gebhart/patrepeval huggingface dataset:
Alielic exchange in Pseudomonas aeruginosa using novel ColE1‐type vectors and a family of cassettes containing a portable oriT and the counter‐selectable Bacillus subtilis sacB marker (1992)

An improved method for allele replacement in Pseudomonas aeruginosa was developed. The two main ingredients of the method are: (i) novel ColE1-type cloning vectors derived from pBR322 and pUC19; and (ii) a family of cassettes containing a portable oriT, the sacB gene from Bacillus subtilis as a counter-selectable marker, and a chloramphenicol-resistance gene allowing positive selection of both oriT and sacB. Introduction of plasmid-borne DNA into the chromosome was achieved in several steps. The DNA to be exchanged was first cloned into the new ColE1-type vectors. After insertion of the oriT and sacB sequences, these plasmid were conjugally transferred into P. aeruginosa and plasmid integrants were selected. Plating on sucrose-containing medium allowed positive selection for both plasmid excision and curing since Pseudomonas aeruginosa strains containing the sacB gene in single- or multiple copy were highly sensitive to 5% sucrose in rich medium. This procedure was successfully used to introduce an agmR mutation into P. aeruginosa wild-type strain PAO1 and should allow the exchange of any DNA segment into any non-essential regions of the P. aeruginosa chromosome.
Expression of intercellular adhesion molecule (ICAM)-1 mRNA and protein is enhanced in endometriosis versus endometrial stromal cells in culture (1998)

The relationship between the immune and the endometrial systems has been recently suggested to be critical to the development of endometriosis. We previously showed that one of the molecules involved in the complex events that allow this interaction is the adhesion molecule intercellular adhesion molecule (ICAM)-1. This study was designed to evaluate whether differences in ICAM-1 mRNA and protein expression might exist between eutopic endometrial cells and ectopic cells derived from endometriomas. Stromal cells were dispersed from samples of endometrium and ovarian endometriomas biopsied synchronously from 24 patients with endometriosis. We established that the relative expression of ICAM transcript was significantly higher in ectopic cells than that found in cultures derived from endometrial samples. Moreover, ectopic cells demonstrated a significant overexpression of ICAM-1 protein in both its cell-bound and soluble form (sICAM-1) (P < 0.05). Interestingly, endometrial secretion of sICAM-1 was shown to vary during the menstrual cycle as proliferative phase samples released significantly higher concentrations of the soluble protein compared to the secretory phase. In contrast, this cycle-dependent pattern was absent in stromal cells derived from endometriomas. Moreover, interleukin (IL-1beta) was able to increase sICAM-1 shedding from endometrial cells in a concentration-dependent manner and this IL-1beta-mediated induction could be slightly enhanced by oestradiol. As sICAM-1 is able to interfere with ICAM-1-mediated immune functions, the release of higher concentrations from ectopic samples may be the mechanism by which ectopic endometrial cells escape immunosurveillance.
Excessive Intake of Zinc Impairs Immune Responses (1984)

The effect of administration of large amounts of zinc on immune response and serum lipoproteins was examined. Eleven healthy adult men ingested 150 mg of elemental zinc twice a day for six weeks. This was associated with a reduction in lymphocyte stimulation response to phytohemagglutinin as well as chemotaxis and phagocytosis of bacteria by polymorphonuclear leukocytes. Serum high-density lipoprotein concentration decreased significantly and low-density lipoprotein level increased slightly. The common food fad of zinc supplementation with resultant excessive intake could have deleterious effects in healthy persons.
Yersinia pestis infection in three dogs (1995)

Yersinia pestis infection was diagnosed in 3 dogs. Clinical signs included lethargy (3 dogs), pyrexia (2 dogs), and a purulent skin lesion in the cervical region (2 dogs). Yersinia pestis infection is a potentially fatal zoonotic disease of human beings. Human cases have resulted from contact with infected domestic cats; however, the risk of human infection from contact with infected domestic dogs is unknown. Dogs frequently are exposed to Y pestis in areas in which there are plague epizootics; however, clinical illness in dogs is rare. In the western United States, where Yersinia pestis is endemic, plague should be considered in the differential diagnosis when examining dogs with nonspecific fever and lethargy.
Immunochemical and amino-terminal sequence comparison of two cytoadhesins indicates they contain similar or identical beta subunits and distinct alpha subunits. (1987)

Platelet membrane glycoprotein (GP) IIb-IIIa is functionally and antigenically related to proteins present on many cell types, suggesting that it is a member of the proposed cytoadhesin family of membrane proteins. We have compared the purified tissue vitronectin receptor (VnR) with GP IIb-IIIa. Anti-VnR immunoprecipitated GP IIb-IIIa and a related endothelial cell protein. In immunoblots, GP IIIa reacted with anti-VnR and the beta subunit of the VnR reacted with poly and monoclonal anti-GP IIIa. In contrast, the alpha subunit of the VnR failed to react either with a polyclonal anti-GP IIb or with monoclonal anti-GP IIb. Furthermore, the amino-terminal sequence of GP IIIa and the beta subunit of VnR were identical at determined residues while the alpha subunit and the GP IIb were different, but showed 33% identity. These data indicate the identity or close homology of GP IIIa and the beta subunit of the VnR. In contrast, the alpha subunit and GP IIb are distinct polypeptides which may be homologous. Since GP IIb-IIIa and the VnR differ in ligand recognition specificity, the data also suggest that this specificity may be governed by the alpha subunit of cytoadhesins.
Uptake of 2-Oxoglutarate in Synechococcus Strains Transformed with the Escherichia coli kgtP Gene (2000)

A number of cyanobacteria from different taxonomic groups exhibited very low levels of uptake of 2-[U-(14)C]oxoglutarate. Synechococcus sp. strain PCC 7942 was transformed with DNA constructs carrying the Escherichia coli kgtP gene encoding a 2-oxoglutarate permease and a kanamycin resistance gene cassette. The Synechococcus sp. strains bearing the kgtP gene incorporated 2-oxoglutarate into the cells through an active transport process. About 75% of the radioactivity from the 2-[U-(14)C]oxoglutarate taken up that was recovered in soluble metabolites was found as glutamate and glutamine. 2-Oxoglutarate was, however, detrimental to the growth of a Synechococcus sp. strain bearing the kgtP gene.
Synthetic Design for Combinatorial Chemistry. Solution and Polymer-Supported Synthesis of Polycyclic Lactams by Intramolecular Cyclization of Azomethine Ylides (1997)

The rapidly expanding field of combinatorial chemistry has stimulated the development of new methods and synthetic strategies for assembly of compound libraries. We propose four criteria that are desirable for synthetic routes to such libraries: (1) the sequence involves a small number of steps; (2) no more than one variable is introduced in any step; (3) starting materials are readily obtained with a diverse selection of substituents, and (4) cyclic, nonoligomeric structures represent the most interesting targets. Guided by these criteria, we have explored an intramolecular version of the azomethine ylide cycloaddition reaction which utilizes readily available amino acids, aldehydes, and 2° amines as inputs. We prepared a number of cycloadducts in solution to optimize conditions and examine the scope of the process and to identify a synthetic strategy that would be amenable to solid-phase synthesis of these compounds. Transfer of the sequence to solid phase was demonstrated by the synthesis of a number of representative compounds, indicating that the chemistry is suitable for construction of a combinatorial library.
EVH1 domains: structure, function and interactions (2001)

Drosophila enabled/vasodilator-stimulated phosphoprotein homology 1 (EVH1) domains are 115 residue protein-protein interaction modules which provide essential links for their host proteins to various signal transduction pathways. Many EVH1-containing proteins are associated closely with actin-based structures and are involved in re-organization of the actin cytoskeleton. EVH1 domains are also present in proteins enriched in neuronal tissue, thus implicating them as potential mediators of synaptic plasticity, linking them to memory formation and learning. Like Src homology 3, WW and GYF domains and profilin, EVH1 domains recognize and bind specific proline-rich sequences (PRSs). The binding is of low affinity, but tightly regulated by the high specificity encoded into residues in the protein:peptide interface. In general, a small (3-6 residue) 'core' PRS in the target protein binds a 'recognition pocket' on the domain surface. Further affinity- and specificity-increasing interactions are then formed between additional domain epitopes and peptide 'core-flanking' residues. The three-dimensional structures of EVH1:peptide complexes now reveal, in great detail, some of the most important features of these interactions and allow us to better understand the origins of specificity, ligand orientation and sequence degeneracy of target peptides, in low affinity signalling complexes.
Formation of Thiolate and Phosphonate Adlayers on Indium−Tin Oxide:  Optical and Electronic Characterization (2002)

Variable angle reflectance Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy were used to investigate adlayers on indium−tin oxide (ITO) and fluorine-doped tin oxide surfaces. A close-packed, ordered adlayer was observed to form on both surfaces by 1-hexadecanethiol through thiolate−indium or thiolate−tin bonding on the two surfaces, respectively. Additionally, a close-packed, ordered adlayer of 12-phosphonododecanoic acid was observed to form on ITO through a phosphonate−indium bonding interaction. The chain length dependence of adlayer formation was studied using alkane thiols of varying chain lengths, and the enthalpic factors affecting adlayer formation were modeled using density functional theory calculations along with periodic boundary conditions.
BASIC GUIDELINES FOR GROUNDWATER MODELLING STUDIES (2003)

ABSTRACT Groundwater flow modelling studies are required to resolve groundwater and catchment issues. A model, no matter how sophisticated, will never describe the groundwater system under investigation without deviation of model simulations from the actual physical processes. As a consequence, in applying a numerical model to a field study, the model user should always understand the implications of simplifying assumptions. This paper addresses groundwater modelling concepts and outlines the approach for commissioning and understanding groundwater modelling studies. It will encourage best practice and help avoid potential problems.
A simplified model and optimal design of a multiwavelength backward-pumped fiber Raman amplifier (2001)

A simplified model to calculate the small-signal optical gain and noise figure of a multiwavelength backward-pumped fiber Raman amplifier under the triangle Raman profile approximation is developed for the first time. The application of the developed model in pump optimization design for flattening the gain spectrum profile is also discussed.
Low complexity data detection using fast Fourier transform decomposition of channel correlation matrix (2002)

This paper presents an efficient FFT based channel-equalization method for data detection. The data detection method is applicable to multiuser detection in the downlink, and single user detection in the uplink. It can operate for chip rate sampling as well as higher sampling rates. The FFT implementation is enabled by approximating the channel correlation matrix by a right circulant matrix. Furthermore, the circulant matrix approximation is optimized via a simple permutation procedure. The solution offers very low complexity relative to other receivers. For instance, for twelve codes with spreading factor 16 each, the complexity of the proposed solution is about 25% of the complexity of the approximate Cholesky based joint detector. The proposed FFT based solution significantly outperforms the matched filter (MF) and is comparable in performance to the approximate Cholesky based joint detector.
Recessive Symptomatic Focal Epilepsy and Mutant Contactin-Associated Protein-like 2 (2006)

Contactin-associated protein-like 2 (CASPR2) is encoded by CNTNAP2 and clusters voltage-gated potassium channels (K(v)1.1) at the nodes of Ranvier. We report a homozygous mutation of CNTNAP2 in Old Order Amish children with cortical dysplasia, focal epilepsy, relative macrocephaly, and diminished deep-tendon reflexes. Intractable focal seizures began in early childhood, after which language regression, hyperactivity, impulsive and aggressive behavior, and mental retardation developed in all children. Resective surgery did not prevent the recurrence of seizures. Temporal-lobe specimens showed evidence of abnormalities of neuronal migration and structure, widespread astrogliosis, and reduced expression of CASPR2.
A Discriminative Convolutional Neural Network with Context-aware Attention (2020)

Feature representation and feature extraction are two crucial procedures in text mining. Convolutional Neural Networks (CNN) have shown overwhelming success for text-mining tasks, since they are capable of efficiently extracting n -gram features from source data. However, vanilla CNN has its own weaknesses on feature representation and feature extraction. A certain amount of filters in CNN are inevitably duplicate and thus hinder to discriminatively represent a given text. In addition, most existing CNN models extract features in a fixed way (i.e., max pooling) that either limit the CNN to local optimum nor without considering the relation between all features, thereby unable to learn a contextual n -gram features adaptively. In this article, we propose a discriminative CNN with context-aware attention to solve the challenges of vanilla CNN. Specifically, our model mainly encourages discrimination across different filters via maximizing their earth mover distances and estimates the salience of feature candidates by considering the relation between context features. We validate carefully our findings against baselines on five benchmark datasets of classification and two datasets of summarization. The results of the experiments verify the competitive performance of our proposed model.
Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps (2001)

The molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets.
Subtly Modulating Glycogen Synthase Kinase 3 β: Allosteric Inhibitor Development and Their Potential for the Treatment of Chronic Diseases (2017)

Glycogen synthase kinase 3 β (GSK-3β) is a central target in several unmet diseases. To increase the specificity of GSK-3β inhibitors in chronic treatments, we developed small molecules allowing subtle modulation of GSK-3β activity. Design synthesis, structure-activity relationships, and binding mode of quinoline-3-carbohydrazide derivatives as allosteric modulators of GSK-3β are presented here. Furthermore, we show how allosteric binders may overcome the β-catenin side effects associated with strong GSK-3β inhibition. The therapeutic potential of some of these modulators has been tested in human samples from patients with congenital myotonic dystrophy type 1 (CDM1) and spinal muscular atrophy (SMA) patients. We found that compound 53 improves delayed myogenesis in CDM1 myoblasts, while compounds 1 and 53 have neuroprotective properties in SMA-derived cells. These findings suggest that the allosteric modulators of GSK-3β may be used for future development of drugs for DM1, SMA, and other chronic diseases where GSK-3β inhibition exhibits therapeutic effects.
Individually Suspended Single-Walled Carbon Nanotubes in Various Surfactants (2003)

Individual single-walled carbon nanotubes (SWNTs) have been suspended in aqueous media using various anionic, cationic, nonionic surfactants and polymers. The surfactants are compared with respect to their ability to suspend individual SWNTs and the quality of the absorption and fluorescence spectra. For the ionic surfactants, sodium dodecylbenzene sulfonate (SDBS) gives the most well resolved spectral features. For the nonionic systems, surfactants with higher molecular weight suspend more SWNT material and have more pronounced spectral features.
Cannabidiol: Pharmacology and potential therapeutic role in epilepsy and other neuropsychiatric disorders (2014)

To present a summary of current scientific evidence about the cannabinoid, cannabidiol (CBD) with regard to its relevance to epilepsy and other selected neuropsychiatric disorders. We summarize the presentations from a conference in which invited participants reviewed relevant aspects of the physiology, mechanisms of action, pharmacology, and data from studies with animal models and human subjects. Cannabis has been used to treat disease since ancient times. Δ(9) -Tetrahydrocannabinol (Δ(9) -THC) is the major psychoactive ingredient and CBD is the major nonpsychoactive ingredient in cannabis. Cannabis and Δ(9) -THC are anticonvulsant in most animal models but can be proconvulsant in some healthy animals. The psychotropic effects of Δ(9) -THC limit tolerability. CBD is anticonvulsant in many acute animal models, but there are limited data in chronic models. The antiepileptic mechanisms of CBD are not known, but may include effects on the equilibrative nucleoside transporter; the orphan G-protein-coupled receptor GPR55; the transient receptor potential of vanilloid type-1 channel; the 5-HT1a receptor; and the α3 and α1 glycine receptors. CBD has neuroprotective and antiinflammatory effects, and it appears to be well tolerated in humans, but small and methodologically limited studies of CBD in human epilepsy have been inconclusive. More recent anecdotal reports of high-ratio CBD:Δ(9) -THC medical marijuana have claimed efficacy, but studies were not controlled. CBD bears investigation in epilepsy and other neuropsychiatric disorders, including anxiety, schizophrenia, addiction, and neonatal hypoxic-ischemic encephalopathy. However, we lack data from well-powered double-blind randomized, controlled studies on the efficacy of pure CBD for any disorder. Initial dose-tolerability and double-blind randomized, controlled studies focusing on target intractable epilepsy populations such as patients with Dravet and Lennox-Gastaut syndromes are being planned. Trials in other treatment-resistant epilepsies may also be warranted. A PowerPoint slide summarizing this article is available for download in the Supporting Information section here.
Crystal structures and magnetic behavior of two novel copper(II) halide chains. (C7H10N)4Cu5Cl14 and (C5H14N)4Cu5Cl14: multiple copper(II) halide coordination geometries (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal structures and magnetic behavior of two novel copper(II) halide chains. (C7H10N)4Cu5Cl14 and (C5H14N)4Cu5Cl14: multiple copper(II) halide coordination geometriesMarcus R. Bond, Roger D. Willett, and Gerald V. RubenackerCite this: Inorg. Chem. 1990, 29, 15, 2713–2720Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/ic00340a004https://doi.org/10.1021/ic00340a004research-articleACS PublicationsRequest reuse permissionsArticle Views195Altmetric-Citations27LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Synthesis and anticancer activity of nordihydroguaiaretic acid (NDGA) and analogues. (2001)

Nordihydroguaiaretic acid (NDGA) 1 is a constituent of the creosote bush Larrea divaricata and is well known to be a selective inhibitor of lipoxygenases. NDGA can also inhibit the platelet derived growth factor receptor and the protein kinase C intracellular signalling family, which both play an important role in proliferation and survival of cancers. Moreover, NDGA induces apoptosis in tumour xenografts. Although it is likely to have several targets of action, NDGA is well tolerated in animals. These encouraging results have prompted interest in the compound for clinical study. However, high concentrations of NDGA are required for efficacy and more potent analogues are required. We have synthesized five analogues of NDGA with different lengths of carbon bridge between the two catechol moieties in order to establish the spacing required for optimum anticancer effect and to compare their activities with NDGA. In order to ascertain if the catechol moieties are essential for anticancer activity, we prepared five analogues of NDGA containing only one hydroxyl group on each aromatic ring. NDGA 1, its racemic form 2, the catechol derivatives 5, 6 with five or six carbon atom bridges and the phenol analogues 8-11 with bridges of three to six carbon atoms all showed similar activity, with IC50 values of approximately 3-5 microM against the H-69 small cell lung cancer cell line. Analogues with shorter (3) or longer bridges (7, 12) were much less active. The most potent analogue was the biscatechol with a four-carbon bridge 4 which was > 10 times more active than NDGA and therefore represents a new lead compound in this area. Surprisingly, the tetramethyl ether 14 of this compound was slightly more active than NDGA, but the trihydroxy analogue 13 was less active than NDGA. The conformationally restricted analogue 15 was also less active than NDGA. In summary, simplification of the structure of NDGA by removal of the methyl groups has produced a new lead compound 4, which is >10 times more potent than NDGA as a proliferative inhibitor of H-69 small cell lung cancer cells.