polypeptide. Directly bonded 14N/13C pairs are correlated through J and residual dipolar coupling under magic-angle spinning using a HMQC-type pulse sequence. The 14N quadrupolar coupling is measured from the isotropic second-order quadrupolar shift obtained by comparing the 14N peak positions with the 15N chemical shifts. The high spectral resolution and sensitivity through 13C detection make this method applicable to many organic, inorganic, and biological molecules for the measurement and the use of 14N quadrupolar coupling as a probe for molecular structure and dynamics.
Central Role for ENaC in Development of Hypertension (2005)

Na(+) reabsorption by the epithelial Na(+) channel (ENaC) in cortical collecting duct provides the final renal adjustment to Na(+) balance, there being no further downstream Na(+) transport system. This fact coupled with the responsiveness of ENaC to aldosterone, which conveys stimulation inversely proportional to the state of Na(+) balance, places ENaC in a pivotal position to influence the risk for hypertension. Although several molecular variants of ENaC subunits have been identified, there has been no consistent demonstration of an association of any of the variants with hypertension. More compelling is the notion that ENaC activity does not fully adjust to an increase in Na(+) reabsorption occurring elsewhere in the nephron, there being overstimulation by inappropriately elevated aldosterone levels. Additional evidence that the maintenance of hypertension can be dependent on ENaC is derived from the observed responses to the treatment of hypertensive individuals with inhibitors of ENaC. Described is a clinical trial in which black hypertensive individuals who did not fully respond to more traditional therapy were given amiloride, spironolactone, a combination of the two drugs, or placebo. Treatment with either of the active inhibitors of ENaC resulted in a substantial improvement in BP. In conclusion, evidence to date is supportive of the concept that an increase in Na(+) transport by ENaC may be a common and requisite component of salt-dependent forms of hypertension.
The Composition of Fluoride Solutions (2005)

Aqueous fluoride solutions underpin much of silicon processing because they are used to strip oxide layers and for cleaning. Depending on their composition and reaction conditions they can be used to create either flat, hydrogen-terminated surfaces or nanocrystalline porous silicon. Nonetheless, confusion reigns regarding the identity and quantity of different solution species as a function of the formal concentration of HF and other additives. The literature is critically surveyed, data and results are reanalyzed, and analytical expressions are derived that allow for the calculation of solution species activities. Above , fluoride solutions are highly nonideal. It is shown that the main constituents of acidic fluoride solutions are , , HF, , and in the range of and even as high as . In these concentration ranges the derived analytical expressions exhibit excellent and approximate agreement with experimental data, respectively. The nature of the HF species that exists in solution, whether it exists as a contact ion pair or as a solvated molecule, remains in doubt.
Ending Aging in Super Glassy Polymer Membranes (2014)

Aging in super glassy polymers such as poly(trimethylsilylpropyne) (PTMSP), poly(4-methyl-2-pentyne) (PMP), and polymers with intrinsic microporosity (PIM-1) reduces gas permeabilities and limits their application as gas-separation membranes. While super glassy polymers are initially very porous, and ultra-permeable, they quickly pack into a denser phase becoming less porous and permeable. This age-old problem has been solved by adding an ultraporous additive that maintains the low density, porous, initial stage of super glassy polymers through absorbing a portion of the polymer chains within its pores thereby holding the chains in their open position. This result is the first time that aging in super glassy polymers is inhibited whilst maintaining enhanced CO2 permeability for one year and improving CO2/N2 selectivity. This approach could allow super glassy polymers to be revisited for commercial application in gas separations.