gebhart/patrepeval huggingface dataset:
Benchtop study of leakages across the Portex, TaperGuard and Microcuff Endotracheal tubes under simulated clinical conditions (2013)

OBJECTIVES. To compare three endotracheal tubes for leakage across the cuff (microaspiration) under a comprehensive set of simulated clinical situations. These were the Mallinckrodt TaperGuard (Covidien, US) with a tapered polyvinyl chloride cuff; the KimVent Microcuff (Kimberly-Clark Health Care, US) with a cylindrical polyurethane cuff; and a conventional Portex (Smiths Medical International Ltd, UK) with a globular polyvinyl chloride cuff. DESIGN. A benchtop experimental study. SETTING AND MATERIALS. A silicone cylinder serving as the model trachea was intubated with each of the three endotracheal tubes, one at a time. A total of 20 mL of water were added above the cuff and leakage measured every minute for 20 minutes under five simulated mechanical ventilation scenarios, including different positive end-expiratory pressure levels, and disconnection with and without spontaneous breathing efforts. Each scenario was studied under three cuff pressures of 10, 20 and 30 cm H2O, and then repeated with the application of a continuous suction force of 200 cm H2O, and leakage measured every minute for 3 minutes. RESULTS. The outcome of interest was the cumulative amount of leakage. The Microcuff endotracheal tubes with an ultrathin polyurethane cuff consistently provided the best protection against microaspiration under all simulated clinical situations, followed by TaperGuard with a tapered cuff, and lastly Portex with a globular polyvinyl chloride cuff. Clinical scenarios associated with the greatest leakage were mechanical ventilation with zero positive end-expiratory pressure, circuit disconnection with spontaneous breathing efforts, application of suction, and a low cuff pressure. CONCLUSIONS. Microcuff endotracheal tubes outperformed TaperGuard and Portex endotracheal tubes in preventing microaspiration, which is one of the major mechanisms for ventilator-associated pneumonia.
Biochemical and functional characteristics of the human leukocyte membrane antigen family LFA‐1, Mo‐1 and p!50,95 (1985)

The human leukocyte function-associated (LFA-1) antigen, the monocyte differentiation antigen Mo-1 which is characterized as the C3bi receptor and the glycoprotein p150,95 are characterized biochemically. Immunoprecipitations carried out with 6 different monoclonal antibodies (mAb) against LFA-1 indicated that four mAb (SPV-L1, SPV-L5, SPV-L7 and SPV-L11) were directed against the alpha chain, whereas mAb CLB54 and MHM-23 were found to react with the common beta chain of LFA-1, Mo-1 and p150,95. LFA-1 and Mo-1 expressed on KG-1 cells or lymphocytes, monocytes and granulocytes from one donor were homogeneous. Interestingly the alpha chain of p150,95 showed heterogeneity. The molecular weight of the alpha chain expressed on monocytes was consistently higher than that of the alpha chain on granulocytes. The beta subunits of LFA-1 and Mo-1 (as detected by mAb Bear-1) are not only similar in molecular weight and isoelectric focusing patterns, but it is demonstrated here that they are also identically glycosylated and have similar protein backbones as judged by tryptic peptide mapping. In spite of their structural similarities. LFA-1 and Mo-1 differ completely in some of their biological functions. Anti-LFA-1 mAb strongly inhibited monocyte-dependent T cell proliferation induced by tetanus toxoid or Helix pomatia hemocyanin and pokeweed mitogen-driven specific antibody production in vitro, whereas the anti-Mo-1 antibody Bear-1 was ineffective. These results suggest that the differences in these biological functions of LFA-1 and Mo-1 may be related to their different alpha subunits, which may recognize specific counter structures.
Agmatine Suppresses Proliferation by Frameshift Induction of Antizyme and Attenuation of Cellular Polyamine Levels (1998)

Polyamines are required for entry and progression of the cell cycle. As such, augmentation of polyamine levels is essential for cellular transformation. Polyamines are autoregulated through induction of antizyme, which represses both the rate-limiting polyamine biosynthetic enzyme ornithine decarboxylase and cellular polyamine transport. In the present study we demonstrate that agmatine, a metabolite of arginine via arginine decarboxylase (an arginine pathway distinct from that of the classical polyamines), also serves the dual regulatory functions of suppressing polyamine biosynthesis and cellular polyamine uptake through induction of antizyme. The capacity of agmatine to induce antizyme is demonstrated by: (a) an agmatine-dependent translational frameshift of antizyme mRNA to produce a full-length protein and (b) suppression of agmatine-dependent inhibitory activity by either anti-antizyme IgG or antizyme inhibitor. Furthermore, agmatine administration depletes intracellular polyamine levels to suppress cellular proliferation in a transformed cell line. This suppression is reversible with polyamine supplementation. We propose a novel regulatory pathway in which agmatine acts as an antiproliferative molecule and potential tumor suppressor by restricting the cellular polyamine supply required to support growth.
Problems of Translating Heterologous Genes in Expression Systems: The Role of tRNA (1996)

tRNA can have large effects on the expression and overexpression of heterologous genes in microbial expression systems through reduced translation and errors in amino acid sequences of protein products. Examples are given of large effects on gene expression related to tRNA content and to tRNA base modifications, both of which differ in heterologous expression systems compared to the cells from which the genes originally came. tRNA should be of greater concern in the expression of heterologous genes.
MADS domain proteins in plant development. (1997)

The MADS domain (MCM1, AGAMOUS, DEFICIENS, and SRF, serum response factor) is a conserved DNA-binding/dimerization region present in a variety of transcription factors from different kingdoms. MADS box genes represent a large multigene family in vascular plants. In angiosperms, many of the genes of the MADS family are involved in different steps of flower development, most notably in the determination of floral meristem and organ identity. The roles that MADS box genes play, however, are not restricted to control the development of the plant reproductive structures. The genetic, molecular, and biochemical basis of the action of the MADS domain proteins in the plant life cycle are reviewed here.
Segmentation of Complex Sentences ⋆ (2008)

Abstract. The paper describes a method of dividing complex sentences into segments, easily detectable and linguistically motivated units that may be subsequently combined into clauses and thus provide a structure of a complex sentence with regard to the mutual relationship of individual clauses. The method has been developed for Czech as a language representing languages with relatively high degree of word-order freedom. The paper introduces important terms, describes a segmentation chart, the data structure used for the description of mutual relationship between individual segments and separators. It also contains a simple set of rules applied for the segmentation of a small set of Czech sentences. The segmentation results are evaluated against a small hand-annotated corpus of Czech complex sentences. 1
Recombinant Human DNA (Cytosine-5) Methyltransferase (1999)

Initial velocity determinations were conducted with human DNA (cytosine-5) methyltransferase (DNMT1) on unmethylated and hemimethylated DNA templates in order to assess the mechanism of the reaction. Initial velocity data with DNA and S-adenosylmethionine (AdoMet) as variable substrates and product inhibition studies with methylated DNA and S-adenosylhomocysteine (AdoHcy) were obtained and evaluated as double-reciprocal plots. These relationships were linear for plasmid DNA, exon-1 from the imprinted small nuclear ribonucleoprotein-associated polypeptide N, (CGG.CCG)(12), (m(5)CGG. CCG)(12), and (CGG.CCG)(73) but were not linear for (CGG. Cm(5)CG)(12). Inhibition by AdoHcy was apparently competitive versus AdoMet and uncompetitive/noncompetitive versus DNA at </=20 microM AdoMet. Addition of the product (methylated DNA) to unmethylated plasmid DNA increased V(max(app)) resulting in mixed stimulation and inhibition. Velocity equations indicated a two-step mechanism as follows: first, activation of DNMT1 by methylated DNA that bound to an allosteric site, and second, the addition of AdoMet and DNA to the catalytic site. The preference of DNMT1 for hemimethylated DNA may be the result of positive cooperativity of AdoMet binding mediated by allosteric activation by the methylated CG steps. We propose that this activation plays a role in vivo in the regulation of maintenance methylation.
Total Synthesis of Spinosyn A. 2. Degradation Studies Involving the Pure Factor and Its Complete Reconstitution (1998)

A total synthesis of natural levorotatory spinosyn A (1) has been achieved. The first objective, to confirm the absolute configurational assignment of tricyclic ketone 2 prepared earlier, was accomplished by oxidative degradation of the macrocyclic lactone ring in 1. The route began with the implementation of a four-step one-pot process that resulted in the efficient conversion of 6 into 18. A combination of periodate cleavage and peracid oxidation events then led to 2. In the reconstruction phase, a Pd-catalyzed coupling of a vinylstannane with an acid chloride reestablished the great majority of the structure in an enantiocontrolled manner. Once macrolactonization had been effected, the 2,3,4-tri-O-methylrhamnose unit was introduced first with exceptionally good stereocontrol. The final glycosidation, which involved a 2-mercaptopyrimidine derivative of d-forosamine, was met with an expectedly diminished percentage of the desired β-anomer.
Minimum Amino Acid Residues of an α-Helical Peptide Leading to Lipid Nanodisc Formation (2014)

Nanodiscs are a relatively new class of nanoparticles composed of amphiphilic α-helical scaffold peptides and a phospholipid bilayer, and find potential applications in various fields. In order to identify the minimum number of amino acid residues of an amphiphilic α-helical peptide that leads to nanodisc formation, seven peptides differing in lengths (22-, 18-, 14-, 12-, 10-, 8-, and 6-mers) that mimic and modify the C-terminal domain of apoA-I (residues 220-241) were synthesized. At a concentration of 0.3 mM, the 6- and 8-mer peptides did not present any surface activity. In case of the 10-mer peptide, the aqueous surface tension initially decreased and reached a constant value of 51.9 mN/m with the 14-, 18-, and 22-mer peptides. Moreover, upon mixing the surface-active peptides (14-, 18-, and 22-mers) with dipalmitoylphosphatidylcholine (DMPC) liposomes (2.5:1, peptide : DMPC), the turbid DMPC liposome solution rapidly became transparent. Further analysis of this solution by negative-stain transmission electron microscopy (NS-TEM) indicated the presence of disk-like nanostructures. The average diameter of the nanodiscs formed was 9.5 ± 2.7 nm for the 22-mer, 8.1 ± 2.7 nm for the 18-mer, and 25.5 ± 8.5 nm for the 14-mer peptides. These results clearly demonstrate that the surface properties of peptides play a critical role in nanodisc formation. Furthermore, the minimum length of an amphiphilic peptide from the C-terminal of apoA-I protein that can lead to nanodisc formation is 14 amino acid residues.
Synthesis of aminomethyl-substituted cyclic imide derivatives for evaluation as anticonvulsants (1983)

A series of aminomethyl-substituted cyclic imides (II) based on the 2,5-pyrrolidinedione (X = CH2, succinimide) and 2,4-imidazolidinedione (X = NH, hydantoin) ring systems have been prepared. The compounds were designed on the basis of a potential interaction in the gamma-aminobutyric acid (GABA) neurotransmitter system and evaluated for anticonvulsant activity. The 3-(aminomethyl)-2,5-pyrrolidinediones were prepared by a dehydration procedure beginning with N-benzyl-2-(aminomethyl)succinic acid, whereas the 3-(aminomethyl)-3-methyl-2,3-pyrrolidinediones were best obtained by fusion of the amine salts of 2-(aminomethyl)-2-methylsuccinic acid. The hydantoin derivative, 5-(aminomethyl)-5-methyl-2,4-imidazolidinedione, was obtained by standard procedures. Although none of the compounds tested showed significant activity against convulsions induced by pentylenetetrazole (PTZ), some showed significant activity against maximal electroshock seizures in mice. Possible reasons for the lack of anti-PTZ activity and directions for further testing are discussed.
Propagation loss measurement for surface plasmon-polariton modes at metal waveguides on semiconductor substrates (2004)

Propagation losses were measured for surface plasmon-polariton (SPP) modes at metal waveguides on semiconductor substrates. The waveguides are simple strips of Au or Al deposited on InP substrates or 300-nm-thick SiO2 film covering the InP substrates. We used a direct method that can clearly discriminate SPP modes in vidicon-camera images, thereby allowing quantitative measurements. The loss coefficients measured at a wavelength of 1.55 μm were, as predicted by theory, in the range of 8.5–17 dB/mm, which shows the waveguides are feasible for practical applications.
Radiolytic Preparation of Ultrafine Colloidal Gold Particles in Aqueous Solution:  Optical Spectrum, Controlled Growth, and Some Chemical Reactions (1999)

Orange− or yellow−orange-colored aqueous dispersions of ultrafine gold particles (∼2 nm) result from the γ-irradiation of deaerated solutions containing hydrolyzed AuCl4- and poly(vinyl alcohol) or poly(vinylpyrrolidone), respectively. The particles have a weak and very broad plasmon absorption band with maximum in the 490 to 500 nm range, i.e., at substantially shorter wavelengths than expected from classical Mie theory using bulk dielectric data; moreover, the specific UV absorption increases as the particles become smaller. The particles are used as seeds in the radiolytic reduction of added Au(CN)2- to yield larger particles of any desired size and improved monodispersity. The particles partially react with oxygen. Chemisorption of 3-mercapto propionic acid strongly affects the electronics of the particles, as indicated by the changes in optical absorption. The early stages of AuCl4- reduction are also investigated. The reduction occurs essentially in two steps: (1) formation, and (2) reduction of Au+. A 203-nm absorption band is tentatively attributed to Au+. Without further irradiation, Au+ disappears thermally within hours to yield larger particles (20−70 nm).
Geophone Coupling and QC of Vector Fidelity (2002)

E-01 GEOPHONE COUPLING AND QC OF VECTOR FIDELITY Abstract 1 We have observed two different types of coupling problems in marine multicomponent (4C) data. The ”poor and stable” coupling response seen in figure 1 and the ”highly variable” coupling response seen in figure 2. We relate this to interaction and contact coupling respectively. Also since the coupling responses tend to be different for inline and crossline geophones we very often find that the horizontal components have a non-uniform azimuth response. If we have enough redundancy we regard it as possible to use the direct arrival to detect and correct for
Targeted therapy of cancer with radiolabeled antibodies. (2002)

This review focuses on the use of radiolabeled antibodies in the therapy of cancer, termed radioimmunotherapy (RAIT). Basic problems concerning the choice of antibody and radionuclide and the physiology of tumor and host are discussed. Then follows a review of pertinent clinical publications on various radioantibody constructs in the treatment of hematopoietic and solid tumors of diverse histopathologies, grades, and stages, and in different clinical settings. Factors such as dose rate delivered, tumor size, and radiosensitivity play a major role in determining therapeutic response, while target-to-nontarget ratios and, particularly, circulating radioactivity to the bone marrow determine the major dose-limiting toxicities. RAIT appears to be gaining a place in the therapy of hematopoietic neoplasms, such as non-Hodgkin's lymphoma, with several agents advancing in clinical trials toward registration, of which one has just been approved by the FDA. Although RAIT of solid tumors has shown less progress, pretargeting strategies, such as an affinity-enhancement system consisting of bispecific antibodies separating targeting from delivery of the radiotherapeutic, appear to enhance tumor-to-nontumor ratios and may increase rad doses to tumor more selectively than directly labeled antibodies.
Noncompetitive Removal of Heavy Metal Ions from Aqueous Solutions by Poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid-co-itaconic acid] Hydrogel (2009)

Noncompetitive removal of Pb2+, Cu2+, and Cd2+ ions from aqueous solutions by the copolymer of 2-(acrylamido)-2-methyl-1-propanesulfonic acid with itaconic acid and its homopolymer poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid] was investigated. Both poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid] and poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid-co-itaconic acid] removed the maximum and same amounts (1.74 mmol Pb2+/g polymer) of Pb2+ ion among the ions investigated in this work. The equilibrium swelling values of poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid] and poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid-co-itaconic acid] showed that the swelling of the copolymer is dominated by its completely ionizable constituent 2-(acrylamido)-2-methyl-1-propanesulfonic acid. Although the incorporation of itaconic acid into poly[2-(acrylamido)-2-methyl-1-propane sulfonic acid] did not affect the removal rates of poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid-co-itaconic acid] for Pb2+ and Cd2+ ions, it considerably enhanced the removal rates of the copolymer for the Cu2+ ion. The trends in the single-ion sorption of ions on poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid] and poly[2-(acrylamido)-2-methyl-1-propanesulfonic acid-co-itaconic acid] followed the orders Pb2+ > Cd2+ > Cu2+ and Pb2+ > Cu2+ > Cd2+, respectively. Noncompetitive adsorption profiles of Pb2+, Cu2+, and Cd2+ ions on both polymers were demonstrated to fit the pseudo-second-order-type kinetics.
Assessing the Uncertainty in Reservoir Description and Performance Predictions with the Ensemble Kalman Filter (2005)

Abstract Recently, the ensemble Kalman filter (EnKF) has gained popularity in atmospheric science for the assimilation of data and the assessment of uncertainty in forecasts for complex, large-scale problems. A handful of papers have discussed reservoir characterization applications of the EnKF, which can easily and quickly be coupled with any reservoir simulator. Neither adjoint code nor specific knowledge of simulator numerics is required for implementation of the EnKF. Moreover, data are assimilated (matched) as they become available; a suite of plausible reservoir models (the set of ensembles) is continuously updated to honor data without rematching data assimilated previously. Because of these features, the method is far more efficient for history matching dynamic data than automatic history matching algorithms based on optimization algorithms. Moreover, the suite of ensembles provides a way to evaluate the uncertainty in reservoir description and performance predictions. Here we establish a firm theoretical relation between randomized maximum likelihood and the ensemble Kalman filter. We also consider examples where the performance of the EnKF does not provide a reliable characterization of uncertainty in the model or performance predictions. Although we have previously generated reservoir characterization examples where the method worked well, here we also provide examples where the performance of EnKF does not provide a reliable characterization of uncertainty.
CD133-enriched Xeno-Free human embryonic-derived neural stem cells expand rapidly in culture and do not form teratomas in immunodeficient mice (2014)

Common methods for the generation of human embryonic-derived neural stem cells (hNSCs) result in cells with potentially compromised safety profiles due to maintenance of cells in conditions containing non-human proteins (e.g. in bovine serum or on mouse fibroblast feeders). Additionally, sufficient expansion of resulting hNSCs for scaling out or up in a clinically relevant time frame has proven to be difficult. Here, we report a strategy that produces hNSCs in completely "Xeno-Free" culture conditions. Furthermore, we have enriched the hNSCs for the cell surface marker CD133 via magnetic sorting, which has led to an increase in the expansion rate and neuronal fate specification of the hNSCs in vitro. Critically, we have also confirmed neural lineage specificity upon sorted hNSC transplantation into the immunodeficient NOD-scid mouse brain. The future use or adaptation of these protocols has the potential to better facilitate the advancement of pre-clinical strategies from the bench to the bedside.
Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid. (2001)

Four bacterial strains that oxidize L-sorbose to 2-keto-L-gulonic acid, a key intermediate in the synthesis of vitamin C, were isolated from soils of geographically distinct locations. All were Gram-negative, facultatively anaerobic, chemoheterotrophic rods. Comparative analysis revealed nearly identical 16S rDNA sequences amongst them (99.7-100% identical) and identified them as members of the alpha-subclass of the Proteobacteria. Phylogenetic analysis identified the closest taxonomically defined genus as Roseobacter (92.1-92.8% identical). On the basis of phylogenetic, phenotypic and genotypic analyses, a new genus is proposed, Ketogulonigenium gen. nov. Based upon these analyses, we also propose the reclassification of strain DSM 4025TP, originally identified as Gluconobacter oxydans, to the genus Ketogulonigenium. Two species are proposed: the type species Ketogulonigenium vulgare gen. nov., sp. nov., consisting of strains 62A-12APP, 266-13BPP and the type strain K. vulgare DSM 4025TP, and Ketogulonigenium robustum gen. nov., sp. nov., consisting of the type strain K. robustum X6LTP (= NRRL B-21627 = KCTC 0858BP). The species affiliation of the fifth strain (291-19PP) remains unresolved.
Effect of endovascular cooling on myocardial temperature, infarct size, and cardiac output in human-sized pigs (2002)

Mild hypothermia reduces myocardial infarct size in small animals; however, the extent of myocardial protection in large animals with greater thermal mass remains unknown. We evaluated the effects of mild endovascular cooling on myocardial temperature, infarct size, and cardiac output in 60- to 80-kg isoflurane-anesthetized pigs. We occluded the left anterior descending coronary artery for 60 min, followed by reperfusion for 3 h. An endovascular heat-exchange catheter was used to either lower core body temperature to 34 degrees C (n = 11) or maintain temperature at 38 degrees C (n = 11). Additional studies assessed myocardial viability and microvascular perfusion with (99m)Tc-sestamibi autoradiography. Endovascular cooling reduced infarct size compared with normothermia (9 +/- 6% vs. 45 +/- 8% of the area at risk; P < 0.001), whereas the area at risk was comparable (19 +/- 3% vs. 20 +/- 7%; P = 0.65). Salvaged myocardium showed normal sestamibi uptake, confirming intact microvascular flow and myocyte viability. Cardiac output was maintained in hypothermic hearts because of an increase in stroke volume, despite a decrease in heart rate. Mild endovascular cooling to 34 degrees C lowers myocardial temperature sufficiently in human-sized hearts to cause a substantial cardioprotective effect, preserve microvascular flow, and maintain cardiac output.