gebhart/patrepeval huggingface dataset:
Nucleoside diphosphate regulation of overall rates of protein biosynthesis acting at the level of initiation. (1985)

A sensitive assay method developed to examine the effects of subtle, physiologically relevant, changes in the levels of adenine and guanine mono-, di-, and triphosphorylated nucleotides specifically on the initiation of protein synthesis is described. Initiation rates are quantified by measuring the amount of protein synthesis resulting from the run-off of ribosomes which have initiated during defined intervals in a modified in vitro protein-synthesizing system developed from Ehrlich ascites tumor cell lysates (Henshaw, E. C., and Panniers, R. (1983) Methods EnzymoZ. 101, 616-629). The modifications include the attenuation of the ATP-regenerating system so that the relative nucleotide levels more nearly reflect actual intracellular conditions. With this system the rate of initiation is highly sensitive to changes in the ADP:ATP and GDP:GTP ratios, but indifferent to the absolute levels of either diphosphate. While the tight coupling of these two ratios by endogenous nucleoside diphosphate kinase activity prevents the independent manipulation of either ratio, the data do eliminate both AMP and GMP per se as inhibitory species. The close agreement of our data calculated in terms of energy charge to previously published results on overall rates of protein synthesis in rat thymocytes (Mendelsohn, S. K., Nordeen, S. K., and Young, D. A. (1977) Biochem. Biophye. Res. Commun. 79,53-60) continues to suggest a physiologically relevant regulatory influence of subtle changes in nucleotides acting at the level of the initiation reaction.
Synthesis of Alumina Balloons Using a Microcapsulation Method (1998)

The synthesis of alumina balloons using the microcapsulation method has been investigated, and was successful in producing a transparent balloon with a diameter of 50-80μm and a wall thickness of less than 1μm. The process is as follows. 10mass% solution of polystyrene in toluene and boehmite sots of approximately 1mol/kg concentration are mixed by a homogenizer. The resultant W/O emulsion is redispersed in water to obtain a (W/O) W emulsion which produces boehmite sols encapsulated by polystyrene in water. After keeping it for 2 days at 40°C, the products are filtered, dried and then the polystyrene crust is dissolved by toluene. The resultant balloon precursors of boehmite sols are dried, fired and then the alumina balloons are obtained. In this paper, the effects of the concentration of polystyrene or boehmite sots and the addition of ethylene glycol or tricresyl phosphate on the formation of alumina balloons were discussed in detail.
Microbial Hydrocarbon Co-oxidation (1967)

Nocardia cultures, isolated from soil by use of n-paraffins as the sole carbon source, have been shown to bring about significant oxidation of several methyl-substituted mono- and dicyclic aromatic hydrocarbons. Oxygen uptake by washed cell suspensions was not a reliable indicator of oxidation. Under co-oxidation conditions in shaken flasks, o- and p-xylenes were oxidized to their respective mono-aromatic acids, o-toluic and p-toluic acids. In addition, a new fermentation product, 2, 3-dihydroxy-p-toluic acid, was found in the p-xylene oxidation system. Of 10 methyl-substituted naphthalenes tested (1-methyl, 2-methyl, 1, 3-dimethyl, 1, 4-dimethyl, 1, 5-dimethyl, 1, 8-dimethyl, 1, 6-dimethyl, 2, 3-dimethyl, 2, 6-dimethyl, 2, 7-dimethyl), only those containing a methyl group in the beta position were oxidized at this position to the mono acid.
Direct Biomimetic Synthesis of β-Carboline Alkaloids from Two Amino Acids (2018)

The increasing importance of enzyme mimics in organic synthesis inspired us to design a novel biomimetic synthesis of β-carboline alkaloids directly from tryptophan and a second amino acid. This novel one-pot protocol utilizes abundant and readily available starting materials and thus presents a green and user-friendly alternative to conventional methods that rely on stepwise synthesis. Driven by molecular iodine and TFA, decarboxylation, deamination, Pictet-Spengler reaction, and oxidation reactions proceeded sequentially, transforming biomass amino acids into value-added alkaloid motifs.
Putting Health IT on the Path to Success (2013)

The promise of health information technology (HIT) is comprehensive electronic patient records when and where needed, leading to improved quality of care at reduced cost. However, physician experience and other available evidence suggest that this promise is largely unfulfilled.
Controlled electroplating for high-aspect-ratio zone-plate fabrication (2006)

The authors report a method for monitoring, control, and end-point detection of electroplating in nanostructures. The method is demonstrated on nickel plating into polymer molds, which is an important process in the fabrication of soft x-ray zone-plate diffractive optics. The lack of reproducibility presently limits the achievable nickel aspect ratio and, thus, reduces the zone-plate diffraction efficiency. The reported method provides reproducible plating via real-time control of the plating rate. It combines in situ light transmission measurements with current measurements to determine the thickness of the growing layer. The accuracy of the thickness prediction was better than ±4% (1σ) for 100–300nm nickel layers. Furthermore, a slight change in the light transmission signal indicates when a gratinglike zone-plate structure is slightly overplated and the plating should be stopped. This end-point detection provides the optimal filling of high-aspect-ratio molds for improved diffraction efficiency.
Transvascular Argon Laser Ablation of Atrioventricular Conduction in Dogs: Feasibility and Morphological Results (1989)

The purpose of this study was to ablate atrioventricular (AV) conduction in dogs with an argon laser using a transvascular approach. Six dogs were anesthetized and underwent a right thoracotomy and atriotomy. A bipolar #7 French lumen catheter containing a 400 u silica fiber was used to map the region of the AV junction. When a stable His deflection was obtained, the silica fiber was extruded from the end of the catheter and argon laser radiation was delivered for up to 20 s at 3.0-4.5 watts. In five of six dogs, complete heart block was successfully created after 3 to 15 lasings. A continuous His bundle electrogram in one dog showed gradual prolongation of the HV interval before the development of complete infrahisian block. The mean R-R intervals in the five dogs with complete heart block increased from 435 +/- 56 ms to 1216 +/- 197 ms (P less than 0.001), and the QRS duration increased from 78 +/- 26 ms to 91 +/- 19 ms (P = ns). Gross inspection showed multiple 1-2 mm2 craters in the atria just above the tricuspid valve ring. Complications included one instance each of aortic root perforation and creation of a small ventricular septal defect. These lesions were so small that there was no hemodynamic compromise in either animal in which they occurred and the lesions themselves were only detected on careful postmortem examination. Histology revealed two patterns of injury involved in conduction ablation. One was direct vaporization of tissue resulting in a wedge shaped incision and the other was formation of a hematoma and thermal necrosis at the lasing site with little evidence of tissue vaporization. Although catheter modifications are necessary to avoid perforation, this study demonstrates that ablation of conduction can be successfully accomplished using an argon laser.
Leveraging Service Composition Relationship to Improve CPU Demand Estimation in SOA Environments (2008)

Service Oriented Architecture (SOA) helps dynamically construct composite services out of a set of low-level atomic services to satisfy customer requirements. For the purpose of capacity planning and resource provisioning, it is important to understand these services' demand for system resources, e.g., CPU. In this paper, we propose a black-box method for estimating CPU demand of service requests based on linear regression between the observed request throughput and resource utilization level. A key advantage of our method is that its input data (i.e., request-processing throughput and resource utilization) can be easily obtained without intrusive software instrumentation. Moreover, we observe that, in an SOA environment, the service composition relationship (i.e., how low-level atomic services are connected into a composite service) is either known in advance or can be discovered through various means. We leverage this composition relationship to further improve the quality of CPU demand estimation. By analyzing the dependency between a composite service and its constituent low-level atomic services using linear algebra, our method can eliminate the collinear problem introduced by the service composition relationship. Moreover, our method can further reduce the number of unknown variables in the linear regression problem, and hence reduce the time duration needed to collect input data. In a dynamic SOA environment, this translates into faster response to changing workloads and more accurate estimation. We demonstrate these advantages of our method over a baseline method through extensive evaluation.
Calculation of the Ki67 index in pancreatic neuroendocrine tumors: a comparative analysis of four counting methodologies (2014)

Ki67 index is now an essential part of classification of pancreatic neuroendocrine tumors. However, its adaptation into daily practice has been fraught with challenges related to counting methodology. In this study, three reviewers used four counting methodologies to calculate Ki67 index in 68 well-differentiated pancreatic neuroendocrine tumors: (1) 'eye-ball' estimation, which has been advocated as reliable and is widely used; (2) automated counting by image analyzer; (3) manual eye-counting (eye under a microscope without a grid); and (4) manual count of camera-captured/printed image. Pearson's correlation (R) was used to measure pair-wise correlation among three reviewers using all four methodologies. Average level of agreement was calculated using mean of R values. The results showed that: (1) 'eye-balling' was least expensive and fastest (average time <1 min) but had poor reliability and reproducibility. (2) Automated count was the most expensive and least practical with major impact on turnaround time (limited by machine and personnel accessibility), and, more importantly, had inaccuracies in overcounting unwanted material. (3) Manual eye count had no additional cost, averaged 6 min, but proved impractical and poorly reproducible. (4) Camera-captured/printed image was most reliable, had highest reproducibility, but took longer than 'eye-balling'. In conclusion, based on its comparatively low cost/benefit ratio and reproducibility, camera-captured/printed image appears to be the most practical for calculating Ki67 index. Although automated counting is generally advertised as the gold standard for index calculation, in this study it was not as accurate or cost-effective as camera-captured/printed image and was highly operator-dependent. 'Eye-balling' produces highly inaccurate and unreliable results, and is not recommended for routine use.
Use of real-time ultrasound to evaluate live animal carcass traits in young performance-tested beef bulls. (1997)

Young bulls were ultrasonically scanned to 1) study breed differences for 12th rib fat depth (USFAT) and longissimus muscle area (USREA), 2) evaluate the nature and predictability of USFAT and USREA development, and 3) determine the effect of age (YFAT and YREA, respectively) or weight (WREA) adjustments on USFAT and USREA. Angus (AA), Charolais (CH), Hereford (HH), Shorthorn (SS), and Simmental (SM) bulls (n = 886) were studied in 2 yr at two stations. Breed differences were observed for end of test USFAT (AA = SS > HH > CH = SM, P < .05) and USREA (CH = SM > SS = AA > HH, P < .05). Within-breed coefficients of variation were 29.8 to 48.4% for end of test USFAT and from 9.0 to 10.8% for end of test USREA. In most bulls, USFAT development was neither linear nor quadratic (P > .05), but USREA development was linear (P < .05). Prediction equations were characterized by low r2 and high residual standard deviation (RSD) values, although those for d-84 USREA had r2 values from .63 to .70 and RSD values from 4.09 to 5.80 cm2. High associations were obtained between end of test USFAT with YFAT (r = .83 to .91, P < .05) and USREA with YREA (r = .74 to .84, P < .05) but not for end of test USREA with WREA (r = .31 to .56, P < .05). These results indicate that end of test ultrasound measurements may be a useful addition to performance testing programs.
Channel shortening equalization for differential ofdm systems (2005)

In orthogonal frequency division multiplexing (OFDM) systems, the length of the cyclic prefix (CP) has to be greater than the length of the channel impulse response to avoid inter-symbol interference. However, a long CP costs extra bandwidth and reduces power efficiency. This paper designs a channel shortening filter for differential OFDM systems with unknown multipath channels with long delay spreads. Without introducing extra redundancy, our design shortens the length of the effective channel response and bypasses the channel estimation, thus improving bandwidth and power efficiencies. The design is easy to be implemented at both transmitter and receiver with low computational complexity. Simulation results corroborate the merits of our design.
Recombinant CD200 Protein Does Not Bind Activating Proteins Closely Related to CD200 Receptor (2005)

CD200 (OX2) is a cell surface glycoprotein that interacts with a structurally related receptor (CD200R) expressed mainly on myeloid cells and is involved in regulation of macrophage and mast cell function. In mouse there are up to five genes related to CD200R with conflicting data as to whether they bind CD200. We show that mouse CD200 binds the inhibitory receptor CD200R with a comparable affinity (Kd = 4 microM) to those found for the rat and human CD200 CD200R interactions. CD200 gave negligible binding to the activating receptors, CD200RLa, CD200RLb, and CD200RLc, by direct analysis at the protein level using recombinant monomeric and dimeric fusion proteins or to CD200RLa and CD200RLb when expressed at the cell surface. An additional potential activating gene, CD200RLe, found in only some mouse strains also did not bind CD200. Thus, the CD200 receptor family consists of both activatory and inhibitory members like several other paired ligand receptors, such as signal regulatory protein, killer cell Ig-like receptor/KAR, LY49, dendritic cell immunoreceptor/dendritic cell immunoactivating receptor, and paired Ig-like type 2 receptor. Although the ligand for the inhibitory product is a widely distributed host protein, the ligands of the activating forms remain to be identified, and one possibility is that they are pathogen components.
Role of lipopolysaccharide (LPS), interleukin-1, interleukin-6, tumor necrosis factor, and dexamethasone in regulation of LPS-binding protein expression in normal hepatocytes and hepatocytes from LPS-treated rats (1995)

Lipopolysaccharide (LPS)-binding protein (LBP) has been reported to be an acute-phase protein. LBP binds to LPS with a high affinity; LPS-LBP complexes then interact with the receptor CD14, resulting in increased expression of LPS-inducible genes. Hepatocytes represent a major source of LBP, but little is known about the regulation of rodent hepatocyte LBP synthesis. In these studies, undertaken to characterize hepatocyte LBP expression, we show that greater-than-20-fold increases in LBP mRNA levels in hepatocytes occurred following injection of LPS or turpentine in rats. In primary cultures of rat hepatocytes, the addition of interleukin-6 (IL-6) and LPS led to 4.5- and 3.2-fold stimulation in LBP mRNA levels, respectively. The induction of LBP by IL-6 or LPS was attenuated by dexamethasone. In contrast to IL-6 and LPS, in the presence of 10(-6) M dexamethasone, IL-1 and tumor necrosis factor (TNF) led to maximal LBP mRNA induction levels, 4.7- and 3.8-fold, respectively, suggesting that IL-6 and LPS stimulate LBP expression by mechanisms different from those of IL-1 and TNF. Similar induction levels of LBP mRNA were seen in rat H35 hepatoma cells for all four stimuli, and dexamethasone inhibited these responses. Dexamethasone alone increased the spontaneous induction in primary hepatocytes at early time points but suppressed induction at later time points. Furthermore, hepatocytes from rats treated with LPS in vivo exhibited a > 10-fold increase in mRNA expression in response to LPS and enhanced responses to TNF and IL-1. As with the normal hepatocytes, dexamethasone inhibited the LPS-dependent induction in the LPS-treated rat hepatocytes. These data suggest that LBP synthesis by hepatocytes is under the control of LPS, IL-1, TNF, IL-6, and glucocorticoids and that the LPS treatment primes hepatocytes for subsequent responses to LPS, TNF, and IL-1 for LBP synthesis.
HIGH TEMPERATURE LUBRICANTS FOR LOW HEAT REJECTION DIESEL ENGINES (1991)

This paper describes the effort currently underway at Cummins and AKZO Chemicals to develop liquid lubricants capable of satisfying the requirements of advanced low heat rejection diesel engines. These new lubricant formulations are based on a synthetic basestock which decomposes with low deposit formation at high temperatures. Bench testing illustrates the progress being made in the development of this basestock. In addition, replacement of the lubricant overbase additives by an external acid filter is being investigated. Initial engine test results in both conventional and high temperature engines are presented. In addition, the high temperature single cylinder engine being readied for the lubricant screening tests is described. (A) For the covering abstract of the proceedings see IRRD 853538.
Developing an Optimal Helix Angle As a Function of Pressure for Helical Groove Seals (2017)

Helical groove seals are non-contacting annular seals used in pumps between impeller stages and at the balance drum. These seals have helically machined grooves on the surface of the rotor and/or stator. They work to sustain a pressure difference given a mass flow rate of the impeller through two flow phenomena which can be characterized by their flow direction. Fluid flowing axially dissipates kinetic energy through turbulent mixing as fluid is pushed through the jet stream region and mixes in the larger groove region, thus producing a pressure differential. Fluid flowing in the groove direction rotates with the rotor wall and is positively displaced toward the high pressure region, essentially acting as a screw pump. Previous work with optimization of helical groove seals has shown that the ideal helix angle of the seal is steeper for lower pressure applications and shallower for higher pressure applications. This is due to lower pressure applications having higher circumferential velocity in the grooves. In high pressure applications, the groove circumferential velocity has even been shown to be negative, and therefore the fluid leaks out the end of the grooves. The objective of this study is to use computational fluid dynamics simulations to find the optimal helix angle of the seal given the pressure differential. To accomplish this goal, simulations were run in ANSYS CFX for various inlet pressures, given zero gauge outlet pressure, and the helix angle of the grooves are varied. The helical grooves seals in this study have grooves on only the stator surface. The number of grooves is varied with the angle to keep the axial cross section of the seal consistent. By doing this, the study is able to focus in on the pumping mechanism of the helical groove seal without substantially changing the energy dissipation. The mass flow rates from each simulation for a given inlet pressure are plotted and quadratic regression was used to calculate an optimal helix angle as a function of inlet pressure. This study also answers the question of whether is there a limit where circumferentially grooved, i.e. labyrinth, seals outperform helical groove seals for very high pressures. Results comparing the powerloss of helical groove seals versus labyrinth seals and the effect of helix angle on powerloss are also given.
The efficacy of Herceptin therapies is influenced by the expression of other erbB receptors, their ligands and the activation of downstream signalling proteins (2004)

ErbB2 and EGFR are attractive oncology therapeutic targets as their overexpression in tumors predicts a poorer clinical outcome in a variety of epithelial malignancies. However, clinical results with therapeutic compounds targeting these receptors have been mixed. Therefore, there is a need for improved predictive biomarkers for these targeted therapeutics. In this study we analysed tissue microarrays of patients treated with combination chemotherapy and Herceptin for expression or phosphorylation of signalling proteins associated with erbB receptors to identify protein biomarkers that are predictive of breast cancer patient response. A comparison of expression or phosphorylation of these markers with patient outcome revealed that response to Herceptin depended not only on expression levels of erbB2 but also on expression of EGFR, expression of erbB ligands, expression of other receptors and phosphorylation of downstream proteins. Elucidating the biological effects of EGFR/erbB2 targeted therapeutics will enable patient tumor profiling to identify likely responders and the determination of biologically effective doses that allows chronic administration of these agents in order to maximise efficacy.
A Moderate Interaction of Maltosyl-&alpha;-cyclodextrin with Caco-2 Cells in Comparison with the Parent Cyclodextrin (2001)

The cytotoxicity of maltosyl-alpha-cyclodextrin (G2-alpha-CyD) and maltosyl-beta-cyclodextrin (G2-beta-CyD) toward Caco-2 cells was compared with that of natural alpha-cyclodextrin (alpha-CyD), beta-cyclodextrin (beta-CyD) and gamma-cyclodextrin (gamma-CyD). The degree of increase in cytotoxicity was dependent on the CyD's type and the concentration: the cytotoxicity of CyDs at the same concentration increased in the order of gamma-CyD<G2-beta-CyD<G2-alpha-CyD<<alpha-CyD, although beta-CyD could not be compared to other CyDs because of low solubility in water. Alpha-CyD decreased transepithelial electrical resistance (TEER) and increased the apical-to-basolateral (AP-to-BL) transport of [3H]mannitol, a paracellular transport marker, in a concentration-dependent manner, suggesting that alpha-CyD decreased the integrity of Caco-2 cell monolayers. In addition, alpha-CyD increased the AP-to-BL transport of rhodamine 123, a transcellular transport marker, under the experimental conditions being independent of P-glycoprotein. In contrast, G2-alpha-CyD, G2-betaCyD and gamma-CyD had slight effect on both TEER and the transport of mannitol and rhodamine 123 even at relatively high concentrations up to 150 mM. The inability of G2-alpha-CyD and G2-beta-CyD to effect TEER and the transport of mannitol and rhodamine 123 could be explained by the findings that these maltosylated CyDs released only a small amount of membrane constituents from Caco-2 cell monolayers and interacted only weakly with monolayers composed of L-alpha-dipalmitoylphosphatidylcholine (DPPC) formed on water. These results indicate that G2-alpha-CyD has less cytotoxicity and less disturbing ability toward Caco-2 cell monolayers than alpha-CyD, and G2-beta-CyD has, at least, comparable cytotoxicity to beta-CyD toward them. Thus, from the safety point of view, highly water-soluble G2-alpha-CyD and G2-beta-CyD may be particularly useful in various pharmaceutical formulations.