gebhart/patrepeval huggingface dataset:
Cleaning out, sealing and mining through wells penetrating areas of active coal mines in northern West Virginia (1977)

Demonstrations began in 1971 to prove the effectiveness of well plugging as the substitute for the support pillars normally left around oil and gas wells. Wells that are candidates for plugging are abandoned or low-productive wells. The purpose of the demonstrations was to achieve safer mining by elimination of problems--mainly adverse roof stress distribution and disruption of normal haulage and ventilation systems--caused by the presence of the well-support pillars. The recovery of the coal in the well-support pillars was a secondary purpose. This method was developed and fostered as a cooperative effort by several divisions of the U.S. Bureau of Mines. Effectiveness of plugging and sealing to prevent reservoir gas from entering the mine through the well borehole was verified in each case by continuous monitoring of the mine atmosphere for indications of a tracer gas, sulfur hexafluoride (SF/sub 6/), which was placed below the well plug in a pressurized time-bomb capsule. Analyses of samples collected in tests for gas showed the wells to have been effectively sealed. Mining companies in this area are convinced that the methods are economically feasible and are beginning to use the techniques to plug wells at their own expense. Successful 301(c) Petitions have beenmore » granted by the Office of Hearings and Appeals, pursuant to the Federal Coal Mine Health and Safety Act of 1969, which allows substitution of the plugging system for the well-support pillar, as required by regulations. MESA has cooperated with industry and labor in developing the safety precautions incorporated in the petition applications.« less
Combining case-based and rule-based reasoning: a heuristic approach (1989)

Ebola virus (EBOV) is a highly pathogenic filovirus that causes hemorrhagic fever in humans and animals. Here we provide evidence that cell-cell contact promotes infection mediated by the glycoprotein (GP) of EBOV. Interestingly, expression of EBOV GP alone, even in the absence of retroviral Gag-Pol, is sufficient to transfer a retroviral vector encoding Tet-off from cell to cell. Cell-to-cell infection mediated by EBOV GP is blocked by inhibitors of actin polymerization, but appears to be less sensitive to KZ52 neutralization. Treatment of co-cultured cells with cathepsin B/L inhibitors, or an entry inhibitor 3.47 that targets the receptor NPC1 for virus binding, also blocks cell-to-cell infection. Cell-cell contact also enhances spread of rVSV bearing GP in monocytes and macrophages, the primary targets of natural EBOV infection. Altogether, our study reveals that cell-cell contact promotes EBOV GP-mediated infection, and provides new insight into understanding EBOV spread and viral pathogenesis.
REST and Peace for the Neuronal‐Specific Transcriptional Program (2004)

Despite a genetic homogeneity, cells in multicellular organisms are structurally and functionally heterogeneous. The diversity of cell phenotypes exists due to differential transcriptional programs precisely regulated by specific nuclear factors and induced upon differentiation. The differences in gene expression programs arise during development and become heritable during cell proliferation. Over the last few years, research has focused on three molecular mechanisms that mediate epigenetic phenomena: DNA methylation, histone modification, and formation of specialized nuclear domains or territories. All of these processes are dynamic and tightly linked to the organism's development. Here we review advances in understanding the significance of epigenetic mechanisms in the establishment and maintenance of the specialized transcriptional program. We project the accumulated knowledge onto the delineation of the molecular mechanisms by which central nervous system-specific genes are expressed in the nervous system and repressed in other tissues.
Site-directed mutagenesis of residues 164, 170, 171, 179, 220, 237 and 242 in PER-1 β-lactamase hydrolysing expanded-spectrum cephalosporins (1999)

The class A beta-lactamase PER-1, which displays 26% identity with the TEM-type extended-spectrum beta-lactamases (ESBLs), is characterized by a substrate profile similar to that conferred by these latter enzymes. The role of residues Ala164, His170, Ala171, Asn179, Arg220, Thr237 and Lys242, found in PER-1, was assessed by site-directed mutagenesis. Replacement of Ala164 by Arg yielded an enzyme with no detectable beta-lactamase activity. Two other mutants, N179D and A164R+N179D, were also inactive. Conversely, a mutant with the A171E substitution displayed a substrate profile very similar to that of the wild-type enzyme. Moreover, the replacement of Ala171 by Glu in the A164R enzyme yielded a double mutant which was active, suggesting that Glu171 could compensate for the deleterious effect of Arg164 in the A164R+A171E enzyme. A specific increase in kcat for cefotaxime was observed with H170N, whereas R220L and T237A displayed a specific decrease in activity towards the same drug and a general increase in affinity towards cephalosporins. Finally, the K242E mutant displayed a kinetic behaviour very similar to that of PER-1. Based on three-dimensional models generated by homology modelling and molecular dynamics, these results suggest novel structure-activity relationships in PER-1, when compared with those previously described for the TEM-type ESBLs.
RNA interference technologies and their use in cancer research (2006)

Loss-of-function studies offer a potential for validation of known and unrecognized tumor-associated targets. RNA interference-mediated gene knockdown can be exploited to study the reprogrammed circuitry of genes, discover gene interactions restricted to cancer cells and identify mechanisms of chemoresistance in cancer cells. In addition, the simultaneous use of cancer drugs and RNA interference also provides a paradigm to develop strategies to inactivate essential genes promoting neoplastic growth.
Adoptive Cell Transfer for Patients with Metastatic Melanoma: The Potential and Promise of Cancer Immunotherapy (2013)

An example of state-of-the-art personalized medicine, ACT is a potentially curative therapy for patients with metastatic melanoma. Ongoing trials aiming to simplify the regimens may allow a broader range of patients to be treated and enable ACT to be offered by academic cancer centers.
Stereospecific Synthesis of cis-2,4-Pyrrolidinedicarboxylic Acid and cis-2,5-Piperidinedicarboxylic Acid. (1997)

Lactams derived from hetero Diels-Alder adducts were stereospecifically converted into cis-2, 4-pyrrolidinedicarboxylic acid and cis-2, 5-piperidinedicarboxylic acid by ruthenium tetroxide oxidation. Optically active (2S, 4S)-(-)-2, 4-pyrrolidinedicarboxylic acid and (2R, 4R)-(+)-2, 4-pyrrolidinedicarboxylic acid were synthesized from (1S, 4R)-(+)-2-azabicyclo[2.2.1]hept-5-en-3-one and (1R, 4S)-(-)-2-azabicyclo[2.2.1]hept-5-en-3-one, respectively.
Reactivity of Lactones and GHB Formation (2004)

The behavior of lactones in their hydrolysis reactions is a good indicator of their reactivity as electrophilic molecules. The hydrolysis of four- to six-membered lactones was investigated in neutral (water) and slightly acid media and in water/dioxane media. The following conclusions were drawn: (i) The reactivity of beta-propiolactone in neutral water is more than four times greater than that of beta-butyrolactone, due to the flow of charge caused by the latter's methyl substituent. Reactivity is enthalpy-controlled. (ii) The reactivity of beta-lactones diminishes in water/dioxane media when the percentage of dioxane increases. The increase in the dioxane percentage relaxing the intermolecular hydrogen bonds in the ordered structure of the water reduces DeltaH# and simultaneously increases the -DeltaS# value. (iii) An inverse solvent kinetic isotope effect in the acid-catalyzed hydrolysis of gamma-butyrolactone and delta-valerolactone was observed, this being indicative of acyl cleavage. (iv) The DeltaH# and DeltaS# values permit discrimination between alkyl and acyl cleavage. (v) A correlation was found between the chemical reactivity of lactones and their carcinogenic activity. (vi) The results suggest that orally ingested gamma-butyrolactone remains largely in its nonhydrolyzed form in the stomach before passing into the blood. (vii) The concentration equilibrium constant of GHB formation at human body temperature is Keq (37 degrees C)=0.40. (viii) Study of GHB formation shows that, contrary to earlier results, this is an endothermic process, with DeltarH=3.6 kJ mol(-1).
Local area data distribution (1980)

The Information Processing Industry now has available a new link-technology between information and the information user. The new technology is the local radio frequency (RF) voice-grade data broadcast channel.
Herbal Modulation of P‐Glycoprotein (2004)

P-glycoprotein (Pgp) is a 170 kDa phosphorylated glycoprotein encoded by human MDR1 gene. It is responsible for the systemic disposition of numerous structurally and pharmacologically unrelated lipophilic and amphipathic drugs, carcinogens, toxins, and other xenobiotics in many organs, such as the intestine, liver, kidney, and brain. Like cytochrome P450s (CYP3A4), Pgp is vulnerable to inhibition, activation, or induction by herbal constituents. This was demonstrated by using an ATPase assay, purified Pgp protein or intact Pgp-expressing cells, and proper probe substrates and inhibitors. Curcumin, ginsenosides, piperine, some catechins from green tea, and silymarin from milk thistle were found to be inhibitors of Pgp, while some catechins from green tea increased Pgp-mediated drug transport by heterotropic allosteric mechanism, and St. John's wort induced the intestinal expression of Pgp in vitro and in vivo. Some components (e.g., bergamottin and quercetin) from grapefruit juice were reported to modulate Pgp activity. Many of these herbal constituents, in particular flavonoids, were reported to modulate Pgp by directly interacting with the vicinal ATP-binding site, the steroid-binding site, or the substrate-binding site. Some herbal constituents (e.g., hyperforin and kava) were shown to activate pregnane X receptor, an orphan nuclear receptor acting as a key regulator of MDR1 and many other genes. The inhibition of Pgp by herbal constituents may provide a novel approach for reversing multidrug resistance in tumor cells, whereas the stimulation of Pgp expression or activity has implication for chemoprotective enhancement by herbal medicines. Certain natural flavonols (e.g., kaempferol, quercetin, and galangin) are potent stimulators of the Pgp-mediated efflux of 7,12-dimethylbenz(a)-anthracene (a carcinogen). The modulation of Pgp activity and expression by these herb constituents may result in altered absorption and bioavailability of drugs that are Pgp substrates. This is exemplified by increased oral bioavailability of phenytoin and rifampin by piperine and decreased bioavailability of indinavir, tacrolimus, cyclosporine, digoxin, and fexofenadine by coadministered St. John's wort. However, many of these drugs are also substrates of CYP3A4. Thus, the modulation of intestinal Pgp and CYP3A4 represents an important mechanism for many clinically important herb-drug interactions. Further studies are needed to explore the relative role of Pgp and CYP3A4 modulation by herbs and the mechanism for the interplay of these two important proteins in herb-drug interactions.
Dynamical eigenfunction decomposition of turbulent channel flow (1991)

Abstract The results of an analysis of low‐Reynolds‐number turbulent channel flow based on the Karhunen‐Loéve(K‐L) expansion are presented. The turbulent flow field is generated by a direct numerical simulation of the Navier‐Stokes equations at a Reynolds number Re ,= 80 (based on the wall shear velocity and channel half‐width). The K‐L procedure is then applied to determine the eigenvalues and eigenfunctions for this flow. The random coefficients of the K‐L expansion are subsequently found by projecting the numerical flow field onto these eigenfunctions. The resulting expansion captures 90% of the turbulent energy with significantly fewer modes than the original trigonometric expansion. The eigenfunctions, which appear either as rolls or shearing motions, posses viscous boundary layers at the walls and are much richer in harmonics than the original basis functions. Chaotic temporal behaviour is observed in all modes and increases for higher‐order eigenfunctions. The structure and dynamical behaviour of the eigenmodes are discussed as well as their use in the representation of the turbulent flow.
Optical properties of two-dimensional photonic lattices fabricated as honeycomb nanostructures in compound semiconductors (1994)

We have experimentally studied two-dimensional photonic lattices, honeycomb nanostructures, fabricated by electron beam lithography with (Al,Ga)As materials. Surface normal optical properties were investigated by measuring reflectance to determine the effective index of refraction and lattice stability against degradation. Also, continuous wave and time-resolved luminescence spectroscopy was used to assess electron-hole recombination. Finally, light scattering was employed to study photon coupling and propagation through the lattice. These measurements show that the structures are stable, that nonradiative surface recombination is present, and that resonant coupling of light into/out of the lattice occurs at selected wavelengths satisfying a Bragg condition.
Large broadband visible to infrared plasmonic absorption from Ag nanoparticles with a fractal structure embedded in a Teflon AF® matrix (2005)

An unusual almost flat broadband plasmonic absorption, ranging from 400nm to well beyond 2500nm, was observed in a 150nm thin film of Ag nanoparticles embedded in a Teflon AF® matrix. The nanocomposites were synthesized by a simple single-step vapor-phase codeposition method. The Ag nanoparticles of various sizes and shapes, and thus various resonance frequencies, form a fractal percolating network. The broadband absorption, attributed to plasmon excitations within the nanoparticles, could be useful for multicolor applications in the visible and infrared wavelengths region.
Brown Adipose Tissue Can Be Activated or Inhibited within an Hour before 18F‐FDG Injection: A Preliminary Study with MicroPET (2011)

Brown adipose tissue (BAT) is emerging as a potential target for treating human obesity. It has been indicated that BAT is rich in innervations of sympathetic nerve control. Using (18)F-FDG microPET imaging, this study aims at evaluating how factors related to sympathetic activation/inhibition changed BAT metabolism of mice. BAT (18)F-FDG uptake were semiquantitatively evaluated in different groups of mice under temperature (cold or warm stimulus) or pharmacological interventions (norepinephrine, epinephrine, isoprenaline, or propranolol) and were compared with the corresponding controls. It was found that BAT activation can be stimulated by cold exposure (P = 1.96 × 10(-4)), norepinephrine (P = .002), or both (P = 2.19 × 10(-6)) within an hour before (18)F-FDG injection and can also be alleviated by warming up (P = .001) or propranolol lavage (P = .027). This preliminary study indicated that BAT function could be evaluated by (18)F-FDG PET imaging through short-term interventions, which paved the way for further investigation of the relationship between human obesity and BAT dysfunction.
Measurement of small mechanical vibrations of brain tissue exposed to extremely‐low‐frequency electric fields (1986)

Electromagnetic fields can interact with biological tissue both electrically and mechanically. This study investigated the mechanical interaction between brain tissue and an extremely-low-frequency (ELF) electric field by measuring the resultant vibrational amplitude. The exposure cell is a section of X-band waveguide that was modified by the addition of a center conductor to form a small TEM cell within the waveguide structure. The ELF signal is applied to the center conductor of the TEM cell. The applied ELF electric field generates an electrostrictive force on the surface of the brain tissue. This force causes the tissue to vibrate at a frequency equal to twice the frequency of the applied sinusoidal signal. An X-band signal is fed through the waveguide, scattered by the vibrating sample, and detected by a phase-sensitive receiver. Using a time-averaging spectrum analyzer, a vibration sensitivity of approximately 0.2 nmp-p can be achieved. The amplitude of the brain tissue vibrational response is constant for vibrational frequencies below 50 Hz; between 50 and 200 Hz resonant phenomena were observed; and above 200 Hz the amplitude fall-off is rapid.
Molecular Heterogeneity of the SHAP-Hyaluronan Complex (2003)

We previously found that a covalent complex of SHAPs (serum-derived hyaluronan-associated proteins), the heavy chains of inter-alpha-trypsin inhibitor family molecules, with hyaluronan (HA) is accumulated in synovial fluid of patients with rheumatoid arthritis, and the complex is circulated in patient plasma at high concentrations. How the SHAP-HA complex participates in this disease is unknown. To address this question, it is essential to clarify the structural features of this macromolecule. The SHAP-HA complex purified from synovial fluid of the patients by three sequential CsCl isopycnic centrifugations was heterogeneous in density, and the fractions with different densities had distinct SHAP-to-HA ratios. Agarose gel electrophoresis and column chromatography revealed that there was no apparent difference in the size distribution of HA to which SHAPs were bound between the fractions with different densities. The SHAP-HA complex in the higher density fraction had fewer SHAP molecules per HA chain. Therefore, the difference between the fractions with different densities was due to a heterogeneous population of the SHAP-HA complex, namely the different number of SHAP molecules bound to an HA chain. Based on the SHAP and HA contents of the purified preparations, we estimated that an HA chain with a molecular weight of 2 x 106 has as many as five covalently bound SHAPs, which could give a proteinaceous multivalency to HA. Furthermore, we also found that the SHAP-HA complex tends to form aggregates, judging from the migration and elution profiles in agarose gel electrophoresis and gel filtration, respectively. The multivalent feature of the SHAP-HA complex was also confirmed by the negative staining electron micrographic images of the purified fractions. Taken together, those structural characteristics may underlie the aggregate-forming and extracellular matrix-stabilizing ability of the SHAP-HA complex.
Glutamate Dehydrogenase Activity Can Be Transmitted Naturally to Lactococcus lactis Strains To Stimulate Amino Acid Conversion to Aroma Compounds (2006)

Amino acid conversion to aroma compounds by Lactococcus lactis is limited by the low production of alpha-ketoglutarate that is necessary for the first step of conversion. Recently, glutamate dehydrogenase (GDH) activity that catalyzes the reversible glutamate deamination to alpha-ketoglutarate was detected in L. lactis strains isolated from a vegetal source, and the gene responsible for the activity in L. lactis NCDO1867 was identified and characterized. The gene is located on a 70-kb plasmid also encoding cadmium resistance. In this study, gdh gene inactivation and overexpression confirmed the direct impact of GDH activity of L. lactis on amino acid catabolism in a reaction medium at pH 5.5, the pH of cheese. By using cadmium resistance as a selectable marker, the plasmid carrying gdh was naturally transmitted to another L. lactis strain by a mating procedure. The transfer conferred to the host strain GDH activity and the ability to catabolize amino acids in the presence of glutamate in the reaction medium. However, the plasmid appeared unstable in a strain also containing the protease lactose plasmid pLP712, indicating an incompatibility between these two plasmids.
Fast mutual exclusion for uniprocessors (1992)

In this paper we describe restartable atomic sequences, an optimistic mechanism for implementing simple atomic operations (such as Test-And-Set ) on a uniprocessor. A thread that is suspended within a restartable atomic sequence is resumed by the operating system at the beginning of the sequence, rather than at the point of suspension. This guarantees that the thread eventually executes the sequence atomically . A restartable atomic sequence has significantly less overhead than other software-based synchronization mechanisms, such as kernel emulation or software reservation. Consequently, it is an attractive alternative for use on uniprocessors that do no support atomic operations. Even on processors that do support atomic operations in hardware, restartable atomic sequences can have lower overhead. We describe different implementations of restartable atomic sequences for the Mach 3.0 and Taos operating systems. These systems' thread management packages rely on atomic operations to implement higher-level mutual exclusion facilities. We show that improving the performance of low-level atomic operations, and therefore mutual exclusion mechanisms, improves application performance.
Induction of Cytotoxic T–Cell Response Against Hepatitis C Virus Structural Antigens Using A Defective Recombinant Adenovirus (1997)

A replication-defective recombinant adenovirus (RAd), RAdCMV-CE1, containing core and E1 genes of hepatitis C virus (HCV) was constructed. RAdCMV-CE1 was able to express core and E1 proteins both in mice and human cells. Immunization of BALB/c mice with RAdCMV-CE1 induced a specific cytotoxic T-cell response against the two HCV proteins. This response was characterized using a panel of 60 synthetic 14- or 15-mer overlapping peptides (10 amino-acid overlap) spanning the entire sequence of these proteins. Five main epitopes were found in the core protein, four of which had been previously described either in mice or humans. One single novel epitope was found in E1. Fine mapping of this E1 determinant, showed that octamer GHRMAWDM is the minimal epitope recognized by cytotoxic T lymphocytes (CTL). The cytotoxic T-cell response was H-2d restricted, lasted for at least 100 days, and was mediated by T cells with the classic CD4-CD8+ phenotype. This work demonstrates that replication-defective recombinant adenoviruses can efficiently express HCV proteins and are able to induce an in vivo cytotoxic T-cell response against a diversity of epitopes from HCV antigens. These vectors should be taken into consideration in the design of vaccines and also as a means to stimulate specific T-cell responses in chronic HCV carriers.