gebhart/patrepeval huggingface dataset:
Comparison of the extracellular proteomes of <b><i>Escherichia coli</i></b> B and K‐12 strains during high cell density cultivation (2008)

Escherichia coli BL21 (DE3) and W3110 strains, belonging to the family B and K-12, respectively, have been most widely employed for recombinant protein production. During the excretory production of recombinant proteins by high cell density cultivation (HCDC) of these strains, other native E. coli proteins were also released. Thus, we analyzed the extracellular proteomes of E. coli BL21 (DE3) and W3110 during HCDC. E. coli BL21 (DE3) released more than twice the amount of protein compared with W3110 during HCDC. A total of 204 protein spots including 83 nonredundant proteins were unambiguously identified by 2-DE and MS. Of these, 32 proteins were conserved in the two strains, while 20 and 33 strain-specific proteins were identified for E. coli BL21 (DE3) and W3110, respectively. More than 70% of identified proteins were found to be of periplasmic origin. The outer membrane proteins, OmpA and OmpF, were most abundant. Two strains showed much different patterns in their released proteins. Also, cell density-dependent variations in the released proteins were observed in both strains. These findings summarized as reference proteome maps will be useful for studying protein release in further detail, and provide new strategies for enhanced excretory production of recombinant proteins.
Design of a Laser-Induced Breakdown Spectroscopy System for On-Line Quality Analysis of Pulverized Coal in Power Plants (2009)

It is vitally important for a power plant to determine the chemical composition of coal prior to combustion in order to obtain optimal boiler control. In this work, a fully software-controlled laser-induced breakdown spectroscopy (LIBS) system comprising a LIBS apparatus and sampling equipment has been designed for possible application to power plants for on-line quality analysis of pulverized coal. Special attention was given to the LIBS system, the data processing methods (especially the normalization with Bode Rule/DC Level) and the specific settings (the software-controlled triggering source, high-pressure gas cleaning device, sample-preparation module, sampling module, etc.), which gave the best direct measurement for C, H, Si, Na, Mg, Fe, Al, and Ti with measurement errors less than 10% for pulverized coal. Therefore, the apparatus is accurate enough to be applied to industries for on-line monitoring of pulverized coal. The method of proximate analysis was also introduced and the experimental error of A(ad) (Ash, 'ad' is an abbreviation for 'air dried') was shown in the range of 2.29 to 13.47%. The programmable logic controller (PLC) controlled on-line coal sampling equipment, which is designed based upon aerodynamics, and is capable of performing multipoint sampling and sample-preparation operation.
Harmonic/Percussive Sound Separation Based on Anisotropic Smoothness of Spectrograms (2014)

This paper describes a method to separate a monaural music signal into harmonic components e.g., a guitar and percussive components, e.g., a snare drum. Separation of these two components is a useful preprocessing for many music information retrieval applications, and in addition, it can be used as a new kind of music equalizer in itself, which enables a music listener to adjust the ratio of the volume of the guitar and the drum freely by themselves. Because of these potential applications, there have been many attempts to develop such a technique, especially in the last decade. However, some of the state-of-the-art techniques have a drawback that they are based on costly operations, such as the multiplications of large-sized matrix, Monte Carlo method, etc., which may constitute barriers to the practical use on some small computers such as smart phones. In this paper, an efficient method that does not depend on these costly operations is described. In formulating the methods, the authors basically assumed only the “anisotropic smoothness” of music spectrogram, which can be one of the minimalistic model that reflects the natures of these instruments. To be specific, the authors just assumed that harmonic instruments are smooth in time, while the percussive instruments are smooth in frequency on a music spectrogram. In this paper, on the basis of the assumption, source separation methods are formulated as optimization problems that optimize the “anisotropic smoothness” under some conditions. Because of the simplicity of the model, the derived algorithms are quite simple. Experimental results show that the methods were effective compared to a state-of-the-art technique, and the computation time was much shorter than an existing method; specifically, it can process a three-minute song in around 4-20 seconds on a laptop PC.
Structural and antigenic analysis of the nucleic acid-binding proteins of bovine and feline leukemia viruses (1983)

The nucleic acid-binding proteins of bovine leukemia virus (BLV) and feline leukemia virus (FeLV) were isolated in a high state of purity with chloroform-methanol extraction followed by reversed-phase liquid chromatography. Selective solubilization and purity of BLV p12 and FeLV p10 was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The compositions and molecular weights were determined by amino acid analysis. An abundance of lysine and arginine residues along with their size identifies both BLV p12 and FeLV p10 as small basic proteins similar to well-defined type C viral nucleoproteins. NH2-terminal degradation by the semiautomated Edman method provided the sequence of the first 40 amino acids for both proteins. The putative nucleic acid binding site found in several type C viral nucleoproteins was contained within this sequence, with the most homology centered around an eight-amino acid region involving seven identical residues and one substitution. Antisera were developed in rabbits, and specificity and titers were determined by electroblotting and immunoautoradiography. By this technique, an immunological cross-reaction was found between BLV p12 and FeLV p10. The shared antigenic determinant most likely exists in the highly conserved eight-amino acid region. Although this sequence is also highly conserved in the nucleic acid-binding proteins of murine leukemia viruses, the shared antigenic determinant is not found in these or any other type C viruses tested. It is suggested that substitution of arginine (BLV p12/FeLV p10) to lysine (murine leukemia virus p10) is sufficient to elicit a change in antibody specificity.
Studies on the Syntheses of Hydrogenated Quinolines and Isoquinolines as Analgesics. III (1955)

As a preliminary to the synthesis of 9-azamorphinan, 1-azoniabicyclo [3:3:1] nonane chloride was prepared by the condensation of β-(3, 4-dimethoxyphenyl) piperidine with formaldehyde and hydrochloric acid. Attempt to obtain the same compound by the formylation of β-(3, 4-dimethoxyphenyl) piperidine followed by cyclization with phosphoryl chloride ended fruitless, the product being a resinous matter. In short, the Bischler-Napieralski reaction of the acyl compound of phenethylamine, in which the amine nitrogen and the carbon in β-position are bonded with several numbers of methylene groups, is extremely difficult and requires further study.
Solar Magnetism and the Activity Telescope at HSOS (2007)

A new solar telescope system is described, which has been operating at Huairou Solar Observing Station (HSOS), National Astronomical Observatories, Chinese Academy of Sciences (CAS), since the end of 2005. This instrument, the Solar Magnetism and Activity Telescope (SMAT), comprises two telescopes which respectively make measurements of full solar disk vector magnetic field and Hα observation. The core of the full solar disk video vector magnetograph is a birefringent filter with 0.1Å bandpass, installed in the tele-centric optical system of the telescope. We present some preliminary observational results of the full solar disk vector magnetograms and Hα filtergrams obtained with this telescope system.
Plasmene Metasurface Absorbers: Electromagnetic Hot Spots and Hot Carriers (2019)

Light–matter interactions are extremely important, as they sustain life on Earth and can be tailored for diverse applications in areas such as solar energy conversion, chemical sensing, and information storage. One key process of these interactions is the absorption of photons. We demonstrate a novel material capable of absorbing up to 98% of incident visible light. The material comprises a thin sheet of a tightly packed two-dimensional lattice of metal nanoparticles, called plasmene, supported by a thin (subwavelength) dielectric film deposited on top of a mirror. We demonstrate how the resulting metasurface absorbers are useful in surface-enhanced spectroscopy and in the generation of plasmonic hot carriers. These structures hold great promise for applications in structural color, sensing, and photocatalysis.
The Stereoisomerism of Cyclohexane Derivatives. (1954)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTThe Stereoisomerism of Cyclohexane Derivatives.Harold D. OrloffCite this: Chem. Rev. 1954, 54, 3, 347–447Publication Date (Print):June 1, 1954Publication History Published online1 May 2002Published inissue 1 June 1954https://doi.org/10.1021/cr60169a001RIGHTS & PERMISSIONSArticle Views870Altmetric-Citations53LEARN 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 InReddit PDF (5 MB) Get e-Alerts Get e-Alerts
<italic>Helicobacter pylori eradication</italic>: efficacy and side effect profile of a combination of omeprazole, amoxycillin and metronidazole compared with four alternative regimens (1993)

We evaluated eradication of Helicobacter pylori infection in 263 patients by a new 14-day regimen of omeprazole 40 mg mane (a gastric secretory inhibitor) plus two antibiotics: amoxycillin 500 mg three-times daily (tds) plus metronidazole 400 mg tds. The comparative groups included updated results of our previous work with a 14-day course of either standard triple therapy (STT, colloidal bismuth subcitrate 120 mg four times daily (qds) plus tetracycline 500 mg qds and metronidazole 400 mg tds), omeprazole 40 mg once daily plus amoxycillin 500 mg tds (OA), or two modified triple therapy: either Borody's (BTT) of all three components (colloidal bismuth subcitrate 120 mg, tetracycline 500 mg, metronidazole 200 mg) qds instead of tds, or Logan's (LTT) seven-day therapeutic regimen of colloidal bismuth subcitrate 120 mg qds, amoxycillin 500 mg qds and, for the last three days, metronidazole 400 mg five times daily. Omeprazole/amoxycillin/metronidazole (OAM) therapy was better tolerated than STT (course completion 98.1% vs. 81.4%, p < 0.001). H. pylori was eradicated by OAM therapy in 53/55 (96.4%) patients with metronidazole-sensitive organisms and in 54/72 (75.0%) with metronidazole-resistant isolates (p < 0.01). The respective corresponding rates for STT and OA therapy were 20/22 (90.9%) and 14/29 (48.3%), (metronidazole-sensitive organisms) and 7/21 (33.3%) and 15/31 (48.4%) (infections resistant to metronidazole). BTT and LTT were also better tolerated than STT. The eradication rate for BTT was 23/26 (88.5%) but that for LTT, the best tolerated of the five treatment regimens, was only 19/28 (67.9%) when pretreatment isolates were metronidazole-sensitive.(ABSTRACT TRUNCATED AT 250 WORDS)
Human Bak Induces Cell Death in <i>Schizosaccharomyces pombe</i> with Morphological Changes Similar to Those with Apoptosis in Mammalian Cells (1997)

Apoptosis as a form of programmed cell death (PCD) in multicellular organisms is a well-established genetically controlled process that leads to elimination of unnecessary or damaged cells. Recently, PCD has also been described for unicellular organisms as a process for the socially advantageous regulation of cell survival. The human Bcl-2 family member Bak induces apoptosis in mammalian cells which is counteracted by the Bcl-x(L) protein. We show that Bak also kills the unicellular fission yeast Schizosaccharomyces pombe and that this is inhibited by coexpression of human Bcl-x(L). Moreover, the same critical BH3 domain of Bak that is required for induction of apoptosis in mammalian cells is also required for inducing death in yeast. This suggests that Bak kills mammalian and yeast cells by similar mechanisms. The phenotype of the Bak-induced death in yeast involves condensation and fragmentation of the chromatin as well as dissolution of the nuclear envelope, all of which are features of mammalian apoptosis. These data suggest that the evolutionarily conserved metazoan PCD pathway is also present in unicellular yeast.
Pentoxifylline treatment and penile calcifications in men with Peyronie's disease (2010)

This retrospective cohort study from a single clinical practice enrolled patients with evidence of calcified Peyronie's disease (PD) plaques detected on penile ultrasound at the time of initial presentation. The primary objective was to describe the effect of pentoxifylline (PTX) treatment on subtunical calcifications in men with PD. A PD-specific questionnaire was administered and sonographic evaluations were performed at baseline and follow-up visits. Descriptive statistics and χ(2) analysis were used to characterize the effect of PTX on calcified tunical plaques. In all, 71 men (mean age: 51.9 years) with PD and sonographic evidence of calcification were identified. Of them, 62 of these men were treated with PTX for a mean duration of 1 year, and nine with vitamin E or no treatment. Improvement or stabilization in calcium burden at follow-up was noted in 57 (91.9%) of men treated with PTX versus four (44.4%) of those not treated with PTX (P<0.001). PTX users were much less likely to have a subjective worsening of their clinical condition (25.0% versus 78.3%, P=0.002). Treatment with PTX appeared to stabilize or reduce calcium content in PD plaques. A randomized controlled trial is warranted to further explore this effect.
The stem rust resistance gene <i>Rpg5</i> encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains (2008)

We isolated the barley stem rust resistance genes Rpg5 and rpg4 by map-based cloning. These genes are colocalized on a 70-kb genomic region that was delimited by recombination. The Rpg5 gene consists of an unusual structure encoding three typical plant disease resistance protein domains: nucleotide-binding site, leucine-rich repeat, and serine threonine protein kinase. The predicted RPG5 protein has two putative transmembrane sites possibly involved in membrane binding. The gene is expressed at low but detectable levels. Posttranscriptional gene silencing using VIGS resulted in a compatible reaction with a normally incompatible stem rust pathogen. Allele sequencing also validated the candidate Rpg5 gene. Allele and recombinant sequencing suggested that the probable rpg4 gene encoded an actin depolymerizing factor-like protein. Involvement of actin depolymerizing factor genes in nonhost resistance has been documented, but discovery of their role in gene-for-gene interaction would be novel and needs to be further substantiated.
Intrinsic functional connectivity pattern based brain parcellation using normalized cut (2012)

In imaging data based brain network analysis, a necessary precursor for constructing meaningful brain networks is to identify functionally homogeneous regions of interest (ROIs) for defining network nodes. For parcellating the brain based on resting state fMRI data, normalized cut is one widely used clustering algorithm which groups voxels according to the similarity of functional signals. Due to low signal to noise ratio (SNR) of resting state fMRI signals, spatial constraint is often applied to functional similarity measures to generate smooth parcellation. However, improper spatial constraint might alter the intrinsic functional connectivity pattern, thus yielding biased parcellation results. To achieve reliable and least biased parcellation of the brain, we propose an optimization method for the spatial constraint to functional similarity measures in normalized cut based brain parcellation. Particularly, we first identify the space of all possible spatial constraints that are able to generate smooth parcellation, then find the spatial constraint that leads to the brain parcellation least biased from the intrinsic function pattern based parcellation, measured by the minimal Ncut value calculated based on the functional similarity measure of original functional signals. The proposed method has been applied to the parcellation of medial superior frontal cortex for 20 subjects based on their resting state fMRI data. The experiment results indicate that our method can generate meaningful parcellation results, consistent with existing functional anatomy knowledge.
New poly(ester-carbonate) multi-block copolymers based on poly(lactic-glycolic acid) and poly(-caprolactone) segments (1998)

A new family of multi-block copolymers having the structure of poly(ester-carbonate)s was obtained by a chain-extension reaction involving poly(lactic-glycolic acid) oligomers (PLGA) and oligomeric α,ω-bishydroxy-terminated poly(ϵ-caprolactone)s (PCDT). The latter were first transformed into α,ω-bis(chloroformate)s, which were subsequently condensed in the presence of amines with both the hydroxylic and the carboxylic end-groups of PLGA oligomers. Several samples differing in the length of the PCDT segments and in the composition of the PLGA segments were prepared and characterized for their physico-chemical properties. All of them had high molecular weight, good solubility in organic solvents, and modest swellability in aqueous media. As regards their thermal behaviour, some samples showed evidence of the presence of a crystalline phase. Since these products are potentially useful as bioerodible materials in drug delivery systems, some preliminary results on their degradation behaviour under conditions mimicking those found in biological fluids are reported.
On switched-current Δ-Σ A/D converters (2002)

Switched-current oversampling /spl Delta/-/spl Sigma/ A/D converters are the ideal choice for mixed analog/digital design due to their complete compatibility with digital CMOS process and high tolerance to process variation. This paper discusses all the aspects of switched-current oversampling A/D converters, including structures, circuits, and practical issues. Three different modulator structures and six different types of switched-current circuits were used in our design and implementation with an emphasis on low-voltage operation. Four 3.3-V oversampling A/D converters were implemented and measured, and another four 3.3-V and one 1.2-V oversampling A/D converters were also implemented but are yet to be measured.
<i>Pseudomonas aeruginosa</i> acid phosphatase Activation by divalent cations and inhibition by aluminium ion (1992)

In Pseudomonas aeruginosa, the effect of different cations on the acid phosphatase activity was studied in order to acquire more information related to a previously proposed mechanism, involving the coordinated action of this enzyme with phospholipase C. Although the natural substrate of this enzyme is phosphorylcholine, in order to avoid the possible interaction of its positive charge and those of the different cations with the enzyme molecule, the artificial substrate p-nitrophenylphosphate was utilized. Kinetic studies of the activation of acid phosphatase (phosphorylcholine phosphatase) mediated by divalent cations Mg2+, Zn2+ and Cu2+ revealed that all these ions bind to the enzyme in a compulsory order (ordered bireactant system). The Km values obtained for p-NPP in the presence of Mg2+, Zn2+ and Cu2+ were 1.4 mM, 1.0 mM and 3.5 mM, respectively. The KA values for the same ions were 1.25 mM, 0.05 mM and 0.03 mM, respectively. The Vmax obtained in the presence of Cu2+ was about twofold higher than that obtained in the presence of Mg2+ or Zn2+. The inhibition observed with Al3+ seems to be a multi-site inhibition. The K'app and n values, from the Hill plot, were about 0.25 mM and 4.0 mM, respectively, which were independent of the metal ion utilized as activator. It is proposed that the acid phosphatase may exert its action under physiological conditions, depending on the availability of either one of these metal ions.
<i>Xanthomonas</i> T3S Effector XopN Suppresses PAMP-Triggered Immunity and Interacts with a Tomato Atypical Receptor-Like Kinase and TFT1 (2009)

XopN is a virulence factor from Xanthomonas campestris pathovar vesicatoria (Xcv) that is translocated into tomato (Solanum lycopersicum) leaf cells by the pathogen's type III secretion system. Xcv DeltaxopN mutants are impaired in growth and have reduced ability to elicit disease symptoms in susceptible tomato leaves. We show that XopN action in planta reduced pathogen-associated molecular pattern (PAMP)-induced gene expression and callose deposition in host tissue, indicating that XopN suppresses PAMP-triggered immune responses during Xcv infection. XopN is predicted to have irregular, alpha-helical repeats, suggesting multiple protein-protein interactions in planta. Consistent with this prediction, XopN interacted with the cytosolic domain of a Tomato Atypical Receptor-Like Kinase1 (TARK1) and four Tomato Fourteen-Three-Three isoforms (TFT1, TFT3, TFT5, and TFT6) in yeast. XopN/TARK1 and XopN/TFT1 interactions were confirmed in planta by bimolecular fluorescence complementation and pull-down analysis. Xcv DeltaxopN virulence defects were partially suppressed in transgenic tomato leaves with reduced TARK1 mRNA levels, indicating that TARK1 plays an important role in the outcome of Xcv-tomato interactions. These data provide the basis for a model in which XopN binds to TARK1 to interfere with TARK1-dependent signaling events triggered in response to Xcv infection.
Rapid solid-phase peptide synthesis using thermal and controlled microwave irradiation (2006)

A rapid and efficient microwave-assisted solid-phase synthesis method is described for the preparation of the nonapeptide WDTVRISFK, using conventional Fmoc/Bu(t) orthogonal protection strategy. The synthesis protocol is based on the use of cycles of pulsed microwave irradiation with intermittent cooling of the reaction during the removal of the Fmoc protecting group and during the coupling. The desired nonapeptide was obtained in highest yield and purity by employing MicroKan technology. The chemical reactions were carried out in a single-mode microwave reactor, equipped with a fiber-optic probe to monitor the reaction temperature continuously.
Cytochrome C Oxidase in Alzheimer's Disease Brain (1995)

Cytochrome c oxidase (COX) is deficient in both peripheral tissue and brain of Alzheimer's disease (AD) patients and may be of pathogenic significance in AD. We purified COX from AD brains (n = 3) and control brains (n = 3) and characterized the enzyme kinetically and spectrally. Purified AD brain COX displayed anomalous kinetic behavior compared with control brain COX in that the low Km binding site was kinetically unidentifiable. For purposes of comparison, we purified COX from a standard beef heart preparation and found normal kinetic behavior. AD brain COX may be structurally abnormal and may make an important contribution to the bioenergetic defect seen in AD.