gebhart/patrepeval huggingface dataset:
Use of Electroless Silver as the Substrate in Microcontact Printing of Alkanethiols and Its Application in Microfabrication (1998)

We have employed electroless deposition to prepare smooth films (mirrors) of silver that could be used as substrates in microcontact printing (μCP) of alkanethiols. Good-quality SAMs of hexadecanethiolate were formed on thin films of electroless silver by printing with an elastomeric stamp; these SAMs were effective resists in protecting the underlying silver from etching in an aqueous ferricyanide solution. Thin films of silver prepared by electroless deposition show a granular morphology (the grain sizes are ∼30−60 nm) and have a rougher surface than those prepared using e-beam or thermal evaporation. As a result, hexadecanethiol liquid spreads more rapidly on electroless silver than on evaporated silver when μCP is carried out in air. This process of reactive spreading limits the resolution and fidelity of pattern transfer to electroless silver films by μCP, but could also be used as a convenient method for reducing the sizes of features of SAMs generated using μCP. The smallest features that we have fabricated using this method were trenches etched in electroless silver (∼40 nm thick) with lateral dimensions of ∼200 nm. The procedure demonstrated here allows us to form micropatterns and microstructures without the metal evaporation usually used to prepare the substrates for μCP, and thus opens μCP and related techniques of microfabrication to those who do not have access to the equipment required for evaporation or sputtering of silver. It also makes it possible to carry out micropatterning on hidden surfaces that could not be silvered by evaporation (for example, the inside surface of a glass tube or flask).
Layout-based 3D solid modeling for IC (2002)

A software system for 3D solid modeling of IC structures (devices, interconnection, and circuits) based on the layout design and processing information is described. Both the 3D perspective view and 2D cross sections of the structure can be examined using the system. Features of the system include automatic update of the geometry as the layout is changed and dynamic display of the process for constructing a structure layer by layer. Coupled with the process simulator and meshing tool, this modeling system can be used for device simulation. Further analysis of interconnection and circuit performance is made possible with other parameter extraction tools. The system configuration, its software components, and numerical techniques in processing mask data are discussed. The entire process of building an SRAM cell and generating an array of cells is demonstrated as an application example of the system.
New Synthetic Polymers for Enzyme and Liposome Modification (1997)

Although most enzyme and liposome modifications have been carried out using linear forms of poly(ethylene glycol), new polymers of natural or synthetic origin have also been employed and under study. A branched structure that, in many respects was found to be superior to the linear one, is similar to poly(ethylene glycol) in structure and single point attachment. New single point attachment polymers were recently synthesised and among these are poly(vinylpyrrolidone) and poly(acryloylmorpholine) oligomers which were successfully used for both enzyme and liposome modification, and poly(oxazoline) and poly(glycerols) which were used for long lasting liposome protection. Among the multifunctional reagents of note are dextran, divinyl ether-maleic acid anhydride and styrene-maleic acid anhydride that, although giving more complex reaction products with protein in comparison to the previous polymers, convey new and useful properties and in vivo behaviour on the conjugates.
Interleukin 13 Mutants of Enhanced Avidity Toward the Glioma-Associated Receptor, IL13Rα2 (2004)

Interleukin 13 (IL13) binds a receptor that is highly overexpressed in malignant gliomas, IL13Ralpha2. IL13 protein is composed of four helices: alpha-helix A, B, C, and D, and we found a new "hot spot" in alpha-helix D that is crucial for the binding of IL13 to IL13Ralpha2. Lys-105 plus Lys-106 and Arg-109 represent this hot spot. In the current study, we have made substitutions at these three positions in IL13. We examined both neutralization of an IL13-based cytotoxin's glioma cell killing and direct receptor binding of the new IL13 mutants. We observed that Lys-105 and Arg-109 are critical for IL13 binding to IL13Ralpha2, indeed. However, new mutants of important properties were identified with regard to tumor targeting. IL13.K105R mutant, in which lysine was substituted by arginine, neutralized the killing of IL13Ralpha2-positive cells by IL13-based cytotoxin more efficiently than wild-type IL13. However, IL13.K105L or IL13.K105A was deprived of any such activity. Furthermore, IL13.K105R and IL13.R109K competed 77- and 27-fold better, respectively, with the binding of [(125)I]IL13 to the IL13Ralpha2 binding sites when compared with wild-type IL13. Thus, we have uncovered the first forms of IL13 of higher avidity toward IL13Ralpha2. These mutants should prove useful in the further design of anticancer diagnostics/therapeutics.
Synthesis of Magnetite Nanoparticles for Bio‐ and Nanotechnology: Genetic Engineering and Biomimetics of Bacterial Magnetosomes (2007)

Magnetotactic bacteria (MTB) have the ability to navigate along the Earth's magnetic field. This so-called magnetotaxis is a result of the presence of magnetosomes, organelles which comprise nanometer-sized intracellular crystals of magnetite (Fe(3)O(4)) enveloped by a membrane. Because of their unique characteristics, magnetosomes have a high potential for nano- and biotechnological applications, which require a specifically designed particle surface. The functionalization of magnetosomes is possible either by chemical modification of purified particles or by genetic engineering of magnetosome membrane proteins. The second approach is potentially superior to chemical approaches as a large variety of biological functions such as protein tags, fluorophores, and enzymes may be directly incorporated in a site-specific manner during magnetosome biomineralization. An alternative to the bacterial production of magnetosomes are biomimetic approaches, which aim to mimic the bacterial biomineralization pathway in vitro. In MTB a number of magnetosome proteins with putative functions in the biomineralization of the nanoparticles have been identified by genetic and biochemical approaches. The initial results obtained by several groups indicate that some of these proteins have an impact on nanomagnetite properties in vitro. In this article the key features of magnetosomes are discussed, an overview of their potential applications are given, and different strategies are proposed for the functionalization of magnetosome particles and for the biomimetism of their biomineralization pathway.
Epigenetic silencing of BIM in glucocorticoid poor-responsive pediatric acute lymphoblastic leukemia, and its reversal by histone deacetylase inhibition (2010)

Glucocorticoids play a critical role in the therapy of lymphoid malignancies, including pediatric acute lymphoblastic leukemia (ALL), although the mechanisms underlying cellular resistance remain unclear. We report glucocorticoid resistance attributable to epigenetic silencing of the BIM gene in pediatric ALL biopsies and xenografts established in immune-deficient mice from direct patient explants as well as a therapeutic approach to reverse resistance in vivo. Glucocorticoid resistance in ALL xenografts was consistently associated with failure to up-regulate BIM expression after dexamethasone exposure despite confirmation of a functional glucocorticoid receptor. Although a comprehensive assessment of BIM CpG island methylation revealed no consistent changes, glucocorticoid resistance in xenografts and patient biopsies significantly correlated with decreased histone H3 acetylation. Moreover, the histone deacetylase inhibitor vorinostat relieved BIM repression and exerted synergistic antileukemic efficacy with dexamethasone in vitro and in vivo. These findings provide a novel therapeutic strategy to reverse glucocorticoid resistance and improve outcome for high-risk pediatric ALL.
Optimization of Steam Pretreatment of Corn Stover to Enhance Enzymatic Digestibility (2004)

Among the available agricultural byproducts, corn stover, with its yearly production of 10 million t (dry basis), is the most abundant promising raw material for fuel ethanol production in Hungary. In the United States, more than 216 million t of corn stover is produced annually, of which a portion also could possibly be collected for conversion to ethanol. However, a network of lignin and hemicellulose protects cellulose, which is the major source of fermentable sugars in corn stover (approx 40% of the dry matter [DM]). Steam pretreatment removes the major part of the hemicellulose from the solid material and makes the cellulose more susceptible to enzymatic digestion. We studied 12 different combinations of reaction temperature, time, and pH during steam pretreatment. The best conditions (200°C, 5 min, 2% H2SO4) increased the enzymatic conversion (from cellulose to glucose) of corn stover more then four times, compared to untreated material. However, steam pretreatment at 190°C for 5 min with 2% sulfuric acid resulted in the highest overall yield of sugars, 56.1 g from 100 g of untreated material (DM), corresponding to 73% of the theoretical. The liquor following steam explo-sion was fermented using Saccharomyces cerevisiae to investigate the inhibitory effect of the pretreatment. The achieved ethanol yield was slightly higher than that obtained with a reference sugar solution. This demonstrates that baker’s yeast could adapt to the pretreated liquor and ferment the glucose to ethanol efficiently.
Designing nanostructures by glancing angle deposition (2003)

Three-dimensional nanostructures can be fabricated by the glancing angle deposition technique. By rotating the substrate in both polar and azimuthal directions, one can fabricate desired nanostructures, such as nano-rod arrays with different shapes, nano-spring arrays, and even multilayer nanostructures. This method offers a fully three-dimensional control of the nanostructure with additional capability of self-alignment. There is almost no limitation on materials that can be fabricated into desired nanostructures. In this presentation, we will discuss the current status of the glancing angle deposition technology, its potential applications, and its future challenges.
Dictionary of Mechanical Engineering (1996)

This book provides clearly-written, easy-to-understand definitions for over 4,500 terms. In addition to covering the more traditional areas of the field, this fourth edition also defines the terminology of the rapidly advancing areas of small size mechanical engineering: micromachining and nanotechnology. Nomenclature used in the manufacture of composites has also been added. Extensively cross-referenced, the Dictionary is an indispensable desk reference for mechanical engineers worldwide. Co-published by SAE and Butterworth-Heinemann.
Direct search algorithms for optimization calculations (1998)

Many different procedures have been proposed for optimization calculations when first derivatives are not available. Further, several researchers have contributed to the subject, including some who wish to prove convergence theorems, and some who wish to make any reduction in the least calculated value of the objective function. There is not even a key idea that can be used as a foundation of a review, except for the problem itself, which is the adjustment of variables so that a function becomes least, where each value of the function is returned by a subroutine for each trial vector of variables. Therefore the paper is a collection of essays on particular strategies and algorithms, in order to consider the advantages, limitations and theory of several techniques. The subjects addressed are line search methods, the restriction of vectors of variables to discrete grids, the use of geometric simplices, conjugate direction procedures, trust region algorithms that form linear or quadratic approximations to the objective function, and simulated annealing. We study the main features of the methods themselves, instead of providing a catalogue of references to published work, because an understanding of these features may be very helpful to future research.
A multilevel-cell 32 Mb flash memory (2002)

A flash memory with multilevel cell significantly reduces the memory per-bit cost. A 32 Mb multilevel-cell (MLC) flash memory storing two bits of data per cell achieves 32 Mb memory storage capacity using 16 M flash memory cells. This 32 Mb flash memory on a 0.6 /spl mu/m process has a 2.0/spl times/1.8 /spl mu/m/sup 2/ flash cell. In MLC operation, the logical flash memory cell achieves two bits per cell using four possible states, defined by four flash cell threshold voltage ranges. The relationship between the threshold voltage ranges stored in the flash memory cell and the corresponding logic levels is shown in this paper, which also shows a plot of the four threshold voltage distributions, each with a separation range.
Prothrombin Complex Concentrate Versus Recombinant Factor VIIa for Reversal of Hemodilutional Coagulopathy in a Porcine Trauma Model (2010)

In a pilot study involving an in vivo large-animal model of spleen trauma, PCC accelerated hemostasis and augmented thrombin generation compared with rFVIIa. Further investigations are warranted on PCC as a hemostatic agent in trauma.
A nonlinear wide‐range immobilized pH gradient for two‐dimensional electrophoresis and its definition in a relevant pH scale (1993)

A new nonlinear immobilized pH gradient (IPG) is proposed as the first dimension for two-dimensional electrophoresis. In comparison to conventional carrier ampholyte techniques, it offers better resolution and greater reproducibility whilst allowing application of higher protein loads. Furthermore, we have checked and supplemented existing data on pK values for the immobilized groups in the presence of 8M urea. This is necessary for pH gradients to be defined in a pH scale relevant to the focusing conditions such that spot positions can be related to amino acid compositions. The data will allow definition of pH scales for the temperature range 10-25 degrees C and for a pH range covering the major part of the nonlinear pH gradient. With the latter, focusing positions are neither influenced by urea concentration nor by the choice or the concentration of detergent or carrier ampholyte. Temperature is the only parameter affecting focusing reproducibility and here any changes in focusing positions can be related to the amino acid compositions of peptides.
The Performance of a Heat Exchanger Designed for Cooling Electric Vehicle Car Battery System by Use Base Fluid and Nano-Fluid (2015)

This study examines the design of heat exchanger made of copper tube for cooling electric vehicle car battery system and the effects of base fluid and nanofluid (as coolants) channeling inside the heat exchanger to increase heat transfer between the compartment of the electric vehicle car and the heat exchanger and comparison between them. The nanofluid (CuO/pure water) was prepared by dispersing a nanoparticle (CuO) in base fluid (pure water). nanofluid (CuO/pure water) with a nominal diameter of 50 nm at volume concentrations (0.27 Vol. %) at batteries’ compartment temperature was used for these investigations. The analysis showed that secondary cooling system by means of nanofluid (CuO/pure water) has advantages in improving the thermal conductivity and heat transfer coefficient, better from base fluid (pure water) also in Nusselt number. This results work on reducing the electric power loss in the form of thermal energy from batteries. This led to increase in the efficiency of the electric vehicle car battery, hence also improved the performance of the EV car and battery lifetime.
Exisulind-induced apoptosis in a non-small cell lung cancer orthotopic lung tumor model augments docetaxel treatment and contributes to increased survival. (2003)

We reported previously a significant increase in survival of nude rats harboring orthotopic A549 human non-small cell lung cancer tumors after treatment with a combination of exisulind (Sulindac Sulfone) and docetaxel (D. C. Chan, Clin. Cancer Res., 8: 904-912, 2002). The purpose of the current study was to determine the biochemical mechanisms responsible for the increased survival by an analysis of the effects of both drugs on A549 orthotopic lung tumors and A549 cells in culture. Orthotopic A549 rat lung tissue sections from drug-treated rats and A549 cell culture responses to exisulind and docetaxel were compared using multiple apoptosis and proliferation analyses [i.e., terminal deoxynucleotidyl transferase-mediated nick end labeling, active caspase 3, the caspase cleavage products cytokeratin 18 and p85 poly(ADP-ribose) polymerase, and Ki-67]. Immunohistochemistry was used to determine cyclic GMP (cGMP) phosphodiesterase (PDE) expression in tumors. The cGMP PDE composition of cultured A549 cells was resolved by DEAE-Trisacryl M chromatography and the pharmacological sensitivity to exisulind, and additional known PDE inhibitors were determined by enzyme activity assays. Exisulind inhibited A549 cell cGMP hydrolysis and induced apoptosis of A549 cells grown in culture. PDE5 and 1 cGMP PDE gene family isoforms identified in cultured cells were highly expressed in orthotopic tumors. The in vivo apoptosis rates within the orthotopic tumors increased 7-8-fold in animals treated with the combination of exisulind and docetaxel. Exisulind increased the in vivo apoptosis rates as a single agent. Docetaxel, but not exisulind, decreased proliferative rates within the tumors. The data indicate that exisulind-induced apoptosis contributed significantly to the increased survival in rats treated with exisulind/docetaxel. The mechanism of exisulind-induced apoptosis involves inhibition of cGMP PDEs, and these results are consistent with a cGMP-regulated apoptosis pathway.
Identification of Triadin 1 as the Predominant Triadin Isoform Expressed in Mammalian Myocardium (1999)

Triadin is an integral membrane protein of sarcoplasmic reticulum shown to interact with the ryanodine receptor/Ca(2+) release channel, junctin, and calsequestrin. Several triadin isoforms have been postulated to exist in cardiac muscle, but to date none has been conclusively identified. Here, we show that only triadin 1 is significantly expressed. We cloned and sequenced cDNAs encoding canine cardiac triadin 1 and 3 but found no evidence for triadin 2. From deduced primary structures, antibodies against domains common to all triadins and an antibody against the unique C terminus of triadin 1 were raised. All antibodies detected two prominent proteins of molecular masses 35 and 40 kDa on immunoblots from cardiac microsomes, including the antibody that recognizes only triadin 1. The 40-kDa mobility form was shown to correspond to the glycosylated form of triadin 1, not a distinct triadin 2 isoform as previously hypothesized. Confirming this, overexpression of triadin 1 in transgenic mouse hearts produced both the 35-kDa deglycosylated and the 40-kDa glycosylated mobility forms. The glycosylation site of triadin 1 was localized to asparagine residue 75, and its bitopic arrangement in the membrane was confirmed. Although a 92-kDa immunoreactive protein could be tentatively identified in myocardium as triadin 3, its expression level was insignificant (</=5%) compared with that of triadin 1. We conclude that triadin 1 is the triadin isoform most likely to play a role in Ca(2+) release in heart.
Soluble human high-affinity receptor for IgE abrogates the IgE-mediated allergic reaction (1993)

The high-affinity receptor for IgE (Fc epsilon RI) has a tetrameric structure structure composed of one alpha, one beta, and two disulfide-linked gamma subunits, of which the alpha subunit binds IgE with high affinity. A recombinant soluble form of the ectodomain of the human Fc epsilon RI alpha subunit (rsFc epsilon RI alpha) was recently generated by gene engineering and was verified to bind IgE with an affinity as high as that of native Fc epsilon RI on the cell surface. rsFc epsilon RI alpha was prepared on a large scale in order to analyze its biological function. rsFc epsilon RI alpha completely inhibited IgE binding to the cell surface, resulting in abrogation of the chemical mediator release from RBL-2H3 cells. Furthermore it completely abolished the passive cutaneous anaphylaxis (PCA) response by trapping IgE specifically when it was administered into rats prior to IgE sensitization. Even after IgE sensitization, treatment of rsFc epsilon RI alpha substantially reduced the PCA response. It was finally shown that rsFc epsilon RI alpha inhibited IgE binding to human peripheral blood basophils and the histamine release from them. In this paper we address the ability of rsFc epsilon RI alpha to specifically prevent the IgE-mediated allergic reaction.
Effects of K+Channel Blockers on Developing Rat Myelinated CNS Axons: Identification of Four Types of K+Channels (2002)

Four blockers of voltage-gated potassium channels (Kv channels) were tested on the compound action potentials (CAPs) of rat optic nerves in an attempt to determine the regulation of Kv channel expression during the process of myelination. Before myelination occurred, 4-aminopyridine (4-AP) increased the amplitude, duration, and refractory period of the CAPs. On the basis of their pharmacological sensitivity, 4-AP-sensitive channels were divided in two groups, the one sensitive to kaliotoxin (KTX), dendrotoxin-I (DTX-I), and 4-AP, and the other sensitive only to 4-AP. In addition, tetraethylammonium chloride (TEA) applied alone broadened the CAPs. At the onset of myelination, DTX-I induced a more pronounced effect than KTX; this indicates that a fourth group of channels sensitive to 4-AP and DTX-I but insensitive to KTX had developed. The effects of KTX and DTX-I gradually disappeared during the period of myelination. Electron microscope findings showed that the disappearance of these effects was correlated with the ongoing process of myelination. This was confirmed by the fact that DTX-I and KTX enlarged the CAPs of demyelinated adult optic nerves. These results show that KTX- and DTX-sensitive channels are sequestrated in paranodal regions. During the process of myelination, KTX had less pronounced effects than DTX-I on demyelinated nerves, which suggests that the density of the KTX-sensitive channels decreased during this process. By contrast, 4-AP increased the amplitude, duration, and refractory period of the CAPs at all the ages tested and to a greater extent than KTX and DTX-I. The effects of TEA alone also gradually disappeared during this period. However, effects of TEA on CAPs were observed when this substance was applied after 4-AP to the adult optic nerve; this shows that TEA-sensitive channels are not masked by the myelin sheath. In conclusion, the process of myelination seems to play an important part in the regulation and setting of Kv channels in optic nerve axons.
Aminocarbonylation of 4-Iodo-1H-imidazoles with an Amino Acid Amide Nucleophile: Synthesis of Constrained H-Phe-Phe-NH2 Analogues (2013)

A simple and an expedient process to prepare 5-aryl-1-benzyl-1H-imidazole-4-carboxamides by the aminocarbonylation of 5-aryl-4-iodo-1H-imidazoles using ex situ generation of CO from Mo(CO)6 with an amino acid amide nucleophile is reported. Furthermore, a microwave-assisted protocol for the direct C-5 arylation of 1-benzyl-1H-imidazole and a regioselective C-4 iodination method to acquire starting material for our aminocarbonylation are presented. The method can be used to prepare imidazole based peptidomimetics, herein exemplified by the synthesis of constrained H-Phe-Phe-NH2 analogues.