gebhart/patrepeval huggingface dataset:
Use of a quadrupole linear ion trap mass spectrometer in metabolite identification and bioanalysis (2003)

Abstract A new type of quadrupole linear ion trap mass spectrometer, Q TRAP™ LC/MS/MS system (Q TRAP™), was evaluated for its performance in two studies: firstly, the in vitro metabolism of gemfibrozil in human liver microsomes, and, secondly, the quantification of propranolol in rat plasma. With the built‐in information‐dependent‐acquisition (IDA) software, the instrument utilizes full scan MS in the ion trap mode and/or constant neutral loss scans as survey scans to trigger product ion scan (MS 2 ) and MS 3 experiments to obtain structural information of drug metabolites ‘on‐the‐fly’. Using this approach, five metabolites of gemfibrozil were detected in a single injection. This instrument combines some of the unique features of a triple quadrupole mass spectrometer, such as constant neutral loss scan, precursor ion scan and multiple reaction monitoring (MRM), together with the capability of a three‐dimensional ion trap. Therefore, it becomes a powerful instrument for metabolite identification. The fast duty cycle in the ion trap mode allows the use of full product ion scan for quantification. For the quantification of propranolol, both MRM mode and full product ion scan in the ion trap mode were employed. Similar sensitivity, reproducibility and linearity values were established using these two approaches. The use of the product ion scan mode for quantification provided a convenient tool in selecting transitions for improving selectivity during the method development stage. Copyright © 2003 John Wiley & Sons, Ltd.
System identification using frequency domain methodology (1990)

A method for using the frequency domain methodology to identify a linear meta-model is proposed. This involves multiple frequency domain runs to eliminate the effect of gain. The method uses the Fourier transform of the output process, rather than the periodogram or smoothed periodgram estimators. The identification focuses on estimating the coefficients of the model, and is therefore similar in spirit to response surface methodology. The method is tested on two models, one with known structure and the other with unknown structure. The procedure does well as fitting the coefficients, including obtaining the correct sign. >
An evaluation of possible interactions between ethanol and trazodone or amitriptyline. (1984)

The pharmacodynamic effects of single doses of trazodone (100 mg), amitriptyline (50 mg) or placebo either alone or with ethanol (0.5 ml/kg) were investigated in six healthy volunteers in a double-blind crossover study. Plasma concentrations of the drugs and ethanol were also measured. Pharmacodynamic tests were critical flicker fusion frequency threshold (CFF), choice reaction time (CRT), manual dexterity, a digit span test and visual analogue scales. Blood ethanol concentrations were not influenced by the co-administration of either antidepressant. tmax for trazodone was prolonged by ethanol but the other pharmacokinetic parameters for trazodone and amitriptyline were not influenced by ethanol. Trazodone and amitriptyline caused the expected profound depressant effects on CFF, CRT, manual dexterity and on the rating scales for drowsiness, 'clear-headedness', aggression and disinhibition. Ethanol alone impaired manual dexterity, increased drowsiness, reduced 'clear headedness' and also tended to reduce feelings of aggression. In combination with either trazodone or amitriptyline, ethanol caused little additional effect except in the case of manual dexterity which was further impaired. This result may reflect the profound effects of the antidepressants alone and does not suggest that it is safe for patients receiving antidepressant medication to take ethanolic drinks.
Angiotensin-converting enzyme and male fertility (2020)

The angiotensin-converting enzyme (ACE; EC 3.4.15.1) gene (Ace) encodes both a somatic isozyme found in blood and several other tissues, including the epididymis, and a testis-specific isozyme (testis ACE) found only in developing spermatids and mature sperm. We recently used gene targeting to disrupt the gene coding for both ACE isozymes in mice and reported that male homozygous mutants mate normally but have reduced fertility; the mutant females are fertile. Here we explore the male fertility defect. We demonstrate that ACE is important for achieving in vivo fertilization and that sperm from mice lacking both ACE isozymes show defects in transport within the oviducts and in binding to zonae pellucidae. Males generated by gene targeting that lack somatic ACE but retain testis ACE are normally fertile, establishing that somatic ACE in males is not essential for their fertility. Furthermore, male and female mice lacking angiotensinogen have normal fertility, indicating that angiotensin I is not a necessary substrate for testis ACE. Males heterozygous for the mutation inactivating both ACE isozymes sire wild-type and heterozygous offspring at an indistinguishable frequency, indicating no selection against sperm carrying the mutation.
Subsalt pressure prediction from multicomponent seismics (and more!) (2006)

Predrill pore-pressure predictions are vitally important in deepwater arenas where extreme depth and drilling window conditions, typical of current prospects and developments, require expensive rigs and highly trained personnel to successfully plan and execute complex wellbores.
Exact Time-Domain Second-Order Adjoint-Sensitivity Computation for Linear Circuit Analysis and Optimization (2009)

Classical adjoint-sensitivity analysis provides an elegant framework to efficiently compute the first-order sensitivities of a few circuit performances with respect to many circuit parameters. However, the computed sensitivity qualities are incremental in nature, hence only reflecting the performance changes under small perturbations of circuit parameters. In this paper, we rigorously extend the classical adjoint-sensitivity analysis and provide an efficient formulation for computing time-domain second-order adjoint sensitivities for linear circuits. This new formulation not only computes the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">exact</i> second-order sensitivities but also has a linear complexity in the number of parameters. Specifically, it only takes <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> +2 transient runs to compute all <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) first- and second-order performance sensitivities, where <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> is the number of parameters. Circuit examples are included to demonstrate the proposed formulation under the context of parametric circuit analysis and optimization.
CO2 Regenerative Ring Power Amplifiers (1971)

An unidirectional regenerative ring CO2 power amplifier is described. Both below threshold (unconditionally stable) and above threshold (conditionally stable) operation are discussed. Analytic expressions for a homogeneously broadened medium are presented for the power extracted from the active medium, the circulating power, and the total output power of the ring amplifier. Experimental results are presented in support of the theoretical analysis and demonstrate the role of gain saturation in the performance of CO2 regenerative ring amplifiers.
Transarterial platinum coil embolization of carotid-cavernous fistulas. (1991)

Of the 227 embolization procedures performed by our neurointerventional section for symptomatic carotid-cavernous fistulas over the past 10 years, five involved placement of platinum coils in the cavernous sinus from a transarterial route. In four patients, prior transarterial balloon procedures had failed to produce fistula closure. In the fifth patient, with Ehlers-Danlos syndrome, a prior transvenous embolization attempt was unsuccessful. In three patients, complete closure of the carotid-cavernous fistula was achieved with preservation of the parent artery. In one patient, the earliest treated, a portion of a platinum coil projected through the fistula into the parent artery. To eliminate the risk of clot formation and distal embolization, internal carotid occlusion was performed and tolerated without deficits. In the last patient, closure of the anterior drainage was achieved, but complicated by distal migration of the platinum coils with transient aggravation of ocular symptoms. Attempts to occlude the remaining cortical drainage were unsuccessful with platinum coils; therefore, a balloon was used to obliterate the small remaining fistula. Transarterial platinum coil embolization is an alternative treatment for symptomatic carotid-cavernous fistulas that cannot be closed successfully by other embolization techniques. The development of shorter, more thrombogenic, detachable or retrievable coils may make this technique more promising in the future.
Self‐sustaining limbic status epilepticus. (1991)

In prior work, we developed a model of self-sustaining limbic status epilepticus (SSLSE) induced by continuous hippocampal stimulation (CHS). Previous electrographic studies showed that SSLSE was synchronized between the cerebral hemispheres. On the basis of this initial work, we postulated that hippocampal commissures were critical for the initiation and maintenance of SSLSE. In the current experiments, we tested this hypothesis by applying CHS in animals with (CMX) or without (-CMX) hippocampal commissurotomies. In the -CMX group, electrographic SSLSE was synchronized between the stimulated and contralateral sides. In the CMX group, SSLSE developed only on the stimulated sides. Regional cerebral glucose utilization (RCGU) was also studied acutely (1 hour) after CHS using 2-deoxyglucose autoradiography. In the -CMX group, there was symmetrically increased RCGU in the hippocampus, retrohippocampal structures, and associated limbic and subcortical nonlimbic regions. In the CMX group, a similar pattern was found, but confined to the side of stimulation. CMX alone did not change RCGU values from those in control (-CMX, nonstimulated) brain in any of the regions studied. Areas of bilateral neocortical hypometabolism were found in both (CMX and -CMX) SSLSE groups. These results lead to rejection of the hypothesis that hippocampal commissures play an essential role in the initiation and maintenance of SSLSE. Instead, a feedback circuit involving the hippocampus and its adjacent structures seems to be the critical anatomic substrate for SSLSE. The presence of neocortical hypometabolism after CMX indicates that the structures other than the hippocampal commissure (eg, the thalamus or other forebrain commissures) mediate this effect.
Pigging Out (2003)

Research Article| May 01 2003 Pigging Out Timothy C. Davis Timothy C. Davis Search for other works by this author on: This Site PubMed Google Scholar Gastronomica (2003) 3 (2): 11–13. https://doi.org/10.1525/gfc.2003.3.2.11 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Timothy C. Davis; Pigging Out. Gastronomica 1 May 2003; 3 (2): 11–13. doi: https://doi.org/10.1525/gfc.2003.3.2.11 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentGastronomica Search This content is only available via PDF. Regents of the University of California Article PDF first page preview Close Modal You do not currently have access to this content.
A full adder implementation using SET based linear threshold gates (2003)

In this paper, we investigate single electron tunneling (SET) devices from the logic design perspective, using the SET tunnel junction's ability to control the transport of individual electrons. In particular, we present the implementation of a full adder using SET threshold gates. First, we augment the threshold gates with an active buffer in order to overcome feedback effects which can appear in passive SET networks. Second, we derive the circuit parameters for buffered SET threshold gates, and present the simulation results. Finally, we utilize the buffered threshold gates to build a full adder circuit, and verify the behavior of the resulting circuit via simulation.
<i>TP53</i> and <i>KRAS2</i> Mutations in Plasma DNA of Healthy Subjects and Subsequent Cancer Occurrence: A Prospective Study (2006)

In cancer patients, plasma often contains mutant DNA released by cancer cells. We have assessed the significance of plasma DNA mutations for subsequent cancer development in healthy subjects in a large longitudinal prospective study. The European Prospective Investigation into Cancer and Nutrition study was analyzed with a nested case-control design. Cases were nonsmokers or ex-smokers for >10 years and newly diagnosed with lung, bladder, or upper aerodigestive tract cancers or leukemia accrued after a median follow-up of 6.3 years. Controls were matched 2:1 for follow-up, age, sex, area of recruitment, and smoking status. KRAS2 mutations were detected by mutant-enriched PCR and sequencing (n = 1,098). TP53 mutations were detected by denaturing high-performance liquid chromatography, temporal temperature gradient electrophoresis, and sequencing (n = 550). KRAS2 or TP53 mutations were detected in 13 of 1,098 (1.2%) and 20 of 550 (3.6%) subjects, respectively, 16 of whom developed cancer on average after 18.3 months of follow-up. Among 137 subjects who developed bladder cancer, 5 had KRAS2 mutations [odds ratio (OR), 4.25; 95% confidence interval (95% CI), 1.27-14.15] and 7 had TP53 mutations (OR, 1.81; 95% CI, 0.66-4.97). There was a nonsignificant trend for association between TP53 mutations and bulky adducts in lymphocyte DNA (OR, 2.78; 95% CI, 0.64-12.17). This is the first report of TP53 or KRAS2 mutations in the plasma of healthy subjects in a prospective study, suggesting that KRAS2 mutation is detectable ahead of bladder cancer diagnosis. TP53 mutation may be associated with environmental exposures. These observations have implications for monitoring early steps of carcinogenesis.
Differentiation stage-specific expression of a gene during granulopoiesis. (1989)

Differential screening of a recombinant cDNA library using cDNAs transcribed from poly(A)+ RNA of normal or leukemic leukocytes revealed a number of recombinants homologous to mRNAs characteristic of particular leukemias. The occurrence of one of these (pCG14) in high abundance was shown to be sufficiently characteristic of the circulating leukocyte population of chronic granulocytic leukemia (CGL) patients to distinguish them from all other populations of leukocytes. We have now characterized the gene encoding this mRNA and shown that its expression is specific to the granulocyte lineage in hemopoietic cells and is, moreover, limited to a narrow stage of differentiation during granulopoiesis. Our results explain why high levels of pCG14 RNA are characteristic of chronic granulocytic leukemia peripheral blood leukocytes.
Structural similarity between the hydrophobic fluorescent probe and lipid A as a ligand of MD‐2 (2006)

Toll-like receptors (TLRs) belong to the family of pattern recognition receptors, as they recognize molecules sharing a broad structural pattern rather than a single defined structure. Bacterial LPS is recognized by MD-2, which is associated with the extracellular domain of TLR4. Understanding the molecular recognition pattern of MD-2 could lead to efficient inhibitors of the excessive LPS signaling needed for early treatment of sepsis. The effect of the acyl chain variability of lipid A on its biological activity indicates that in addition to electrostatic interactions, the recognition must also involve hydrophobic interactions. We show that the fluorescent hydrophobic probe bis-ANS binds to MD-2 with a dissociation constant in the 10 nanomolar range, both to glycosylated and to nonglycosylated MD-2, and requires its native conformation. The binding site of bis-ANS overlaps with the binding site of LPS and is in the proximity of the single tryptophan residue. Furthermore, photoincorporation of bis-ANS by UV light inhibits the ability of MD-2 to confer the LPS responsiveness to the TLR4-transfected HEK293 cell line. Our results show that the structural pattern recognized by MD-2 is defined by the hydrophobic patch and a pair of separated negative charges.
Transport of proteins to the plant vacuole is not by bulk flow through the secretory system, and requires positive sorting information. (1989)

Plant cells, like other eukaryotic cells, use the secretory pathway to target proteins to the vacuolar/lysosomal compartment and to the extracellular space. We wished to determine whether the presence of a hydrophobic signal peptide would result in the transport of a reporter protein to vacuoles by bulk flow; to investigate this question, we expressed a chimeric gene in transgenic tobacco. The chimeric gene, Phalb, used for this study consists of the 1,188-bp 5' upstream sequence and the hydrophobic signal sequence of a vacuolar seed protein phytohemagglutinin, and the coding sequence of a cytosolic seed albumin (PA2). The chimeric protein PHALB cross-reacted with antibodies to PA2 and was found in the seeds of the transgenic plants (approximately 0.7% of total protein), but not in the leaves, roots, or flowers. Immunoblot analyses of seed extracts revealed four glycosylated polypeptides ranging in molecular weight from 29,000 to 32,000. The four polypeptides are glycoforms of a single polypeptide of Mr 27,000, and the heterogeneity is due to the presence of high mannose and endoglycosidase H-resistant glycans. The PHALB products reacted with an antiserum specific for complex plant glycans indicating that the glycans had been modified in the Golgi apparatus. Subcellular fractionation of glycerol extracts of mature seeds showed that only small amounts of PHALB accumulated in the protein storage vacuoles of the tobacco seeds. In homogenates made in an isotonic medium, very little PHALB was associated with the organelle fraction containing the endoplasmic reticulum and Golgi apparatus; most of it was in the soluble fraction. We conclude that PHALB passed through the Golgi apparatus, but did not arrive in the vacuoles. Transport to vacuoles is not by a bulk-flow mechanism, once proteins have entered the secretory system, and requires information beyond that provided by a hydrophobic signal peptide.
Sequence Diversity and Molecular Evolution of the Leukotoxin ( <i>lktA</i> ) Gene in Bovine and Ovine Strains of <i>Mannheimia</i> ( <i>Pasteurella</i> ) <i>haemolytica</i> (2001)

The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella) haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains representing the various evolutionary lineages and serotypes of the species. Eight major allelic variants (1.4 to 15.7% nucleotide divergence) were identified; these have mosaic structures of varying degrees of complexity reflecting a history of horizontal gene transfer and extensive intragenic recombination. The presence of identical alleles in strains of different genetic backgrounds suggests that assortative (entire gene) recombination has also contributed to strain diversification in M. haemolytica. Five allelic variants occur only in ovine strains and consist of recombinant segments derived from as many as four different sources. Four of these alleles consist of DNA (52.8 to 96.7%) derived from the lktA gene of the two related species Mannheimia glucosida and Pasteurella trehalosi, and four contain recombinant segments derived from an allele that is associated exclusively with bovine or bovine-like serotype A2 strains. The two major lineages of ovine serotype A2 strains possess lktA alleles that have very different evolutionary histories and encode divergent leukotoxins (5.3% amino acid divergence), but both contain segments derived from the bovine allele. Homologous segments of donor and recipient alleles are identical or nearly identical, indicating that the recombination events are relatively recent and probably postdate the domestication of cattle and sheep. Our findings suggest that host switching of bovine strains from cattle to sheep, together with inter- and intraspecies recombinational exchanges, has played an important role in generating leukotoxin diversity in ovine strains. In contrast, there is limited allelic diversity of lktA in bovine strains, suggesting that transmission of strains from sheep to cattle has been less important in leukotoxin evolution.
A New Scheme of Finding the Master Sintering Curve (2006)

The master sintering curve approach represents densification data in terms of a master variable that combines sintering time and temperature. Recently, a finite‐element scheme to predict sintering deformation that requires only the master sintering curve instead of a full constitutive law as the input data has been developed. Here, a modification to the original master sintering curve approach, so that it is more suitable for finite‐element analysis, is presented. Finite‐element shape functions are used to represent the densification data as well as the master sintering curve. This approach confers extra flexibility to the master sintering curve approach, even when it is not used with finite‐element analysis. For example, by using shape functions, a varying activation energy can be used to obtain a master sintering curve for a set of densification data that cannot be fitted using a constant activation energy.
Osmium Replica of Mesoporous Silicate MCM-48:  Efficient and Reusable Catalyst for Oxidative Cleavage and Dihydroxylation Reactions (2003)

A three-dimensional networked osmium nanomaterial (N-Os) was prepared by a thermal decomposition of Os3(CO)12 within mesopores of MCM-48. The novel N-Os species shows high catalytic activity and excellent reusability in the oxidation reactions of unsaturated compounds under mild conditions.
Development of Ultrabright Semiconducting Polymer Dots for Ratiometric pH Sensing (2011)

Semiconducting polymer-based nanoparticles (Pdots) have recently emerged as a new class of ultrabright probes for biological detection and imaging. This paper describes the development of poly(2,5-di(3',7'-dimethyloctyl)phenylene-1,4-ethynylene) (PPE) Pdots as a platform for designing Förster resonance energy transfer (FRET)-based ratiometric pH nanoprobes. We describe and compare three routes for coupling the pH-sensitive dye, fluorescein, to PPE Pdots, which is a pH-insensitive semiconducting polymer. This approach offers a rapid and robust sensor for pH determination using the ratiometric methodology where excitation at a single wavelength results in two emission peaks, one that is pH sensitive and the other one that is pH insensitive for use as an internal reference. The linear range for pH sensing of the fluorescein-coupled Pdots is between pH 5.0 and 8.0, which is suitable for most cellular studies. The pH-sensitive Pdots show excellent reversibility and stability in pH measurements. In this paper, we use them to measure the intracellular pH in HeLa cells following their uptake by endocytosis, thus demonstrating their utility for use in cellular and imaging experiments.