gebhart/patrepeval huggingface dataset:
Phenotypic Expression of PCR-Generated Random Mutations in a Pseudomonas putida Gene after Its Introduction into an Acinetobacter Chromosome by Natural Transformation (1999)

Localized sets of random point mutations generated by PCR amplification can be transferred efficiently to the chromosome of Acinetobacter ADP1 (also known as strain BD413) by natural transformation. The technique does not require cloning of PCR fragments in plasmids: PCR-amplified DNA fragments are internalized by cells and directly incorporated into their genomes by homologous recombination. Previously such procedures for random mutagenesis could be applied only to Acinetobacter genes affording the selection of mutant phenotypes. Here we describe the construction of a vector and recipient that allow for mutagenesis, recovery, and expression of heterologous genes that may lack a positive selection. The plasmid carries an Acinetobacter chromosomal segment interrupted by a multiple cloning site next to a kanamycin resistance marker. The insertion of heterologous DNA into the multiple cloning site prepares the insert as a target for PCR mutagenesis. PCR amplifies the kanamycin resistance marker and a flanking region of Acinetobacter DNA along with the insert of heterologous DNA. Nucleotide sequence identity between the flanking regions and corresponding chromosomal segments in an engineered Acinetobacter recipient allows homologous recombination of the PCR-amplified DNA fragments into a specific chromosomal docking site from which they can be expressed. The recipient strain contains only a portion of the kanamycin resistance gene, so donor DNA containing both this gene and the mutagenized insert can be selected by demanding growth of recombinants in the presence of kanamycin. The effectiveness of the technique was demonstrated with the relatively GC-rich Pseudomonas putida xylE gene. After only one round of PCR amplification (35 cycles), donor DNA produced transformants of which up to 30% carried a defective xylE gene after growth at 37 degrees C. Of recombinant clones that failed to express xylE at 37 degrees C, about 10% expressed the gene when grown at 22 degrees C. The techniques described here could be adapted to prepare colonies with an altered function in any gene for which either a selection or a suitable phenotypic screen exists.
Properties of (trifluoromethanesulfonato)pentacarbonylmanganese(I) and -rhenium(I). Reactions in superacid solvents (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProperties of (trifluoromethanesulfonato)pentacarbonylmanganese(I) and -rhenium(I). Reactions in superacid solventsJay Nitschke, Steven P. Schmidt, and William C. TroglerCite this: Inorg. Chem. 1985, 24, 13, 1972–1978Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://pubs.acs.org/doi/10.1021/ic00207a005https://doi.org/10.1021/ic00207a005research-articleACS PublicationsRequest reuse permissionsArticle Views349Altmetric-Citations43LEARN 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
A role for glycine in the gating of plant NMDA‐like receptors (2003)

The amino acid glycine has a well-established role in signalling in the mammalian central nervous system. For example, glycine acts synergistically with the major excitatory neurotransmitter, glutamate, to regulate the influx of ions such as calcium, through N-methyl-d-aspartate (NMDA) receptors. Plants possess NMDA-like receptors, generically referred to as glutamate receptors (GLRs), named on the basis of their presumed ligand, glutamate. Previously, glycine has not been implicated in plant GLR activity or any other aspect of plant signalling. Using transgenic Arabidopsis seedlings expressing aequorin to monitor ligand-mediated changes in the cytosolic concentration of Ca2+ ([Ca2+]cyt), the data presented herein show that glutamate and glycine act synergistically to control ligand-mediated gating of calcium in plants. Glutamate and glycine synergism also regulates hypocotyl elongation. Transient increases in [Ca2+]cyt mediated by glutamate and glycine, as well as hypocotyl elongation, were inhibited by 6,7-dinitroquinoxaline-2,3 dione (DNQX), a competitive inhibitor of animal GLRs. Using a multiscale docking algorithm in combination with a molecular model of the ligand-binding domain of plant GLRs, evidence is provided indicating that glycine, and not glutamate, is likely to be the natural ligand for most plant GLR subunits. These findings uncover a hitherto unconsidered role for glycine signalling in plants, and suggest that the synergistic action of glutamate and glycine at NMDA-like receptors predates the divergence of plants and animals.
Surface Ligand Dynamics in Growth of Nanocrystals (2007)

Amine ligands were identified to bond on the surface of CdSe nanocrystals in a dynamic fashion under elevated temperatures in the reproducible growth domain of the specific designed growth reactions. The surface ligand dynamics was found to strongly depend on the growth temperature, the ligand concentration, and the ligand chain length. The strong chain-length dependence was originated from the interligand interactions in the ligand monolayer of a nanocrystal, provided fatty amines being weak ligands for CdSe nanocrystals. When the growth reaction was above the boiling point of an amine ligand, the surface ligand dynamics was violent, a quasi-gas-phase state, indicated by strong temperature-dependent and fast growth rates of the nanocrystals. Approximately below its boiling point, a significantly weak temperature dependence of the growth rate of the nanocrystals associated with the quasi-liquid state of the surface ligands was observed. A direct result of studying the surface ligand dynamics of this well-established nanocrystal system was the formation of high-quality CdSe nanocrystals under much reduced temperature, 150 degrees C, in comparison to the standard 250-350 degrees C temperature range. This was achieved by using fatty amines with a short hydrocarbon chain at a low ligand concentration in the solution. Preliminary results indicate that a similar temperature (160 degrees C) also worked for the growth of InP nanocrystals.
A new multichannel bladder stimulator (2002)

An integrated circuit intended for neural stimulation applications is described. The device has been designed and implemented in CMOS 3- mu m technology. The major advantages of the chip are its programmability and versatility. The intensity, format, and timing of the current pulses available at the eight channel outputs are serially and fully programmable. The different components of the device are controlled by a finite-state machine implemented by a PLA (programmable logic array). This implant can be placed inside the human body for long-term neural stimulation, and it can be used for many neurologic stimulation applications with minor modification of the implant.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antibiotic treatment of Crohn's disease: results of a multicentre, double blind, randomized, placebo‐controlled trial with rifaximin (2006)

Rifaximin 800 mg b.d. was superior to placebo in inducing clinical remission of active Crohn's disease. Although this difference was not statistically significant, the number of the failures in the placebo group was significantly higher than those who received rifaximin 800 mg b.d.
Crosstalk Between the PI3K/mTOR and MEK/ERK Pathways Involved in the Maintenance of Self-Renewal and Tumorigenicity of Glioblastoma Stem-Like Cells (2010)

The molecular signaling pathways orchestrating the biology of cancer stem-like cells (CSLCs), including glioblastoma, remain to be elucidated. We investigated in this study the role of the MEK/extracellular signal-regulated kinase (ERK) pathway in the control of self-renewal and tumorigenicity of glioblastoma CSLCs, particularly in relation to the PI3K/mTOR (mammalian target of rapamycin) pathway. Targeted inactivation of MEK alone using pharmacological inhibitors or siRNAs resulted in reduced sphere formation of both cell line- and patient-derived glioblastoma CSLCs, accompanied by their differentiation into neuronal and glial lineages. Interestingly, this effect of MEK inactivation was apparently augmented in the presence of NVP-BEZ235, a dual inhibitor of PI3K and mTOR. As a potential explanation for this observed synergy, we found that inactivation of either the MEK/ERK or PI3K/mTOR pathway triggered activation of the other, suggesting that there may be mutually inhibitory crosstalk between these two pathways. Significantly, inactivation of either pathway led to the reduced activation of p70S6K, and siRNA-mediated knockdown of p70S6K resulted in the activation of both pathways, which no longer maintained the cross-inhibitory relationship. Finally, combinational blockade of both pathways in glioblastoma CSLCs suppressed their tumorigenicity, whether transplanted subcutaneously or intracranially, more efficiently than blockade of either alone. Our findings suggest that there is p70S6K-mediated, cross-inhibitory regulation between the MEK/ERK and PI3K/mTOR pathways, in which each contribute to the maintenance of the self-renewal and tumorigenic capacity of glioblastoma CSLCs. Thus, combinational disruption of these pathways would be a rational and effective strategy in the treatment of glioblastoma.
Using SIMD registers and instructions to enable instruction-level parallelism in sorting algorithms (2007)

Most contemporary processors offer some version of Single Instruction Multiple Data (SIMD) machinery - vector registers and instructions to manipulate data stored in such registers. The central idea of this paper is to use these SIMD resources to improve the performance of the tail of recursive sorting algorithms. When the number of elements to be sorted reaches a set threshold, data is loaded into the vector registers, manipulated in-register, and the result stored back to memory. Three implementations of sorting with two different SIMD machineries - x86-64's SSE2 and G5's AltiVec - demonstrate that this idea delivers significant speed improvements. The improvements provided are orthogonal to the gains obtained through empirical search for a suitable sorting algorithm [11]. When integrated with the Dynamically Tuned Sorting Library (DTSL) this new code generation strategy reduces the time spent by DTSL up to 22% for moderately-sized arrays, with greater relative reductions for small arrays. Wall-clock performance of d-heaps is improved by up to 39% using a similar technique.
Inhibition of the Interaction of Urokinase-Type Plasminogen Activator (uPA) with Its Receptor (uPAR) by Synthetic Peptides (1997)

Focusing of the serine protease urokinase-type plasminogen activator (uPA) to the cell surface via interaction with its specific receptor (uPAR, CD87) is an important step for tumor cell invasion and metastasis. The ability of a synthetic peptide derived from the uPAR-binding region of uPA (comprising amino acids 16-32 of uPA; uPA(16-32)) to inhibit binding of fluorescently labeled uPA to uPAR on human promyeloid U937 cells was assessed by quantitative flow cytofluorometric analysis (FACS) and compared to the inhibitory capacities of other synthetic peptides known to interfere with uPA/uPAR-interaction. An about 3000-fold molar excess of uPA(16-32) resulted in 50% inhibition of pro-uPA binding to cell surface-associated uPAR. Using a solid-phase uPA-ligand binding assay employing recombinant soluble uPAR coated to microtiter plates, the minimal binding region of wild-type uPA was determined. The linear peptide uPA(19-31) and its more stable disulfide-bridged cyclic form (cyclo(19,31)uPA(19-31)) displayed uPAR-binding activity whereas other peptides such as uPA(18-30), uPA(20-32) or uPA(20-30) did not react with uPAR. Cyclic peptide derivatives of cyclo(19,31)uPA(19-31) in which certain amino acids were deleted and/or replaced by other amino acids as well as uPAR-derived wild-type peptides did also not inhibit uPA/uPAR-interaction. Therefore, the present investigations identified cyclo(19,31)uPA(19-31) as a potential lead structure for the development of uPA-peptide analogues to block uPA/uPAR-interaction.
Dynamic Topic Modeling for Monitoring Market Competition from Online Text and Image Data (2015)

We propose a dynamic topic model for monitoring temporal evolution of market competition by jointly leveraging tweets and their associated images. For a market of interest (e.g. luxury goods), we aim at automatically detecting the latent topics (e.g. bags, clothes, luxurious) that are competitively shared by multiple brands (e.g. Burberry, Prada, and Chanel), and tracking temporal evolution of the brands' stakes over the shared topics. One of key applications of our work is social media monitoring that can provide companies with temporal summaries of highly overlapped or discriminative topics with their major competitors. We design our model to correctly address three major challenges: multiview representation of text and images, modeling of competitiveness of multiple brands over shared topics, and tracking their temporal evolution. As far as we know, no previous model can satisfy all the three challenges. For evaluation, we analyze about 10 millions of tweets and 8 millions of associated images of the 23 brands in the two categories of luxury and beer. Through experiments, we show that the proposed approach is more successful than other candidate methods for the topic modeling of competition. We also quantitatively demonstrate the generalization power of the proposed method for three prediction tasks.
Reduction of Self-Quenching Effect in Organic Electrophosphorescence Emitting Devices via the Use of Sterically Hindered Spacers in Phosphorescence Molecules (2001)

The incorporation of a sterically demanding pinene moietyinto the ligand of a phosphorescent iridium complex prevents self-quenching by neighboring molecules, raising its photoluminescence quantum yield to 0.71 in solution. The compound is highly interesting as a dopant in electroluminescent devices, as shown for various concentrations of the complex in 4,4′-bis-(carbazolyl)-biphenyl (CBP) (see Figure).
RAC1: An Emerging Therapeutic Option for Targeting Cancer Angiogenesis and Metastasis (2013)

Angiogenesis and metastasis are well recognized as processes fundamental to the development of malignancy. Both processes involve the coordination of multiple cellular and chemical activities through myriad signaling networks, providing a mass of potential targets for therapeutic intervention. This review will focus on one master regulator of cell motility, RAC1, and the existing data with regard to its role in cell motility, including particular roles for tumor angiogenesis and invasion/metastasis. We also emphasize the preclinical investigations carried out with RAC1 inhibitors to evaluate the therapeutic potential of this target. Herein, we explore potential future directions as well as the challenges of targeting RAC1 in the treatment of cancer. Recent insights at the molecular and cellular levels are paving the way for a more directed and detailed approach to target mechanisms of RAC1 regulating angiogenesis and metastasis. Understanding these mechanisms may provide insight into RAC1 signaling components as alternative therapeutic targets for tumor angiogenesis and metastasis.
Regulated Expression and Subcellular Localization of Syndecan Heparan Sulfate Proteoglycans and the Syndecan-Binding Protein CASK/LIN-2 during Rat Brain Development (1999)

The syndecan family of cell surface heparan sulfate proteoglycans interacts via their cytoplasmic C-terminal tail with the PDZ domain of CASK/LIN-2, a membrane-associated guanylate kinase homolog. The syndecan-CASK interaction may be involved in intercellular signaling and/or cell adhesion. Here we show that syndecan-1 to syndecan-4 have distinctive mRNA distributions in adult rat brain by in situ hybridization, with syndecan-2 and -3 being the major syndecans expressed in neurons of the forebrain. At the protein level, syndecan-2 and -3 are differentially localized within neurons; syndecan-3 is concentrated in axons, whereas syndecan-2 is localized in synapses. The synaptic accumulation of syndecan-2 occurs late in synapse development. CASK is a cytoplasmic-binding partner for syndecans, and its subcellular distribution changes strikingly during development, shifting from a primarily axonal distribution in the first 2 postnatal weeks to a somatodendritic distribution in adult brain. This change in CASK distribution correlates temporally and spatially with the expression patterns of syndecan-3 and -2, consistent with the association of both of these syndecans with CASK in vivo. In support of this, we were able to coimmunoprecipitate a complex of CASK and syndecan-3 from brain extracts. Our results indicate that specific syndecans are differentially expressed in various cell types of the brain and are targeted to distinct subcellular compartments in neurons, where they may serve specialized functions. Moreover, CASK is appropriately expressed and localized to interact with both syndecan-2 and -3 in different compartments of the neuron throughout postnatal development.
Studies on the biosynthesis of cholesterol. 10. Mevalonic kinase and phosphomevalonic kinase from liver (1960)

After the discovery that mevalonic acid was a key intermediate in the biosynthesis of cholesterol (Tavormnina, Gibbs & Huff, 1956), it was shown that liver preparations (Popjak, Gosselin, Gore & Gould, 1958) as well as yeast extracts (Amdur,
Estrogen formation in human prostatic tissue from patients with and without benign prostatic hyperplasia (1986)

Prostatic tissue removed at the time of cystoprostatectomy was separated into periurethral and peripheral zones. Homogenized tissue was incubated with [1,2,6,7(3)H] androstenedione in the presence or absence of an aromatase inhibitor, 4-hydroxyandrostenedione (4-OHAD) and a 5 alpha-reductase inhibitor 4-MA (N,N-diethyl-4-methyl-3-oxo-4-aza-5 alpha-androstane 17 beta-carboxamide). Estrogen formation was determined by reverse isotope dilution of [3H] estrone and [3H] estradiol and crystallization to constant specific activity. Control incubations were carried out in parallel utilizing heated prostatic tissue. Total estrogens produced in the periurethral zone in patients with benign prostatic hyperplasia (BPH) was 223 fmol/mg protein/hr (SE +/- 57) compared to 102 fmol (SE +/- 17) in patients without BPH. Estrogen formation in the peripheral zone was 175 fmol (SE +/- 69) and 105 fmol (SE +/- 26) in patients with and without BPH, respectively. The prostatic aromatase exhibits Michaelis-Menton kinetics with an apparent Km of 90 nM. 4-OHAD inhibited aromatization in the prostatic tissue by 57-93%. Aromatization was also strongly inhibited by 4-MA, indicating that 4-MA is a potent aromatase as well as a 5 alpha-reductase inhibitor in this tissue. These results suggest that aromatization of androgens to estrogens in the human prostate proceeds at a substantial rate and that local estrogen formation could preexist and be a factor in the etiology of BPH and prostatic cancer.
ChemInform Abstract: (BaTiO3)m(Gd,Ce)3Cu2O7: A New Homologous Series of Layered Cuprates Containing Various Layers of Perovskite Units. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Regiospecific Synthesis of 1,4,5-Trisubstituted-1,2,3-triazole via One-Pot Reaction Promoted by Copper(I) Salt (2005)

A method for the regiospecific synthesis of 1,4,5-trisubstituted-1,2,3-triazole catalyzed by copper(I) iodide was developed. This is the first example of a regiospecific synthesis of 5-iodo-1,4-disubstituted-1,2,3-triazole, which can be further elaborated to a range of 1,4,5-trisubstituted-1,2,3-triazole derivatives.
Low temperature selectively inhibits fusion between pinocytic vesicles and lysosomes during heterophagy of 125I-asialofetuin by the perfused rat liver. (1980)

Galactose-terminating ligands are specifically recognized by mammalian hepatocytes, internalized, and degraded within lysosomes. We have studied the effects of temperature on this process using 125I-asialofetuin and the perfused rat liver. Uptake and catabolism of 125I-asialofetuin continued but were progressively slowed as the temperature decreased from 35 degrees C to 20 degrees C. At 20 degrees C, lysosomal degradation completely stopped. Results of subcellular fractionation experiments and in situ electron microscopic autoradiography revealed that fusion between pinocytic vesicles and lysosomes did not occur below 20 degrees C, despite the continued endocytosis of 125I-asialofetuin and movement of pinocytic vesicles into the lysosome-Golgi region of the cell. Below 10 degrees C, endocytosis essentially stopped. Inhibition of the fusion step was reversed upon rewarming the liver to physiological temperature. By examining the reversal process the half-time for fusion between pinocytic vesicles and lysosomes was determined to be 7 min. This is the slowest metabolic event involved in the catabolism of asialofetuin by the liver both in the perfused organ and in vivo.