gebhart/patrepeval huggingface dataset:
Outer membrane protein H1 of Pseudomonas aeruginosa: purification of the protein and cloning and nucleotide sequence of the gene (1989)

Overexpression of the divalent cation-regulated outer membrane protein H1 of Pseudomonas aeruginosa is associated with resistance to polymyxin B, aminoglycosides, and EDTA. Protein H1 is believed to act by replacing divalent cations at binding sites on lipopolysaccharide, thereby preventing disruption of the sites and subsequent self-promoted uptake of the antibiotics. Protein H1 purified by two cycles of anion-exchange chromatography was apparently associated with lipopolysaccharide. Lipopolysaccharide-free protein H1 was purified in high yield by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis and was subjected to N-terminal amino sequencing. Complementary oligodeoxyribonucleotides were used to clone the structural gene for protein H1, oprH, into Escherichia coli. Successful cloning was confirmed by nucleotide sequence analysis. Southern hybridization suggested that oprH was present as a single-copy gene in P. aeruginosa. The deduced amino acid sequence revealed that H1 was a slightly basic polypeptide of 178 residues, with a leader sequence typical of an exported procaryotic protein. It had little similarity, however, to other bacterial surface proteins for which sequence data were available. No expression of protein H1, from its own or the lac promoter, was detected in E. coli. We concluded that, as for some other regulated Pseudomonas genes, expression of oprH, at least under some conditions, is blocked in E. coli.
Multifunctional nanocomposite hollow fiber membranes by solvent transfer induced phase separation (2017)

The decoration of porous membranes with a dense layer of nanoparticles imparts useful functionality and can enhance membrane separation and anti-fouling properties. However, manufacturing of nanoparticle-coated membranes requires multiple steps and tedious processing. Here, we introduce a facile single-step method in which bicontinuous interfacially jammed emulsions are used to form nanoparticle-functionalized hollow fiber membranes. The resulting nanocomposite membranes prepared via solvent transfer-induced phase separation and photopolymerization have exceptionally high nanoparticle loadings (up to 50 wt% silica nanoparticles) and feature densely packed nanoparticles uniformly distributed over the entire membrane surfaces. These structurally well-defined, asymmetric membranes facilitate control over membrane flux and selectivity, enable the formation of stimuli responsive hydrogel nanocomposite membranes, and can be easily modified to introduce antifouling features. This approach forms a foundation for the formation of advanced nanocomposite membranes comprising diverse building blocks with potential applications in water treatment, industrial separations and as catalytic membrane reactors.
Multiple metal-carbon bonds. 7. Preparation and characterization of Ta(.eta.5-C5H5)2(CH2)(CH3), a study of its decomposition, and some simple reactions (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultiple metal-carbon bonds. 7. Preparation and characterization of Ta(.eta.5-C5H5)2(CH2)(CH3), a study of its decomposition, and some simple reactionsR. R. Schrock and P. R. SharpCite this: J. Am. Chem. Soc. 1978, 100, 8, 2389–2399Publication Date (Print):April 1, 1978Publication History Published online1 May 2002Published inissue 1 April 1978https://pubs.acs.org/doi/10.1021/ja00476a022https://doi.org/10.1021/ja00476a022research-articleACS PublicationsRequest reuse permissionsArticle Views1332Altmetric-Citations181LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Naturally occurring antibodies against nine common antigens in humans sera. II. High incidence of monoclonal Ig exhibiting antibody activity against actin and tubulin and sharing antibody specificities with natural antibodies. (1982)

Abstract In a previous work, we consistently detected in normal human serum, natural antibodies directed against tubulin, actin, thyroglobulin, myoglobin, fetuin, albumin, and transferrin. These results prompted us to check the sera of patients carrying either a multiple myeloma or a Waldenstrom’s macroglobulinemia for the presence of monoclonal Ig (Mlg) having antibody activity against the same antigens. Among the 62 Mlg studied against the seven above-mentioned antigens, one (IgAκ) was shown to bind extensively to tubulin, and four (1lgGк, 1IgGλ, IgMк and 1lgAλ) bound mainly to actin, but a significant binding was also found to occur with tubulin and thyroglobulin. In all cases, findings were as follows: 1 ) The binding was mediated by light and heavy chain isotypes corresponding to those of the Mlg. 2) The antibody function was located in the Fab fragments prepared by pepsin digestion of these Mlg. 3) The antibody function was inhibited by the antigens. Mlg with anti-tubulin activity was exclusively inhibited by tubulin, whereas the four Mlg binding mainly to actin were predominantly inhibited by actin, but they were also strongly inhibited by tubulin and thyroglobulin. Similar results were obtained with either the serum or the F(ab’)2 fragments. 4) The Fab fragments were tested for their capacity to stain, by immunocytologic procedures, cultured human hepatic cells previously treated with vinblastine. In the case of the serum exhibiting anti-tubulin activity, only paracrystals of tubulin were stained, whereas for the four Mlg exhibiting anti-actin activity, simultaneous staining of actin filaments and tubulin paracrystals was observed. Three main conclusions emerge: 1) There is a high incidence of Mlg possessing antibody activity directed against the cytoskeleton proteins. 2) These Mlg seem to share antibody specificities with natural antibodies. 3) In the latter case, it can be postulated that, at least for some patients, the Mlg may constitute the expansion of a clone producing a natural antibody.
Random search for hyper-parameter optimization (2012)

Grid search and manual search are the most widely used strategies for hyper-parameter optimization. This paper shows empirically and theoretically that randomly chosen trials are more efficient for hyper-parameter optimization than trials on a grid. Empirical evidence comes from a comparison with a large previous study that used grid search and manual search to configure neural networks and deep belief networks. Compared with neural networks configured by a pure grid search, we find that random search over the same domain is able to find models that are as good or better within a small fraction of the computation time. Granting random search the same computational budget, random search finds better models by effectively searching a larger, less promising configuration space. Compared with deep belief networks configured by a thoughtful combination of manual search and grid search, purely random search over the same 32-dimensional configuration space found statistically equal performance on four of seven data sets, and superior performance on one of seven. A Gaussian process analysis of the function from hyper-parameters to validation set performance reveals that for most data sets only a few of the hyper-parameters really matter, but that different hyper-parameters are important on different data sets. This phenomenon makes
Biologically important interactions between synthetic peptides of the N-terminal region of troponin I and troponin C. (1992)

The interaction between troponin I and troponin C plays a critical role in the regulation of muscle contraction. In this study the interaction between troponin C (TnC) and the N-terminal region of TnI was investigated by the synthesis of three TnI peptides (residues 1-40/Rp, 10-40, and 20-40). The regulatory peptide (Rp) on binding to TnC prevents the ability of TnC to release the inhibition of the acto-S1-tropomyosin ATPase activity caused by TnI or the TnI inhibitory peptide (Ip), residues 104-115. A stable complex between TnC and Rp in the presence of Ca2+ was demonstrated by polyacrylamide gel electrophoresis in the presence of 6 M urea. Rp was able to displace TnI from a preformed TnI.TnC complex. In the absence of Ca2+, Rp was unable to maintain a complex with TnC in benign conditions of polyacrylamide gel electrophoresis which demonstrates the Ca(2+)-dependent nature of this interaction. Size-exclusion chromatography demonstrated that the TnC.Rp complex consisted of a 1:1 complex. The results of these studies have shown that the N-terminal region of TnI (1-40) plays a critical role in modulating the Ca(2+)-sensitive release of TnI inhibition by TnC.
Oxidation of silicon nitride films in an oxygen plasma (1999)

The fabrication of oxynitrides using low thermal budget process technology is a key component in the production of advanced devices. This work focuses on the use of plasma anodization of low-pressure chemical vapor deposition (LPCVD) silicon nitride films to produce silicon oxynitride films, which are characterized structurally and electrically. The oxynitride dielectric films have a three layer structure, with “SiO2”-like layers at the surface and near the interface, and a “Si3N4”-like layer between them. Hence, nitrogen atoms are replaced by oxygen atoms at the surface of the film and near the Si/dielectric interface. The conductivity of the silicon nitride film was found to be higher than the silicon oxynitride film, whereas the conductivity of the oxynitride and, therefore, its trapping characteristics are more temperature dependent. Furthermore, the activation energy required to release an electron from a trap in the silicon oxynitride film (0.218 eV) is 1.7× that of the silicon nitride film (0.130 eV). Although oxidation of the LPCVD silicon nitride film did not reduce the interface trap density (≅1012 cm−2 eV−1 for both Si3N4 and SiON films), the density of traps, which are thought to be silicon dangling bonds in the form of an sp3 state near midgap, have reduced. A model to explain the conduction properties of the silicon oxynitride film—based on the Fowler–Nordheim conduction mechanism—was developed. Moreover, this model takes into account the trapping dynamics of the film. It was found that the best theoretical fit to the experimental current density data was obtained by assuming that the areal trap density, No,=5×1012 cm−2 and the trap capture cross section, σ=1×10−16 cm2.
Systematic review: The relation between nutrition and nosocomial pneumonia: randomized trials in critically ill patients (1997)

Abstract Objective To review the effect of enteral nutrition on nosocomial pneumonia in critically ill patients as summarized in randomized clinical trials. Study identification and selection Studies were identified through MEDLINE, SCISEARCH, EMBASE, the Cochrane Library, bibliographies of primary and review articles, and personal files. Through duplicate independent review, we selected randomized trials evaluating approaches to nutrition and their relation to nosocomial pneumonia. Data abstraction In duplicate, independently, we abstracted key data on the design features, population, intervention and outcomes of the studies. Results We identified four trials of enteral vs total parenteral nutrition, one trial of early enteral nutrition vs delayed enteral nutrition, one trial of gastric vs jejunal tube feeding, one trial of intermittent vs continuous enteral feeding, and three trials evaluating different enteral feeding formulae. Sample sizes were small, pneumonia definitions were variable and blinded outcome assessment was infrequent. Randomized trial evidence is insufficient to draw conclusions about the relation between enteral nutrition and nosocomial pneumonia. Conclusions Nutritional interventions in critically ill patients appear to have a modest and inconsistent effect on nosocomial pneumonia. This body of evidence neither supports nor refutes the gastropulmonary route of infection.
Metabolic effects of a D-β-hydroxybutyrate infusion in septic patients (1994)

Exogenous ketone-bodies infusion decreased lipolysis and glucose production in septic patients but had no beneficial effect on protein metabolism, as evaluated with L[1-13C]leucine.
A Polyvalent Cellular Vaccine Induces T-cell Responses Against Specific Self-antigens Overexpressed in Chronic Lymphocytic B-cell Leukemia (2008)

B cell-derived chronic lymphocytic leukemia (CLL) is an incurable disease that requires innovative therapeutic regimens. Experimental approaches of immunotherapy aiming at induction of systemic T-cell responses have been developed. Trioma cells provide a potent vaccine derived from malignant B cells that allows multiple antigens (Ags) from the parental tumor to be ingested by Ag-presenting cells. Like other strategies using modified whole tumor cells, this approach induces polyvalent responses. Using trioma cell-pulsed dendritic cells (DCs) for T-cell activation in vitro, we asked whether specific Ags overexpressed by CLL can be identified as target structures of such responses and what is the nature of these Ags. Expression levels of several genes in CLL samples were quantitated by reverse transcriptase-polymerase chain reaction. T lymphocytes were polyvalently stimulated by trioma-pulsed DCs and specificities were tested by determining cytokine secretion in the presence of target cells transfected with RNA coding for those Ags that were found to be overexpressed. We demonstrate that DCs pulsed with the modified tumor cells efficiently activate T lymphocytes against CLL and that overexpressed Ags related to leukemogenesis, such as BCL-2, MDM2, and ETV5, serve as targets for those T cells. Immune escape by Ag loss or mutation is less likely to occur if immunity is directed against altered self-proteins that are involved in malignant transformation. Therefore, vaccines based on modified tumor cells such as triomas hold promise for immunotherapy of CLL and other malignancies. Polyvalent vaccines originally designed as individualized therapeutics may be more broadly applicable, at least in patients showing similar Ag patterns.
Stat proteins and oncogenesis (2002)

JAK-STAT signaling in human diseaseThe discovery of Stat proteins' key role in IFN signaling, initially described over ten years ago, provided the first molecular link of growth factor receptor stimulation to the direct activation of a transcription factor (1). Since that time a large number of growth factor receptors and some nonreceptor tyrosine kinases have been found to lead to the activation of these transcription factors (2).The contributions of individual Stat proteins to normal cytokine signaling and development have been studied in various cell culture systems and in vivo in mice made deficient for one or more of these proteins (3).This approach has identified some related roles, as well as many unique, nonoverlapping physiological roles, for the various members of the Stat family.In summary, Stat1-deficient mice are unable to respond to IFNs and are subsequently susceptible to bacterial and viral pathogens.Likewise, disruption of Stat2 gives rise to animals unable to respond to type 1 IFNs, with increased susceptibility to viral infections (see Candotti et al., this Perspective series, ref. 4).Stat4-and Stat6-deficient animals reveal a requirement for IL-12-or IL-4-mediated proliferation of T cells, respectively (see Decker et al., this series, ref. 5).The phenotypes of Stat5A and Stat5B individual knockouts reveal the importance of Stat5A in breast development and lactation and the importance of Stat5B in the development of sexually dimorphic patterns of gene expression within the liver.In addition to these phenotypes, Stat5A/5B double knockouts are abnormal in their T cell and B cell development.Because Stat3-deficient animals die early in embryogenesis, the role of this protein in a number of biological functions had to be determined in conditional knockouts.As discussed by Levy and Lee in this series (6), Stat3 is implicated in keratinocyte migration, T cell apoptosis, IL-10-mediated signaling in macrophages, and the induction of apoptosis in the involuting breast.Beyond these various roles in normal cellular and physiological processes, the Stat proteins are now known to participate in cellular transformation and oncogenesis.Here, I consider the evidence implicating these molecules, particularly Stats 1, 3, and 5, in tumor formation and progression.
The Yak1 protein kinase of Saccharomyces cerevisiae moderates thermotolerance and inhibits growth by an Sch9 protein kinase-independent mechanism. (1994)

The growth defect associated with the loss of yeast A kinase activity can be alleviated by the overexpression or deletion of two other kinases, Sch9 and Yak1, respectively. Using tests of epistasis, we have shown that Sch9 and Yak1 define separate signaling pathways and must, therefore, suppress the A kinase defect by different mechanisms. Nevertheless, the Yak1 kinase appears to regulate cellular processes that are under A kinase control. For example, acquisition of heat resistance is correlated with Yak1 kinase activity, such that YAK1-overexpressing cells are over 200-fold more resistant than isogenic yak1 strains. These results, for the first time, associate a phenotype, other than suppression of the A kinase growth defect, with the loss of Yak1 activity and argue a broader role for the Yak1 kinase in cell growth.
Microphone Array for Headset with Spatial Noise Suppressor (2005)

This paper presents a hybrid microphone array architecture used for processing the signals from a small microphone array that is used in a headset. The processing chain consists of fixed end-fire beamforming, adaptive spatial noise reduction and stationary noise suppression. The far-field design algorithm used for the fixed beamformer is adapted to the specifics of the headset by compensating for the directivity of the mouth and the sound diffraction around the head. The spatial noise reduction generalizes the suppression rule for optimal MMSE power noise reduction to multiple dimensions. The algorithm was tested with a headset that used a three element microphone array. It is computationally effective and provides up to 18 dB of ambient noise suppression. 1.
IMGT, the international ImMunoGeneTics database (1999)

IMGT, the international ImMunoGeneTics database (http://imgt.cnusc.fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Universit Montpellier II, CNRS, Montpellier, France (lefranc@ligm.igh.cnrs.fr). IMGT comprises three databases: LIGM-DB, a comprehensive database of Ig and TcR, MHC/HLA-DB, and PRIMER-DB (the last two in development); a tool, IMGT/DNAPLOT, developed for sequence analysis and alignments; and expertised data based on the IMGT scientific chart, the IMGT repertoire. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutic approaches (antibody engineering), genome diversity and genome evolution studies.
Stable transformation of soybean by electroporation and root formation from transformed callus (1987)

Soybean protoplasts from a number of commercially important cultivars have been genetically engineered by way of electroporation using chimeric genes coding for resistance to the aminoglycoside antibiotics kanamycin and G418. Effective electroporation conditions were determined by monitoring transient expression from aminoglycoside 3'-phosphotransferase II (APHII) expression plasmids. Electroporation of protoplasts with a chimeric APHII gene and subsequent selection on media supplemented with kanamycin resulted in the recovery of calli resistant to the antibiotic. Enzyme assays for APHII activity and Southern blot hybridization confirmed the expression of the foreign DNA and its stable integration into the soybean genome. Root formation was induced from transformed calli, and these roots maintained expression of the APHII gene.
Purification, composition, and physical properties of a thermal hysteresis "antifreeze" protein from larvae of the beetle Tenebrio molitor (1982)

Proteins which produce a thermal hysteresis (difference between the freezing and melting points) in aqueous solution are well-known for their antifreeze activity in polar marine fishes. Much less is known about the biology and biochemistry of similar antifreeze proteins found in certain insects. A thermal hysteresis protein was purified from cold acclimated larvae of the beetle, Tenebrio molitor, by using ethanol fractionation, DEAE ion-exchange chromatography, gel filtration, and high-pressure liquid chromatography. The purified protein had a molecular mass of 17 000 daltons and its N terminus was lysine. The amino acid composition of the antifreeze protein contained more hydrophilic amino acids than the fish antifreezes. This is consistent with the compositions of previously purified insect thermal hysteresis proteins. However, the percentage of hydrophilic amino acids in this Tenebrio antifreeze protein was considerably less than that of other insect thermal hysteresis proteins. The freezing point depressing activity of the Tenebrio antifreeze was less than that of fish proteins and glycoproteins at low protein concentrations but was greater at high protein concentrations.
Regulative development of the sea urchin embryo: Signalling cascades and morphogen gradients (1999)

Differentiation of sea urchin embryo ectoderm, endoderm and mesenchyme cells, whose anlagen are arrayed along the animal-vegetal axis, relies on both maternally regulated localized transcription factor activities and cell-cell signalling. Classic models proposed that fates are determined by opposing animal and vegetal morphogenetic gradients, whereas current models emphasize unidirectional and sequential vegetal-to-animal signalling cascades between adjacent blastomeres. Recent data support aspects of both models: the vegetal micromeres send one or more signals, which depend on a nuclear beta-catenin-dependent pathway, that both activate Notch signalling required for secondary mesenchyme fate and promote endoderm differentiation and gastrulation. This is opposed by an animalizing domain of BMP4 signals that regulates ectodermal cell fates and establishes the ectoderm-endoderm border.