gebhart/patrepeval huggingface dataset:
Control of glycoprotein synthesis. (1983)

Hen oviduct membranes have been shown to catalyze the transfer of GlcNAc from UDP-GlcNAc to GlcNAc-beta 1-2Man alpha 1-6(GlcNAc beta 1-2 Man alpha 1-3) Man beta 1-4GlcNAc beta 1-4GlcNAc-Asn-X (GnGn) to form the triantennary structure GlcNAc beta 1-2Man alpha 1-6[GlcNAc beta 1-2(GlcNAc beta 1-4)Man alpha 1-3]Man beta 1-4GlcNAc beta 1-4GlcNAc-Asn-X. The enzyme has been named UDP-GlcNAc:GnGn (GlcNAc to Man alpha 1-3) beta 4-N-acetylglucosaminyltransferase IV (GlcNAc-transferase IV) to distinguish it from three other hen oviduct GlcNAc-transferases designated I, II, and III. Since GlcNAc-transferases III and IV both act on the same substrate, concanavalin A/Sepharose was used to separate the products of the two enzymes. At pH 7.0 and at a Triton X-100 concentration of 0.125% (v/v), GlcNAc-transferase IV activity in hen oviduct membranes is 7 nmol/mg of protein/h. The product was characterized by high resolution proton NMR spectroscopy at 360 MHz and by methylation analysis. In addition to triantennary oligosaccharide, hen oviduct membranes produced about 20% of bisected triantennary material, GlcNAc beta 1-2Man alpha 1-6[GlcNAc beta 1-2(GlcNAc beta 1-4)Man alpha 1-3] [GlcNAc beta 1-4]Man beta 1-4GlcNAc beta 1-4GlcNAc-Asn-X. Maximal GlcNAc-transferase IV activity requires the presence of both terminal beta 1-2-linked GlcNAc residues in the substrate. Removal of the GlcNAc residue on the Man alpha 1-6 arm or of both GlcNAc residues reduces activity by at least 80%. A Gal beta 1-4GlcNAc disaccharide on the Man alpha 1-6 arm reduces activity by 68% while the presence of this disaccharide on the Man alpha 1-3 arm reduces activity to negligible levels. A similar substrate specificity was found for GlcNAc-transferase III, the enzyme which adds a bisecting GlcNAc in beta 1-4 linkage to the beta-linked Man residue. Since a bisecting GlcNAc was found to prevent GlcNAc-transferase IV action, the bisected triantennary material found in the incubation must have been formed by the sequential action of GlcNAc-transferase IV followed by GlcNAc-transferase III. Activities similar to GlcNAc-transferase IV were also detected in rat liver Golgi-rich membranes (0.4 nmol/mg/h) and pig thyroid microsomes (0.1 nmol/mg/h).
Cardioprotective Effect of Hydrogen Sulfide in Ischemic Reperfusion Experimental Rats and Its Influence on Expression of Survivin Gene (2009)

Hydrogen sulfide (H(2)S), as an endogenous gas signaling molecule with important biological function that has been found recently, may play a protection in ischemic reperfusion (I/R) myocardium. We investigated the cardioprotective effect of H(2)S in rats model of ischemic reperfusion in vivo and a probably influence on the expression of survivin, an anti-apoptosis gene. Animals were randomly divided into 3 groups and received either vehicle, sodium hydrosulfide (NaHS) or DL-propargylglycine (PAG) respectively everyday for 1 week before surgery and the treatment continued for a further 2 d after I/R till the animals were sacrificed. We investigated the plasma H(2)S concentration and blood pressure, with the electrocardiogram (ECG) together, to prove the effect of H(2)S to the heart function. We also compared the heart infarct size and the expression of an anti-apoptosis gene, survivin, among groups. As the data shown, the NaHS group had great improvement in blood pressure and electrocardiogram situation. And the remarkable shrink of the infarct size and up-regulation of survivin in NaHS group comparing with the other two groups also showed the cardio protective effect of H(2)S in our study.
Functional Effects of Glycosylation at Asn-579 of the Epidermal Growth Factor Receptor (2005)

We have investigated functional effects of glycosylation at N(579) of the epidermal growth factor receptor (EGFR). Our previous study showed that the population of cell-surface expressed EGFRs in A431 cells, a human epidermoid carcinoma cell line, is composed of two subpopulations that differ by glycosylation at N(579) [Zhen et al. (2003) Biochemistry 42, 5478-5492]. To characterize the subpopulation of receptors not glycosylated at N(579), we established a 32D cell line expressing a point mutant of the EGFR (N579Q), which cannot be glycosylated at this position. Analysis of epitope accessibility suggests that the lack of glycosylation at N(579) weakens auto-inhibitory tether interactions, and cross-linking experiments suggest a somewhat elevated level of preformed N579Q-EGFR dimers in the absence of ligand relative to wild-type EGFR (WT-EGFR). However, ligand drives the majority of N579Q-EGFR dimerization, suggesting that untethering, while necessary, is not sufficient to drive dimerization. Ligand-binding experiments reveal a much greater fraction of N579Q-EGFRs in a high-affinity state compared to the fraction of WT-EGFRs in a high-affinity state. However, differences in the kinetic association and dissociation rates indicate that the high-affinity states of the WT and the N579Q receptors are distinct. EGF-stimulated phosphorylation in cells expressing N579Q-EGFRs results in notable differences in the pattern of tyrosine phosphorylated proteins compared with that obtained in cells expressing WT-EGFRs. Moreover, although WT-EGFRs confer cell survival in 32D cells in the absence of interleukin-3 and EGF, we found that receptors lacking glycosylation at N(579) do not. This is the first study of which we are aware to show that selective glycosylation of a specific N-glycosylation site can produce two functionally distinct receptors.
High K gate dielectrics for the silicon industry (2002)

The exponential growth of the silicon industry can be attributed to that fact that silicon has a native oxide that is silicon dioxide. With SiO/sub 2/ soon approaching fundamental limit, we must find an alternate to SiO/sub 2/ or a new switch to replace MOSFET. In this paper we focus on leading alternate gate dielectrics. We first discuss the selection criteria for alternate gate dielectrics and why it is important to have an amorphous gate dielectric. SiO/sub 2/ and aluminum oxide remain amorphous at very high temperatures. For dielectrics with K > 15 and gate power < 100mW/cm/sup 2/, it may be necessary to stabilize the amorphous phase of metal oxides by adding Al or Si into the oxide; and thus forming multi-component dielectrics such as aluminates or silicates. At present, the most critical issue facing the high K research is the reduced mobility and therefore the effective fixed charge at the dielectric/Si interface. In this paper, we also shed some light on the effective fixed charge in group-three metal oxides.
Nonsteroidal anti-inflammatory drug use and breast cancer risk. (2001)

Findings from previous epidemiological studies are inconclusive, though they suggest nonsteroidal anti-inflammatory drug (NSAID) use is associated with a reduction in breast cancer risk. In addition, animal studies report that NSAIDs inhibit mammary tumor development. The association between NSAID use and breast cancer risk was evaluated using a case-control study design. Cases were a random sample of women diagnosed with a first primary cancer of the breast, aged 25-74 years, identified through the Ontario Cancer Registry, and diagnosed between July 1996 and September 1998. Controls were an age-matched random sample of the female population of Ontario. Cases (n = 3133) and controls (n = 3062) completed a mailed questionnaire with information on their past use of NSAID and other medications, as well as many risk factors thought to be associated with breast cancer. Multivariate logistic regression analysis was used to obtain adjusted odds ratio (OR) estimates. Use of any NSAID medication (daily use for > or =2 months) was found to be associated with a significant 24% reduction in breast cancer risk (OR = 0.76; 95% confidence interval: 0.66, 0.88). The reduced risk was strongest for use lasting > 8 years, compared with nonusers (OR = 0.68; 95% confidence interval: 0.54, 0.86). No marked trends were observed for time since first use or last use or age at first use. Our results suggest a reduction in breast cancer risk associated with any regular NSAID use. NSAID use is a modifiable factor, and any protective effect attributed to its use could be of great public health importance.
Effects of substrate bias on CoCrPt-SiO2 magnetic recording media (2006)

CoCrPt and CoCrPt-SiO2 magnetic layers were investigated as a function of substrate bias. It was found that the use of substrate bias greatly modified the CoCrPt-SiO2 film microstructure. This was due to a large change in the SiO2 content during bias sputtering. Biasing had an effect of reducing the amount of oxide in the growing films and promoting the growth of larger grains, but it was also found to be very effective in decoupling the grains as determined by ΔM curves. In addition, in the biased films, a large dependence of the coercivity on film thickness was observed. The in-plane coercivity nearly doubled its value from 2400 to 4300 Oe as the thickness increased from 5 to 15 nm.
Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea (2009)

Proteins from halophilic organisms, which live in extreme saline conditions, have evolved to remain folded at very high ionic strengths. The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids, a low frequency of lysine, and a high occurrence of amino acids with a low hydrophobic character. Using extensive mutational studies on the protein surfaces, we show that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form. NMR studies demonstrate complete preservation of the three-dimensional structure of extreme mutants and confirm that salt dependency is conferred exclusively by surface residues. In spite of the statistically established fact that most halophilic proteins are strongly acidic, analysis of a very large number of mutants showed that the effect of salt on protein stability is largely independent of the total protein charge. Conversely, we quantitatively demonstrate that halophilicity is directly related to a decrease in the accessible surface area.
Bone morphogenetic proteins 2 and 6, expressed in arthritic synovium, are regulated by proinflammatory cytokines and differentially modulate fibroblast‐like synoviocyte apoptosis (2003)

BMP-2 and BMP-6 are expressed in arthritic synovium and are strongly up-regulated by proinflammatory cytokines. Although BMP signaling has been proposed to be involved in cartilage and bone repair in arthritis, this pathway may be equally important in modulating FLS cell populations in inflamed synovium.
Diospyros lotus: micropropagation and antioxidant activity (2008)

Diospyros lotus is a deciduous tree that is native to the Middle East and south Asia, especially China, Korea, and Japan. It bears edible small fruits in autumn and leaves are used widely in folk medicine for their medicinal properties. A protocol for the date plum (Diospyros lotus) was developed. For shoot proliferation, in vitro nodal and apical explants were cultured on various media containing 0.5-2.0 mg/l BA, kinetin, or TDZ. WPM medium supplemented with 0.5 m/l BA displayed the highest proliferation rate (4-7 shoots per explant). The rooting was optimized using MS medium supplemented with 0.5 mg/l IBA with 3-5 roots after 2 months of culture. The rooted plantlets were successfully acclimatized and transferred to potting mix with 92% survival. Antioxidant properties of in vivo grown tissues were evaluated using various assays. The levels of total phenolics and flavonoids of the leaves extracts were also determined. The alcohol extract of date plum leaves had good phenolic (445. 6 mg/g) and flavonoid (260.9 mg/g) contents, and showed the strong antioxidant and free-radical scavenging activity (scavenged 92.1% of DPPH at 250 ug/ml). Leaf extracts had higher activities of anti-oxidant-related enzymes including superoxide dismutase (SOD; 20.5 U/mg protein), catalase (CAT; 4.9 U/mg protein), and ascorbate peroxidase (APX; 105.8 U/mg protein) than mature seed extracts (SOD, 2.1 U/mg protein; CAT, 74.5 U/mg protein; APX, 3.7 U/mg protein). These results establish the antioxidant potential of date plum, which could be used as natural antioxidant source.
Microarrays and Gene Expression (2001)

This chapter contains sections titled: Introduction to Microarray Data, Probabilistic Modeling of Array Data, Clustering, Gene Regulation
Persistence of Cotton (Gossypium hirsutum) Herbicides and Injury to Replacement Soybeans (Glycine max) after Stand Failure (1982)

Soybeans [ Glycine max (L.) Merr.] are often the replacement crop when cotton ( Gossypium hirsutum L.) is abandoned because of stand failure in the southern United States. Injury from cotton herbicides may be reduced if the soybean planting is delayed more than 4 weeks after cotton planting or if the original herbicide-treated area is fully tilled and a new seedbed formed. Planting delay intervals were compared with five cotton preemergence herbicides on Calloway silt loam at one location. Seedbed-preparation methods were included in a similar experiment at two locations on Sharkey silty clay. Herbicides compared were fluometuron [1,1-dimethyl-3-(α,α,α-trifluoro- m -tolyl)urea], norflurazon [4-chloro-5-(methylamino)-2-(α,α,α-trifluoro- m -tolyl)-3(2 H )-pyridazinone], cyanazine {2-[[4-chloro-6-(ethylamino) -s -triazin-2-yl] amino]-2-methylpropionitrile}, perfluidone {1,1,1-trifluoro- N- [2-methyl-4-phenylsulfonyl)phenyl] methanesulfonamide}, fluridone {1-methyl-3-phenyl-5-[3-(trifluoromethyl)phenyl]-4(1 H )-pyridinone}, and diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea]. Seedbeds compared were no-till and conventional (fully tilled). Soybean planting delays after cotton planting were 20, 29, and 56 days (first year), and 15 and 29 or 15 and 30 days (second year). We found in the 2-yr studies that fluridone severely damaged soybeans both years. Fluometuron and diuron also caused damage the second year when we experienced wet, cool conditions in the spring. Most injury occurred on the clay, with yield reductions occurring even after the 30-day delay. Norflurazon was most injurious at this location. The no-tillage planting method resulted in the least herbicide injury on the silt loam and the conventional tillage method was better on the clay. Detailed studies with fluometuron under incubation conditions showed that degradation was inhibited most by low temperatures and high soil moisture.
Limiting deflection during the slewing of flexible spacecraft using deflection sampling (1996)

This paper describes a control scheme for slewing flexible spacecraft with deflection suppression during the maneuver. The method minimizes the maneuver time subject to constraints on residual vibration magnitude, sensitivity to modeling errors, and rest-torest slew distance, as well as, the transient deflection amplitude. Furthermore, a solution is sought which provides inherent fuel efficiency. Techniques for verifying the time-optimality of the solution are discussed. The deflection reduction during the slew is demonstrated with computer simulations.
Software advances in measurement and instrumentation (1993)

National Instruments (NI) software architecture combines low-level device drivers for their hardware and high-level application development software. With this combination one has a scalable development system with the flexibility to handle a very wide range of measurement and instrumentation applications. To build virtual instruments, one needs software that easily integrates any or all of the four hardware instrumentation options in a single system. At the lowest level, with standardized driver software packages one can control the four acquisition hardware options. The NI driver packages include function libraries for programming hardware. The NI-488.2 driver is the industry standard for programming GPIB. NI-VXI is the driver software for programming VXI. NI-DAQ is driver software for programming plug-in data acquisition boards. Most computers include RS-232 driver software. With NI's application software, LabVIEW, you can build your own instruments. LabVIEW works with all aspects of an instrumentation system, including data acquisition and control, data analysis, and data presentation. LabVIEW also features modular, reusable, high-level instrument drivers for specific instruments and applications that dramatically reduce your software development task. By using NI's application software packages, you are free to choose the components necessary to m your application cost and performance requirements.
Membrane translocation of diphtheria toxin A-fragment: role of carboxy-terminal region (1993)

The C-terminal end of diphtheria toxin A-fragment was altered and the consequences for toxicity and translocation of the A-fragment to the cytosol were studied. Mutations and deletions in the protease-sensitive, disulfide-bridged region linking the two functional parts of the toxin, the A- and B-fragments, reduced the toxicity of the protein as such, but when the mutant toxins were cleaved ("nicked") by trypsin before being added to cells, the toxicity was restored. Prevention of disulfide formation by removal of Cys186 resulted in complete loss of toxicity. To circumvent the nicking step, toxin was formed by reconstitution from separate A- and B-fragments where the A-fragments varied in the C-terminal sequences. The amino acids C-terminal to Cys186 were found not to be required for translocation. Furthermore, both charged and uncharged residues near the C-terminal end were compatible with translocation. The data indicate that the C-terminal amino acid sequence is not decisive for translocation of diphtheria toxin A-fragment to the cytosol.
Signal-to-noise ratio degradation with channel mismatch (in magnetic recording) (1991)

Sensitivities of different run-length-limited coding and equalization/detection schemes to channel response variations have been investigated. Channel variations considered are due to the head-medium velocity variations and head-medium spacing fluctuations, reflected in the height and width changes in the read pulse. Given equalizers/detectors are first tuned to a specific value of PW50, the half-height width of the read pulse. The signal-to-noise ratio degradation was observed as the actual PW50 is varied around this nominal value. The results show that the sensitivity varies widely across different detectors. For example, the partial response maximum likelihood (PRML) schemes, which achieve large performance advantages over peak detection under ideal conditions, are highly sensitive to channel variations and perform worse than peak detection as the PW50 mismatch becomes large. On the other hand, the recently introduced fixed-delay tree search with decision feedback (FDTS/DF) exhibits good resistance to channel variations while achieving favorable nominal performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene Expression Profiling and its Practice in Drug Development (2007)

The availability of sequenced genomes of human and many experimental animals necessitated the development of new technologies and powerful computational tools that are capable of exploiting these genomic data and ask intriguing questions about complex nature of biological processes. This gave impetus for developing whole genome approaches that can produce functional information of genes in the form of expression profiles and unscramble the relationships between variation in gene expression and the resulting physiological outcome. These profiles represent genetic fingerprints or catalogue of genes that characterize the cell or tissue being studied and provide a basis from which to begin an investigation of the underlying biology. Among the most powerful and versatile tools are high-density DNA microarrays to analyze the expression patterns of large numbers of genes across different tissues or within the same tissue under a variety of experimental conditions or even between species. The wide spread use of microarray technologies is generating large sets of data that is stimulating the development of better analytical tools so that functions can be predicted for novel genes. In this review, the authors discuss how these profiles are being used at various stages of the drug discovery process and help in the identification of new drug targets, predict the function of novel genes, and understand individual variability in response to drugs.
Free-Running Droplets (1995)

We present a detailed study of an original spreading behavior observed with nonvolatile droplets containing surface-active agents: The droplet moves spontaneously on the surface with velocities on the order of a few centimeters per second. For small droplets, this self-supported motion may be interpreted in terms of capillary models, which gives precise information about the reaction mechanism that occurs at the surface. For large droplets, gravity intervenes and we observed an important change in the profile of the droplets and different spreading regimes.
Thermodynamic Components of the Atom Transfer Radical Polymerization Equilibrium: Quantifying Solvent Effects (2009)

A thermodynamic scheme representing the atom transfer radical polymerization (ATRP) equilibrium as the formal sum of equilibria involving carbon−halogen bond homolysis and three additional distinct thermodynamic contributions related to the catalyst is rigorously evaluated. The reduction/oxidation of both the metal complex and the halogen atom, and the affinity of the higher oxidation state of the catalyst for halide anions (or “halidophilicity”), are measured. The validity and self-consistency of the model are verified by independently measuring, computing, or calculating the overall ATRP equilibrium constant and all four contributing equilibrium constants for one catalyst/alkyl halide combination in acetonitrile. As a thorough demonstration of the value and effectiveness of the scheme, the different equilibrium constants were measured or calculated in 11 different organic solvents, and a comparison of their values was used to both understand and predict catalyst activity in ATRP with high accuracy. The scheme explains quite well, for example, why the ATRP equilibrium constant is greater in dimethyl sulfoxide than in acetone by a factor of about 80 and why in acetonitrile and three different alcohols it is nearly identical. The solvent effects are also quantitatively analyzed in terms of Kamlet−Taft parameters, and linear solvation energy relationships are employed to extrapolate catalyst activity over 7 orders of magnitude in 17 more organic solvents and water.
<title>Analysis of clot formation with acoustic radiation force</title> (2002)

Inappropriate blood coagulation plays an important role in diseases including stroke, heart attack, and deep vein thrombosis (DVT). DVT arises when a blood clot forms in a large vein of the leg. DVT is detrimental because the blood flow may be partially or completely obstructed. More importantly, a potentially fatal situation may arise if part of the clot travels to the arteries in the lungs, forming a pulmonary embolism (PE). Characterization of the mechanical properties of DVT could improve diagnosis and suggest appropriate treatment. We are developing a technique to assess mechanical properties of forming thrombi. The technique uses acoustic radiation force as a means to produce small, localized displacements within the sample. Returned ultrasound echoes are processed to estimate the time dependent displacement of the sample. Appropriate mechanical modeling and signal processing produce plots depicting relative mechanical properties (relative elasticity and relative viscosity) and force-free parameters (time constant, damping ratio, and natural frequency). We present time displacement curves of blood samples obtained during coagulation, and show associated relative and force-free parameter plots. These results show that the Voigt model with added mass accurately characterizes blood behavior during clot formation.