gebhart/patrepeval huggingface dataset:
A Study of Low Speed Preignition Mechanism in Highly Boosted SI Gasoline Engines (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The authors investigated the reasons of how a preignition occurs in a highly boosted gasoline engine. Based on the authors' experimental results, theoretical investigations on the processes of how a particle of oil or solid comes out into the cylinder and how a preignition occurs from the particle. As a result, many factors, such as the in-cylinder temperature, the pressure, the equivalence ratio and the component of additives in the lubricating oil were found to affect the processes. Especially, CaCO&lt;sub&gt;3&lt;/sub&gt; included in an oil as an additive may be changed to CaO by heating during the expansion and exhaust strokes. Thereafter, CaO will be converted into CaCO&lt;sub&gt;3&lt;/sub&gt; again by absorbing CO&lt;sub&gt;2&lt;/sub&gt; during the intake and compression strokes. As this change is an exothermic reaction, the temperature of CaCO&lt;sub&gt;3&lt;/sub&gt; particle increases over 1000K of the chemical equilibrium temperature determined by the CO&lt;sub&gt;2&lt;/sub&gt; partial pressure. The possibility of a preignition due to particles including CaCO&lt;sub&gt;3&lt;/sub&gt; particles is numerically simulated comparing with the experimental results.&lt;/div&gt;&lt;/div&gt;
Development of a Real-time RT-PCR Assay for Detecting EGFRvIII in Glioblastoma Samples (2008)

This assay will facilitate accurate assessment of EGFRvIII in clinical samples and may aid in the development of strategies for stratifying patients for EGFRvIII-directed therapies.
Design and Analysis of an Engineered Human Interleukin-10 Monomer (2000)

A monomeric form of human interleukin 10 (IL-10M1) has been engineered for detailed structure-function studies on IL-10 and its receptor complexes. Wild type IL-10 (wtIL-10) is a domain swapped dimer whose structural integrity depends on the intertwining of two peptide chains. wtIL-10 was converted to a monomeric isomer by inserting 6 amino acids into the loop connecting the swapped secondary structural elements. Characterization of IL-10M1 by mass spectroscopy, size exclusion chromatography, cross-linking, and circular dichroism shows that IL-10M1 is a stable alpha-helical monomer at physiological pH whose three-dimensional structure closely resembles one domain of wtIL-10. As previously reported, incubation of wtIL-10 with a soluble form of the IL-10Ralpha (sIL-10Ralpha) generates a complex that consists of 2 wtIL-10 molecules and 4 sIL-10Ralphas. In contrast, IL-10M1 forms a 1:1 complex with the sIL-10Ralpha. Characterization of the interaction using isothermal titration calorimetry confirmed the 1:1 stoichiometry and yielded a dissociation constant of 30 nm with an apparent binding enthalpy of -12.2 kcal/mol. Despite forming a 1:1 complex, IL-10M1 is biologically active in cellular proliferation assays. These results indicate that the 1:1 interaction between IL-10M1 and IL-10Ralpha is sufficient for recruiting the signal transducing receptor chain (IL-10Rbeta) into the signaling complex and eliciting IL-10 cellular responses.
Extension of Sequence-Specific Recognition in the Minor Groove of DNA by Pyrrole−Imidazole Polyamides to 9−13 Base Pairs (1996)

The sequence-specific recognition of the minor groove of DNA by pyrrole−imidazole polyamides has been extended to 9−13 base pairs (bp). Four polyamides, ImPyPy-Py-PyPyPy-Dp, ImPyPy-G-PyPyPy-Dp, ImPyPy-β-PyPyPy-Dp, and ImPyPy-γ-PyPyPy-Dp (Im = N-methylimidazole, Py = N-methylpyrrole, Dp = N,N-dimethylaminopropylamide, G = glycine, β = β-alanine, and γ = γ-aminobutyric acid), were synthesized and characterized with respect to their DNA-binding affinities and specificities at sequences of composition 5‘-(A,T)G(A,T)5C(A,T)-3‘ (9 bp) and 5‘-(A,T)5G(A,T)C(A,T)5-3‘ (13 bp). In both sequence contexts, the β-alanine-linked compound ImPyPy-β-PyPyPy-Dp has the highest binding affinity of the four polyamides, binding the 9 bp site 5‘-TGTTAAACA-3‘ (Ka = 8 × 108 M-1) and the 13 bp site 5‘-AAAAAGACAAAAA-3‘ (Ka = 5 × 109 M-1) with affinities higher than the formally N-methylpyrrole-linked polyamide ImPyPy-Py-PyPyPy-Dp by factors of ∼8 and ∼85, respectively (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl2, and 5 mM CaCl2, pH 7.0). The binding data for ImPyPy-γ-PyPyPy-Dp, which has been shown previously to bind DNA in a “hairpin” conformation, indicates that γ-aminobutyric acid does not effectively link polyamide subunits in an extended conformation. These results expand the binding site size targetable with pyrrole−imidazole polyamides and provide structural elements that will facilitate the design of new polyamides targeted to other DNA sequences.
Axial Pattern Composite Prefabrication of High-Density Porous Polyethylene: Experimental and Clinical Research (2005)

Currently, various alloplastic materials are being used for reconstruction of three-dimensional structures, and high-density porous polyethylene is so far the best and the most commonly used material. Various indications for high-density porous polyethylene have been defined for closure of craniofacial defects, correction of congenital anomalies, and aesthetic augmentations. A common property of various studies published so far is that after being fixed to the bone or underlying structures, high-density porous polyethylene has been covered primarily or by skin flaps. For reconstruction of complex three-dimensional structures such as the ear and nose, the success of current methods is limited by the thinness and pliability of the skin flap. In this study, the authors' aim was to investigate the graftability of high-density porous polyethylene after prefabrication with an axial pedicle and to explore possible clinical applications in light of the new data obtained. In the experimental study, three-dimensional implants (rectangular prism) carved from high-density porous polyethylene were prefabricated using bilateral superficial epigastric arteries and veins of 25 New Zealand rabbits. After a waiting period of 2 to 6 weeks in five groups, control samples were obtained and the prefabricated implants that had been left in place were directly grafted. The results showed that high-density porous polyethylene was vascularized 75 percent after 4 weeks and 90 percent after 5 weeks, and 95 percent of the grafts had survived after 8 weeks. In the clinical study, three nose defects, three ear defects, and one hard palate defect in seven patients ranging in age from 21 to 72 years were reconstructed using the same method. High-density porous polyethylene has been prefabricated and directly grafted for the very first time on a clinical basis. No serious complications have been observed, except for minimal graft loss in two patients. It is obvious that full-thickness skin grafts that are thinner than flaps will adapt better to the fine details of high-density porous polyethylene and will highly increase the detail obtained in the reconstruction of three-dimensional defects.
Diamond waveguides fabricated by reactive ion etching (2008)

We demonstrate for the first time the feasibility of all-diamond integrated optic devices over large areas using a combination of photolithography, reactive ion etching (RIE) and focused ion beam (FIB) techniques. We confirm the viability of this scalable process by demonstrating guidance in a two-moded ridge waveguide in type 1b single crystal diamond. This opens the door to the fabrication of a diamond-based optical chip integrating functional elements such as X-crossings, Y-junctions, evanescent couplers, Bragg reflectors/couplers and various interferometers.
Extremely durable biofouling-resistant metallic surfaces based on electrodeposited nanoporous tungstite films on steel (2015)

Formation of unwanted deposits on steels during their interaction with liquids is an inherent problem that often leads to corrosion, biofouling and results in reduction in durability and function. Here we report a new route to form anti-fouling steel surfaces by electrodeposition of nanoporous tungsten oxide (TO) films. TO-modified steels are as mechanically durable as bare steel and highly tolerant to compressive and tensile stresses due to chemical bonding to the substrate and island-like morphology. When inherently superhydrophilic TO coatings are converted to superhydrophobic, they remain non-wetting even after impingement with yttria-stabilized-zirconia particles, or exposure to ultraviolet light and extreme temperatures. Upon lubrication, these surfaces display omniphobicity against highly contaminating media retaining hitherto unseen mechanical durability. To illustrate the applicability of such a durable coating in biofouling conditions, we modified naval construction steels and surgical instruments and demonstrated significantly reduced marine algal film adhesion, Escherichia coli attachment and blood staining.
ChemInform Abstract: The Synthesis and Evaluation of Functionalized Estratropones: Potent Inhibitors of Tubulin Polymerization. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Novel Method for the Synthesis of Imidazo[5,1-f][1,2,4]triazin-4(3H)-ones (2005)

[reaction: see text] Imidazo[5,1-f][1,2,4]triazinones, as isosteres of purine, are of interest for pharmaceutical research. The syntheses reported in the literature generally require several steps. We report a novel method to access a broad range of diversely substituted derivatives. The key step is the electrophilic N-amination of 3H-imidazoles containing a 4-carbonyl group. Several different substituted imidazoles have been N-aminated in this manner. The resulting N-aminoimidazoles were cyclized under different conditions to the corresponding imidazotriazinones, which allowed for additional diversification. This novel method was applied in a formal synthesis of vardenafil, a well-known representative of this class of compounds. Furthermore, we report the first synthesis of a 7-aryl-imidazotriazinone via bromination of an unsubstituted imidazotriazinone followed by a Suzuki coupling.
Spin-orbit-induced torque in a collinear spin valve: A possible route to design fast magnetic memory (2007)

We argue and show that spin-orbit (SO) interaction can induce a torque for the collinear configuration of spin valve structure (F1/2DEG/F2). Further, it is argued that this SO-induced torque can induce magnetization reversal even in collinear spin valves. The theoretical estimates of this effect that are made are well within the reach of present day experimental observations. In addition, it is shown that the same mechanism allows one to increase the purity of the outgoing current and produces entangled spin states essential for quantum computation. A scattering theory for the spin-density matrix is developed. Using this theory, the SO-induced torque and the associated von Neumann entropy are studied quantitatively.
A powerful tool for acid catalyzed organic addition and substitution reactions (2015)

A novel approach to perform organic reactions using a dried Dowex® H<sup>+</sup>/NaI system has been reported.
A nutritionally-enhanced oil from transgenic Camelina sativa effectively replaces fish oil as a source of eicosapentaenoic acid for fish (2015)

For humans a daily intake of up to 500 mg omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA) is recommended, amounting to an annual requirement of 1.25 million metric tonnes (mt) for a population of 7 billion people. The annual global supply of n-3 LC-PUFA cannot meet this level of requirement and so there is a large gap between supply and demand. The dietary source of n-3 LC-PUFA, fish and seafood, is increasingly provided by aquaculture but using fish oil in feeds to supply n-3 LC-PUFA is unsustainable. Therefore, new sources of n-3 LC-PUFA are required to supply the demand from aquaculture and direct human consumption. One approach is metabolically engineering oilseed crops to synthesize n-3 LC-PUFA in seeds. Transgenic Camelina sativa expressing algal genes was used to produce an oil containing n-3 LC-PUFA to replace fish oil in salmon feeds. The oil had no detrimental effects on fish performance, metabolic responses or the nutritional quality of the fillets of the farmed fish.
Melanin absorption spectroscopy: new method for noninvasive skin investigation and melanoma detection (2008)

We present a new method for studying melanin in vivo based on diffuse reflectance spectroscopy of human skin. We find that the optical absorption spectrum of in vivo melanin exhibits an exponential dependence on wavelength, consistent with, but with a higher decay slope than, in vitro results. We offer theoretical justification for this exponential dependence on the basis of a recently proposed model for the structure of eumelanin protomolecules. Moreover, we report on a new method for analysis of diffuse reflectance spectra, which identifies intrinsic differences in absorption spectra between malignant melanoma and dysplastic nevi in vivo. These preliminary results are confirmed both by analysis of our own clinical data as well as by analysis of data from three independent, previously published studies. In particular, we find evidence that the histologic transition from dysplastic nevi to melanoma in situ and then to malignant melanoma is reflected in the melanin absorption spectra. Our results are very promising for the development of techniques for the noninvasive detection of melanoma and, more generally, for the study and characterization of pigmented skin lesions. It is also a promising approach for a better understanding of the biological role, structure, and function of melanin.
Deciphering the peptide iodination code: Influence on subsequent gas-phase radical generation with photodissociation ESI-MS (2009)

Iodination of tyrosine was recently discovered as a useful method for generating radical peptides via photodissociation of carbon-iodine bonds by an ultraviolet photon in the gas phase. The subsequent fragmentation behavior of the resulting odd-electron peptides is largely controlled by the radical. Although previous experiments have focused on mono-iodination of tyrosine, peptides and proteins can also be multiply iodinated. Tyrosine and, to a lesser extent, histidine can both be iodinated or doubly iodinated. The behavior of doubly iodinated residues is explored under conditions where the sites of iodination are carefully controlled. It is found that radical peptides generated by the loss of a single iodine from doubly iodinated tyrosine behave effectively identically to singly iodinated peptides. This suggests that the remaining iodine does not interfere with radical directed dissociation pathways. In contrast, the concerted loss of two iodines from doubly iodinated peptides yields substantially different results that suggest that radical recombination can occur. However, sequential activation can be used to generate multiple usable radicals in different steps of an MS(n) experiment. Furthermore, it is demonstrated that in actual peptides, the rate of iodination for tyrosine versus mono-iodotyrosine cannot be predicted easily a priori. In other words, previous assumptions that mono-iodination of tyrosine is the rate-limiting step to the formation of doubly iodinated tyrosine are incorrect.
Prostate-specific antigen and diagnosing early malignancies of the prostate (1992)

Prostate-specific antigen is a kallikrein-like serine protease that is produced exclusively by the epithelial cells of all types of prostatic tissue, benign and malignant. Physiologically, it is present in the seminal fluid at high concentration and functions to cleave the high molecular weight protein responsible for the seminal coagulum into smaller polypeptides. This action results in liquefaction of the coagulum. Prostate-specific antigen is also present in the serum and can be measured reliably by several different assays. Although the protein is prostate-specific, it is not prostate-cancer-specific. As a result, benign conditions such as benign prostatic hyperplasia, prostatitis and infarction, as well as prostatic intraepithelial neoplasia, can be associated with elevated serum levels of prostate-specific antigen. Approximately 25% of men with benign prostatic hyperplasia have an elevated serum value of prostate-specific antigen, whereas 35% to 40% of patients with organ-confined prostate cancer have a level within the reference range. Prostate-specific antigen can identify some cancers not detectable by digital rectal examination; alternatively, this examination can identify cancers not detectable from the serum prostate-specific antigen concentration. Thus, the most complete evaluation of the prostate gland is achieved when both the prostate-specific antigen value and the digital rectal examination are used. The density and the rate of change of serum prostate-specific antigen are new concepts to improve the ability of prostate-specific antigen to detect early prostate cancer. Preliminary results are encouraging, but additional studies are required to determine the true usefulness of these new variables. Thus, in 1992, determination of the prostate-specific antigen value is a valuable new tool for the practicing physician and will be instrumental in our campaign to diagnose clinically significant prostate cancer at an early, curable stage.
Cutting Edge: Generation of IL-18 Receptor-Deficient Mice: Evidence for IL-1 Receptor-Related Protein as an Essential IL-18 Binding Receptor (1999)

IL-18 is a proinflammatory cytokine that plays an important role in NK cell activation and Th1 cell response. Recently IL-1R-related protein (IL-1Rrp) has been cloned as the receptor for IL-18. However, the functional role of IL-1Rrp is still controversial due to its low affinity to IL-18 as well as the possibility of the presence of another high-affinity binding receptor. In the present study, we have generated and characterized IL-1Rrp-deficient mice. The binding of murine rIL-18 was not detected in Th1-developing splenic CD4+ T cells isolated from IL-1Rrp-deficient mice. The activation of NF-kappa B or c-Jun N-terminal kinase were also not observed in the Th1 cells. NK cells from IL-1Rrp-deficient mice had defects in cytolytic activity and IFN-gamma production in response to IL-18. Th1 cell development was also impaired in IL-1Rrp-deficient mice. These data demonstrate that IL-1Rrp is a ligand-binding receptor that is essential for IL-18-mediated signaling events.
Analysis of cytokine gene expression during fetal thymic ontogeny using the polymerase chain reaction (1991)

The expression of 12 cytokine and cytokine receptor genes during mouse thymic ontogeny has been studied using the polymerase chain reaction. The data reveal that IL-2 gene transcription does not begin in the thymus until fetal day (Fd) 16. However, IL-2R beta-chain mRNA was detectable throughout the period of investigation, from Fd 14 to 20. This suggests that the potential for high or intermediate affinity IL-2 binding is present in the thymus before the IL-2 gene is actually expressed. Overall, cytokine gene induction occurred in two distinct patterns. In the first group, represented by IL-1 beta, IL-4, IL-5, IL-6, IL-7, IFN-gamma, and lymphotoxin (lymphotoxin or TNF-beta) there was detectable mRNA present from Fd 14 to 20. IL-1 alpha, IL-2, IL-3, and GM-CSF followed a second pattern in which gene induction was delayed until Fd 16. The expression of IL-7 and IL-2 genes showed an interesting temporal relationship. IL-7 mRNA transcription occurred before IL-2 but diminished from Fd 16 after the onset of IL-2 gene induction. Because these data reflect the in vivo progression of gene expression during T cell ontogeny, they provide a guideline for assessing the physiologic significance of thymocyte responses to cytokines at different stages of fetal development.
Activation/Attenuation Model for RNase H (1998)

Ribonucleases H (RNases H) comprise a family of metal-dependent enzymes that catalyze the hydrolysis of the 3'-O---P bond of RNA in RNA.DNA hybrids. The mechanism by which RNases H use active-site metal(s) for catalysis is unclear. Based upon the seemingly contradictory structural observations of one divalent metal bound to Escherichia coli RNase HI and two divalent metals bound to the HIV RNase H domain, two models explaining RNase H metal dependence have been proposed: a one-metal mechanism and a two-metal mechanism. In this paper, we show that the Mn2+-dependent activity of E. coli RNase HI is not consistent with either of these mechanisms. RNase H activity in the presence of Mn2+ is complex, with activation and inhibition of the enzyme at low and high Mn2+ concentrations, respectively. Mutations at Asp-134 result in a partial loss of this inhibition, with little effect on activation. Neutralization of His-124 by mutation to Ala results in an enzyme with a significantly decreased specific activity and an absolute loss of Mn2+ inhibition. Inhibition by high Mn2+ concentrations is shown to be due to a reduction in kcat; this attenuation has a critical dependence on the presence of His-124. Based upon these results, we propose an "activation/attenuation" model explaining the metal dependence of RNase H activity where one metal is required for enzyme activation and binding of a second metal is inhibitory.
ChemInform Abstract: General Method to Trifluoromethyl Ketones. Part 1. Direct Alkylation of Ethyl Trifluoroacetylacetate. (1990)

Abstract Alkylation of the potassium (II) or sodium enolate (VI) of ethyl trifluoroacetylacetate (I) gives rise to the O‐ (III) and C‐alkylated products (IV) and (V).
[Current status of monoclonal antibodies to human melanoma and its application]. (1983)

Monoclonal antibodies to human melanoma associated antigens were reviewed from the viewpoint of a target structure recognized by them. In addition, phase I evaluation of a monoclonal antibody 225.28S in man and fundamental studies of the antibody-cytotoxic agent conjugates in melanoma-bearing nude mice were described.
Functional unit of 30 kDa for proximal tubule water channels as revealed by radiation inactivation. (1991)

The high water permeability of kidney proximal tubules is of paramount importance for isotonic reabsorption of 70% of the glomerular filtrate, and water channels have been postulated to account for the high water permeability. Target analysis following radiation inactivation was used to probe the molecular size of the water channel. Samples of brush border membranes from rat renal cortex were subjected to 3-MeV electron pulses from the Van de Graaff accelerator at a temperature of -130 degrees C. The inactivation of the renal brush border enzymes, alkaline phosphatase, and maltase was used for internal standardization of accumulated dose measurements in target analysis of the water channel. Osmotic water permeability was measured by following the change in scattered light intensity upon rapid mixing of vesicles with a hypertonic solution using stopped-flow spectrophotometry. The vesicle shrinkage response was biphasic and the rate of the fast phase decreased dose dependently by irradiation corresponding to a target size of 30 +/- 3.5 kDa. The total change in scattered light intensity was unaltered, indicating that irradiation did not destroy the lipid barrier. Our results provide strong support for the hypothesis that the high osmotic water permeability of renal proximal tubules results from a water channel-specific protein with a functional unit of 30 kDa.