gebhart/patrepeval huggingface dataset:
Extremely high thermal conductivity of graphene: Prospects for thermal management applications in silicon nanoelectronics (2008)

Graphene, a recently discovered form of carbon, revealed many unique properties, including extremely high electron mobility of ~15000 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs at room temperature (RT). We have experimentally studied the thermal conductivity of graphene suspended over a trench in silicon (Si) wafer. It was found for a given set of samples that RT thermal conductivity of graphene is in the range ~ 3080 - 5150 W/mK. The giant thermal conductivity and demonstrated graphene - Si integration suggest that graphene can become superior material for thermal management of Si nanoelectronic circuits.
Metal ion-mediated polymer superquenching for highly sensitive detection of kinase and phosphatase activities (2004)

An assay technology for high-throughput screening of kinase and phosphatase activities is introduced. The format is based upon superquenching of fluorescent-conjugated polymers by dye-labeled kinase/phosphatase peptide substrates. The sensor platform is composed of highly fluorescent-conjugated polyelectrolytes colocated with the phosphate coordinating metal ion gallium on microspheres. Phosphorylated peptide substrates containing a quencher bind specifically to the metal ions by means of phosphate groups, resulting in quench of polymer fluorescence. The modulation of fluorescence signal is proportional to kinase or phosphatase activity and is monitored as a turn-off or turn-on signal, respectively. The assay is homogeneous and simple and can be run either as an endpoint measurement or in a kinetic mode. The assay meets the sensitivity required for high-throughput screening of kinase or phosphatase inhibitors and is a valuable tool for drug discovery. A modified version of the assay allows for the detection of protein phosphorylation.
The relation of structure to some physical and mechanical properties of poly(vinyl alkyl ethers) (1961)

Abstract The preparation of a homologous series of eighteen poly(vinyl alkyl ethers) by cationic solution polymerization is reported. Physical and mechanical properties of the polymer were found to be highly dependent on the size or bulkiness of the alkyl side chain. Thus, poly(vinyl alkyl ethers) having highly branched alkyl groups exhibited a higher glass transition temperature (T g ), higher softening point, increased hardness, tensile strength, 100% modulus and modulus of elasticity than the corresponding polymers possessing straight chain alkyl groups. In addition, it was found that the higher the degree of steric hindrance about the oxygen atom of the vinyl alkyl ether monomer, the higher the rate of polymerization.
HUMAN NUCLEUS PULPOSUS CAN RESPOND TO A PRO-INFLAMMATORY STIMULUS. (2003)

The role of nucleus pulposus (NP) biology in the genesis of sciatica is being increasingly investigated. The aim of this study was to examine the ability of control and degenerate human nucleus pulposus to respond to an exogenous pro-inflammatory stimulus. Control disc material was obtained from surgical procedures for scoliosis and degenerate disc tissue from surgical procedures for sciatica and low back pain. Disc specimens were cultured using a serumless technique under basal and lipopolysaccharride (LPS) stimulated conditions and the media harvested, aliquoted and stored at –80°C for subsequent analysis. Levels of IL-1β,TNFα, LTB4, GM-CSF, IL-6, IL-8, MCP-1, PGE2, bFGF and TGFβ-1 in the media were estimated using commercially available enzyme linked immunoabsorbent assay kits. Neither basal nor LPS stimulated control or degenerate NP produced detectable levels of IL-1β, TNFα, LTB4 or GM-CSF. Control disc IL-8 secretion increased significantly with LPS stimulation, p LPS induces an increase in both control and degenerate NP mediator production demonstrating the ability of human NP to react to a noxious stimulus by producing pro-inflammatory mediators. The difference in levels of basal and LPS stimulated mediator production between control and degenerate discs show that as a disc degenerates it increases both its level of inflammatory mediator production and its ability to react to a pro-inflammatory stimulus. The increased sensitivity of degenerating human NP to noxious stimuli and increased ability to respond with inflammatory mediator production support the role of NP as an active participant in the genesis of lumbar radiculopathy and discogenic back pain.
Dietary Zinc Deficiency and Tumorigenesis: A Scanning Electron Microscope Study (1984)

The surface morphology of the forestomach squamous mucosa in zinc-deficient and pair-fed zinc-sufficient rats fed N-nitrosodimethylamine (NDMA) was studied by scanning electron microscopy (SEM). Specific changes including squamous papillomas and changes of the superficial keratinocytes were found only in zinc-deficient rats. In these rats, architectural distortion in the arrangement of the surface keratinocytes on the junctional ridge between the fore- and glandular stomachs were present. There was marked flaking and scaling of the keratinocytes. Widening of the intercellular spaces was also present. It is possible that the abnormal mucosa may be more permeable and that local increased tissue exposure may play a role in the pathogenesis of NDMA-induced forestomach tumors in zinc deficiency.
Priming of CD4+ T cells specific for conserved regions of human immunodeficiency virus glycoprotein gp120 in humans immunized with a recombinant envelope protein. (1990)

A nonglycosylated denatured form of human immunodeficiency virus (HIV) 1 glycoprotein gp120 (Env 2-3), which does not bind to CD4, was used with muramyl tripeptide as adjuvant to immunize HIV-seronegative healthy volunteers. In all the volunteers, three 50-micrograms injections of Env 2-3 induced priming of CD4+ T cells specific for conserved regions of the native glycosylated gp120. Moreover, we found that several major histocompatibility complex class II (DR) alleles can function as restriction molecules for presentation of conserved epitopes of gp120 to T cells, implying that a T-cell response to these epitopes can be obtained in a large fraction of the population. The possibility to prime CD4+ T cells specific for conserved epitopes of a HIV protein is particularly important in view of the lack of such cells in HIV-infected individuals and of a possible role that CD4+ T cells may play in the development of protective immunity against AIDS.
The oxygen dependence of mitochondrial oxidative phosphorylation measured by a new optical method for measuring oxygen concentration. (1988)

Oxygen-dependent quenching of phosphorescence has been used to measure the dependence of mitochondrial oxidative phosphorylation on oxygen concentration in suspensions of isolated rat liver mitochondria. An instrument has been designed which simultaneously monitors the phosphorescence lifetime of a fluorophor and the reduction of cytochrome c by dual wavelength spectrophotometry. The phosphorescence lifetime method gives very rapid (less than 100 ms) measure of the oxygen concentration (Vanderkooi, J. M., Maniara, G., Green, T. J., and Wilson, D. F. (1987) J. Biol. Chem. 262, 5476-5482) from concentrations characteristic of air-saturated media to as low as 2 x 10(-8) M. The results may be summarized as follows. For well coupled rat liver mitochondria at pH 7.0 and in the presence of ATP, as the oxygen concentration was lowered, increased cytochrome c reduction was observed to begin at oxygen concentrations greater than 20 microM. For mitochondria in the presence of uncoupler, cytochrome c reduction began at oxygen concentrations less than 1.0 microM. The oxygen dependence of reduction of cytochrome c in well coupled mitochondria treated with ATP was strongly dependent on the pH of the suspending medium. Reduction of cytochrome c began at higher oxygen concentrations as the pH was made more alkaline. The oxygen concentration for half-maximal respiratory rates was much larger for well coupled mitochondria treated with ATP (approximately 0.7 microM) than for mitochondria treated with uncoupler (less than 0.1 microM). It is concluded that the oxygen dependence of mitochondrial oxidative phosphorylation is such that mitochondria could function in their proposed role of tissue oxygen sensors for regulation of such diverse functions as local blood flow and electrical activity in the carotid body.
Images of the DNA Double Helix in Water (1989)

The scanning tunneling microscope can image uncoated DNA submerged in water. The grooves of the double helix were clearly resolved in images of the 146-base pair fragment extracted from calf thymus nucleosome. In contrast to images obtained with dry DNA, the helix pitch varied only a small amount (36 +/- 5 angstroms). The path of the helix shows considerable variation. It is quite straight when the molecules are densely packed, but it curves and bends in isolated molecules.
Unsteady-State Pressure Distributions Created by a Well With a Single Infinite-Conductivity Vertical Fracture (1974)

Introduction During the last few years, there has been an explostion of information in the field of well-test analysis. Because of increased physical understanding of transient fluid flow, it is possible to analyze the entire pressure history of a well test, not just long-time data as in conventional analysis.1 It is now often possible to specify the time of beginning of the correct semilog straight line and determine whether the correct straight lie has been properly identified. It is also possible to identify wellbore storage effects, and the nature of wellbore stimulation as to permeability improvement, or fracturing, and to quantitatively analyze those effects. Such accomplishments have been augmented by attempts to understand the short-time pressure data from well testing - data that were often classified as too complex for analysis. One recent study of short-time pressure behavior2 showed that it was important to specify the physical nature of the stimulation in considering the behavior of a stimulated well. That is, stating that the van Everdingen-Hurst infinitesimal skin effect was negative was not sufficient to define short-time well behavior. For instance, acidized (but not acid-fractured) and hydraulically fractured wells might not necessarily exhibit the same behavior at early times, even though they could possess the same value of negative skin effect. In the same manner, hydraulic fracturing leading to horizontal or vertical fractures could produce the same skin effect, but with possibly different short-time pressure data. This could then provide a way to determine the orientation of fractures created by this type of well stimulation. In fact, it is generally agreed that hydraulic fracturing usually results in one vertical fracture, the plane of which includes the wellbore. Most studies of the flow behavior for a fractured well consider vertical fractures only.3–11 Yet it is also agreed that horizontal fractures could occur in shallow formations. Furthermore, it would appear that notch-fracturing would lead to horizontal fractures. Surprisingly, no detailed study of the horizontal fracture case had been performed until recently.12 A solution to this problem was presented by Gringarten and Ramey.13 In the course of their study, it was found that a large variety of new transient pressure behavior solutions useful in well and reservoir analysis could be constructed from instantaneous Green's functions.14 Possibilities included a well with a single vertical fracture in an infinite reservoir, or at any location in a rectangle.
Specificity of the wound‐induced leucine aminopeptidase (LAP‐A) of tomato (2000)

Wounding of tomato leaves results in the accumulation of an exoprotease called leucine aminopeptidase (LAP‐A) that preferentially hydrolyzes amino acid ‐p‐ nitroanilide and ‐β‐naphthylamide substrates with N‐terminal Leu, Met and Arg residues. To determine the substrate specificity of LAP‐A on more natural substrates, the rates of hydrolysis of 60 dipeptide and seven tripeptide substrates were determined. For comparison, the specificities of the porcine and Escherichia coli LAPs were evaluated in parallel. Several marked differences in substrate specificities for the animal, plant and prokaryotic LAP enzymes were observed. Substrates with variable N‐terminal (P1) residues (Xaa) were evaluated; these substrates had Leu or Gly in the penultimate (P1′) position. The plant, animal, and prokaryotic LAPs hydrolyzed dipeptides with N‐terminal nonpolar aliphatic (Leu, Val, Ile, and Ala), basic (Arg), and sulfur‐containing (Met) residues rapidly, while P1 Asp or Gly were cleaved inefficiently from peptides. Significant differences in the cleavage of dipeptides with P1 aromatic residues (Phe, Tyr, and Trp) were noted. To systematically evaluate the impact of the P1′ residue on cleavage of dipeptides, three series of dipeptides (Leu‐Xaa, Gly‐Xaa, and Arg‐Xaa) were evaluated. The P1′ residue strongly influenced hydrolysis of dipeptides and the magnitude of its effect was dependent on the P1 residue. P1′ Pro, Asp, Lys and Gly slowed the hydrolysis rates of the tomato LAP‐A, porcine LAP, and E. coli PepA markedly. Analysis six Arg‐Gly‐Xaa tripeptides showed that more diversity was tolerated in the P2′ position. P2′ Arg inhibited tripeptide cleavage by all three enzymes, while P2′ Asp enhanced hydrolysis rates for the porcine and prokaryotic LAPs.
Borehole gravity gradiometry (1989)

Abstract Gravity gradients measured in a borehole are of interest due to their direct, simple relation to the density of the formations surrounding the hole. Borehole gravity meters (BHGMs) are used to measure gravity differences along the borehole and from these differences, we compute averaged values for a linear combination of the gravity gradient tensor elements. One way to implement a borehole gravity gradiometer (BHGGM) is to measure the torque exerted on a pair of masses separated by a beam. A BHGGM directly measures all the elements of the gravity gradient tensor. Knowledge of these elements provides information about the direction to density anomalies in the vicinity of the borehole and enhances the analysis of dipping beds. The BHGGM may be superior to the BHGM for resolving the density of thin beds. Density variations remote from the borehole are best detected and characterized by joint interpretation of BHGM and BHGGM data.
Development of a reporter system for the study of gene expression for solvent production in Clostridium beijerinckii NRRL B592 and Clostridium acetobutylicum ATCC 824 (1998)

To study the regulation of gene expression, a good reporter system is very useful. The lack of a good reporter system for the solvent-producing clostridia hindered the progress of research in this area. The objective of this study was to develop a reporter system to facilitate the elucidation of the control mechanism for the expression of solvent-producing genes. A potential reporter gene was found in Clostridium beijerinckii NRRL B593, which contains an adh gene encoding a primary-secondary alcohol dehydrogenase and this adh gene is not present in Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NRRL B592. The adh gene was cloned into the E. coli -Clostridium shuttle vectors to generate plasmids. An electro-transformation procedure was developed for C. beijerinckii NRRL B592. Shuttle plasmids were transformed into C. beijerinckii NRRL B592 or C. acetobutylicum ATCC 824. The copy number of the plasmids in C. beijerinckii was 4. Isopropanol production suggested that the adh gene was expressed in transformants of C. acetobutylicum ATCC 824 and C. beijerinckii NRRL B592. Northern analysis indicated that the expression of the adh gene was regulated at the transcriptional level in the transformants of C. beijerinckii. The transcriptional start site for the adh gene was identified by the primer extension method. A promoter-probing vector was constructed and tested with the promoter from the ferredoxin(fer) gene. The expression of the adh gene under the control of the fer promoter was at a low and similar level during acidogenesis and solventogenesis. The expression pattern of the adh gene under the control of the promoter of the adh gene differed from that under the control of the promoter of the fer gene.
Z-DNA binding and inhibition by GTP of Drosophila topoisomerase II (1993)

A Z-DNA binding protein has been isolated and characterized by biochemical means from Drosophila melanogaster tissue culture cells and embryos. This protein shares the following properties with the known, cloned Drosophila topoisomerase II: (1) expression of an ATP-dependent relaxation activity on supercoiled DNA; (2) a monomer mass of 165 kDa in SDS denaturing gels; (3) a sedimentation coefficient, S20,w, of approximately 10 S for the active enzyme; (4) cross-reactivity for the respective monoclonal and polyclonal antibodies; (5) generation of covalent enzyme-DNA intermediates at preferred cutting sites in the Drosophila HSP70 intergenic spacer region; (6) inhibition of DNA relaxation activity by antitumor drugs, e.g., the etoposide VM26, and by monospecific antibodies raised against the protein; and (7) in vitro phosphorylation by a casein kinase activity. However, we have identified new properties for our topoisomerase II preparation not previously reported for the conventionally isolated enzyme: (1) The enzyme binds to Z-DNA with an affinity 2 orders of magnitude greater than that for B-DNA. (2) The binding to Z-DNA is increased 5-10-fold by GTP or GTP-gamma-S. (3) GTP and GTP-gamma-S inhibit the catalytic activity of topoisomerase II through a proposed allosteric mechanism. (4) Z-DNA inhibits the relaxation of closed circular supercoiled DNA. (5) The preparation consists of a single polypeptide chain of 165 kDa on denaturing SDS gels with no evidence of proteolytic degradation. We postulate that the Z-DNA binding activity of undegraded topoisomerase II may be important in targeting the enzyme both to structural motifs required for chromatin organization and to sites of local supercoiling. Some of these features arise during processes such as replication and gene expression and may be more frequent during embryogenesis and early development.
Persistent elevation of high mobility group box-1 protein (HMGB1) in patients with severe sepsis and septic shock* (2005)

This is the first prospective study assessing the release over time of HMGB1 in a population of patients with sepsis, severe sepsis, or septic shock. Levels remained high in the majority of patients up to 1 wk after admittance, indicating that the cytokine indeed is a downstream and late mediator of inflammation. Further studies are required to fully define the relationship of HMGB1 to severity of disease.
Activation of Interleukin-6 Gene Expression through the NF-κB Transcription Factor (1990)

The promoter region of the interleukin-6 (IL-6) gene has a putative NF-kappa B-binding site. We found that a fragment of the IL-6 promoter containing the site specifically binds highly purified NF-kappa B protein and the NF-kappa B protein in nuclear extracts of phorbol ester-induced Jurkat cells. Mutations of the NF-kappa B site abolished complex formation with both purified NF-kappa B and the nuclear extract protein. Transient expression of chloramphenicol acetyltransferase (CAT) plasmids containing the IL-6 promoter revealed very little activity of the promoter in U-937 monocytic cells and in HeLa cells before stimulation. However, stimulation of U-937 and HeLa cells by inducers of NF-kappa B led to a dramatic increase in CAT activity. Mutations in the NF-kappa B-binding site abolished inducibility of IL-6 promoter-cat constructs in U-937 cells by lipopolysaccharide, tumor necrosis factor alpha, the double-stranded RNA poly(IC), or phytohemagglutinin and in HeLa cells by tumor necrosis factor alpha and drastically reduced but did not completely eliminate inducibility in HeLa cells stimulated by double-stranded RNA poly(IC) or phorbol 12-myristate 13-acetate. These results suggest that NF-kappa B is an important mediator for activation of the IL-6 gene by a variety of IL-6 inducers in both U-937 and HeLa cells and that alternative inducible enhancer elements contribute in a cell-specific manner to IL-6 gene induction. Because NF-kappa B is involved in the control of a variety of genes activated upon inflammation, NF-kappa B may play a central role in the inflammatory response to infection and tissue injury.
Planarized, Extendible, Multilayer Fabrication Process for Superconducting Electronics (2014)

We report on technique and results for superconductor electronics fabrication process, featuring customizable number of planarized superconducting layers. The novel technique enhanced yield on stackable vias of our standard planarized process (RIPPLE) by eliminating the need for an additional deposition of aluminum as an etch stop in the metal-via stack. The drawback of the previous approach was the difficulty in processing aluminum using either wet or dry etch mechanisms. Here, we discuss details of the novel fabrication process flow and its realization for 4.5 kA/cm2 fabrication process with six Nb layers with two fully planarized layers. We report test results of various planarization diagnostics structures, accounting the influence of topology on Josephson junction quality, as well as yield and critical current of via stacks. We also report on inductance measurement results providing information on interlayer dielectric thickness for planarized layers; confirming a good uniformity over the wafer. Basic components of superconducting logic such as dc/SFQ, SFQ/dc converters, Josephson transmission lines (JTLs), and simple digital circuits such as half-adder (HA) have been designed, fabricated and tested using either conventional (RSFQ) or energy-efficient (ERSFQ) approach. The ERSFQ HA cells with bias inductors fabricated in two planarized layers were shown to function with the operational margins of +/-22%.
Nanostructure and magnetic properties of polycrystalline FePdPt/MgO thin films (2002)

Atomic ordering, nanostructure and the magnetic properties of polycrystalline FePdPt thin films deposited with MgO underlayers have been investigated. The film thickness was fixed at 5 nm in all films, a thickness where perpendicular anisotropy is dominant. Films deposited at ambient temperature were postannealed at various temperatures to study the kinetics of atomic ordering. The Pd additions to FePt were effective in reducing the temperature needed for atomic ordering. The mean grain size determined by transmission electron microscopy is about 10 nm in annealed films. Within the limits of our observations, FePdPt films do not show phase separation into more than one phase of the L10 structure. The maximum coercivity (Hc) for annealed FePdPt films is about ∼3000–4000 Oe. In situ ordered FePdPt films at 530 °C show no indication of a lower temperature for atomic ordering.