gebhart/patrepeval huggingface dataset:
Chemistry of the neomycins. XIII. Synthesis of aminocyclitols and aminosugars via nitromethane condensations (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of the neomycins. XIII. Synthesis of aminocyclitols and aminosugars via nitromethane condensationsSeiichiro Ogawa, Kenneth L. Rinehart Jr., Goro Kimura, and Robert P. JohnsonCite this: J. Org. Chem. 1974, 39, 6, 812–821Publication Date (Print):March 1, 1974Publication History Published online1 May 2002Published inissue 1 March 1974https://pubs.acs.org/doi/10.1021/jo00920a015https://doi.org/10.1021/jo00920a015research-articleACS PublicationsRequest reuse permissionsArticle Views130Altmetric-Citations16LEARN 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
The cell cycle and Wnt (2010)

Comment on: Davidson G, et al. Dev Cell 2009; 17:788-99.
The Writer's Workbench: Computer Aids for Text Analysis (1982)

This paper describes the Writer's Workbench programs, which analyze English prose and suggest improvements. Some limited data on the use of the Writer's Workbench and its acceptance are also presented. The Writer's Workbench incorporates the style and diction programs, described in a previous paper of this TRANSACTIONS, into a more extensive system to help writers improve their writing. The system runs under the UNIX <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> operating system, and includes programs to: 1) proofread, 2) comment on stylistic features of text, and 3) provide reference information about the English language. Among other writing faults, the programs detect split infinitives, errors in spelling and punctuation, overly long sentences, wordy phrases, and passive sentences.
Suppression of ongoing experimental allergic encephalomyelitis (EAE)in Lewis rats: synergistic effects of myelin basic protein (MBP) peptide68–86 and IL-4 (2000)

Mucosal myelin autoantigen administration effectively prevented EAE, but mostly failed to treat ongoing EAE. Patients with multiple sclerosis (MS), for which EAE is considered an animal model, did not benefit from oral treatment with bovine myelin. We anticipated that autoantigen, administered together with a cytokine that counteracts Th1 cell responses, might ameliorate Th1-driven autoimmune disease, and that nasal administration might considerably reduce the amounts of antigen + cytokine needed for treatment purposes. Lewis rats with EAE actively induced with myelin basic protein peptide (MBP 68-86) and Freund's complete adjuvant (FCA), received from day 7 post-immunization, i.e. after T cell priming had occurred, 120 microg MBP 68-86 + 100 ng IL-4 per rat per day for 5 consecutive days. These rats showed later onset, lower clinical scores, less body weight loss and shorter EAE duration compared with rats receiving MBP 68-86 or IL-4 only, or PBS. EAE amelioration was associated with decreased infiltration of ED1+ macrophages and CD4+ T cells within the central nervous system, and with decreased interferon-gamma (IFN-gamma) and tumour necrosis factor-alpha (TNF-alpha) and enhanced IL-4, IL-10 and transforming growth factor-beta (TGF-beta) responses by lymph node cells. Simultaneous administration of encephalitogenic peptide + IL-4 by the nasal route thus suppressed ongoing EAE and induced IL-4, IL-10 and TGF-beta-related regulatory elements.
Analysis of energy-efficient, fair routing in wireless sensor networks through non-linear optimization (2003)

In the area of wireless sensor networks (WSN) there is still a significant gap between theory and practice: system designs and protocols are rapidly out-pacing analysis. We develop formal computational models of a WSN based on non-linear optimization and use them to analyze the impact of fairness constraints on network performance. The optimization framework presented is very general and can also be used to analyze the optimal performance of WSN subject to other design parameters such as the topology, number of nodes, energy levels, source rates, reception power, etc. Our results show that the maximum information that can be extracted for a fixed amount of energy increases and that the minimum energy required outputting a fixed amount of information decreases as we reduce the fairness requirement in the network. We present these functions for a fixed network topology and observe that they exhibit sharp changes in gradient due to qualitative changes in optimal routes.
Protective Role of tolC in Efflux of the Electron Shuttle Anthraquinone-2,6-Disulfonate (2002)

Extracellular electron transfer can play an important role in microbial respiration on insoluble minerals. The humic acid analog anthraquinone-2,6-disulfonate (AQDS) is commonly used as an electron shuttle during studies of extracellular electron transfer. Here we provide genetic evidence that AQDS enters Shewanella oneidensis strain MR-1 and causes cell death if it accumulates past a critical concentration. A tolC homolog protects the cell from toxicity by mediating the efflux of AQDS. Electron transfer to AQDS appears to be independent of the tolC pathway, however, and requires the outer membrane protein encoded by mtrB. We suggest that there may be structural and functional relationships between quinone-containing electron shuttles and antibiotics.
Supramolecular Control of Reactivity in the Solid State: From Templates to Ladderanes to Metal−Organic Frameworks (2008)

We describe how reactivity can be controlled in the solid state using molecules and self-assembled metal-organic complexes as templates. Being able to control reactivity in the solid state bears relevance to synthetic chemistry and materials science. The former offers a promise to synthesize molecules that may be impossible to realize from the liquid phase while also taking advantage of the benefits of conducting highly stereocontrolled reactions in a solvent-free environment (i.e., green chemistry). The latter provides an opportunity to modify bulk physical properties of solids (e.g., optical properties) through changes to molecular structure that result from a solid-state reaction. Reactions in the solid state have been difficult to control owing to frustrating effects of molecular close packing. The high degree of order provided by the solid state also means that the templates can be developed to determine how principles of supramolecular chemistry can be generally employed to form covalent bonds. The paradigm of synthetic chemistry employed by Nature is based on integrating noncovalent and covalent bonds. The templates assemble olefins via either hydrogen bond or coordination-driven self-assembly for intermolecular [2 + 2] photodimerizations. The olefins are assembled within discrete, or finite, self-assembled complexes, which effectively decouples chemical reactivity from effects of crystal packing. The control of the solid-state assembly process affords the supramolecular construction of targets in the form of cyclophanes and ladderanes. The targets form stereospecifically, in quantitative yield, and in gram amounts. Both [3]- and [5]-ladderanes have been synthesized. The ladderanes are comparable to natural ladderane lipids, which are a new and exciting class of natural products recently discovered in anaerobic marine bacteria. The organic templates function as either hydrogen bond donors or hydrogen bond acceptors. The donors and acceptors generate cyclobutanes lined with pyridyl and carboxylic acid groups, respectively. The metal-organic templates are based on Zn(II) and Ag(I) ions. The reactivity involving Zn(II) ions is shown to affect optical properties in the form of solid-state fluorescence. The solids based on both the organic and metal-organic templates undergo rare single-crystal-to-single-crystal reactions. We also demonstrate how the cyclobutanes obtained from this method can be applied as novel polytopic ligands of metallosupramolecular assemblies (e.g., self-assembled capsules) and materials (e.g., metal-organic frameworks). Sonochemistry is also used to generate nanostructured single crystals of the multicomponent solids or cocrystals based on the organic templates. Collectively, our observations suggest that the organic solid state can be integrated into more mainstream settings of synthetic organic chemistry and be developed to construct functional crystalline solids.
Emerging views on tmRNA‐mediated protein tagging and ribosome rescue (2001)

Transfer-messenger RNA (tmRNA), also known as SsrA or 10Sa RNA, is a bacterial ribonucleic acid that recycles 70S ribosomes stalled on problematic messenger RNAs (mRNAs) and also contributes to the degradation of incompletely synthesized peptides. tmRNA acts initially as transfer RNA (tRNA), being aminoacylated at its 3'-end by alanyl-tRNA synthetase, to add alanine to the stalled polypeptide chain. Resumption of translation ensues not on the mRNA on which the ribosomes were stalled but at an internal position in tmRNA. Termination soon occurs, tmRNA recruiting the appropriate termination factors allowing the release of the tagged protein that is subsequently recognized and degraded by specific cytoplasmic and periplasmic proteases, and permits ribosome recycling. Recent data suggest that tmRNA tags bacterial proteins in three other instances; when ribosomes stall at internal sites; during 'readthrough' of canonical termination codons; and when ribosomes are at the termination codon of intact messages. The importance of bacterial tmRNAs for survival, growth under stress, and pathogenesis is also discussed. Recent in vivo and in vitro studies have identified novel ligands of tmRNA. Based on the available experimental evidences, an updated model of tmRNA mediated protein tagging and ribosome rescue in bacteria is presented.
Thin-Film Interference in Lossy, Ultra-Thin Layers (2014)

Although much thinner than conventional optical interference coatings, nanometer-thick films made of optically absorbing materials can display strong interference effects. This new class of coatings shows promise for coloring and labeling, optical filters, tunable absorbers and emitters, and energy harvesting.
CATNIP: Common Architecture for the Internet (1994)

This paper describes a common architecture for the network layer protocol.The Common Architecture for Next Generation Internet Protocol (CATNIP) provides a compressed form of the existing network layer protocols.Each compression is defined so that the resulting network protocol data units are identical in format.The fixed part of the compressed format is 16 bytes in length, and may often be the only part transmitted on the subnetwork.With some attention paid to details, it is possible for a transport layer protocol (such as TCP) to operate properly with one end system using one network layer (e.g.IP version 4) and the other using some other network protocol, such as CLNP.Using the CATNIP definitions, all the existing transport layer protocols used on connectionless network services will operate over any existing network layer protocol.The CATNIP uses cache handles to provide both rapid identification of the next hop in high performance routing as well as abbreviation of the network header by permitting the addresses to be omitted when a valid cache handle is available.The fixed part of the network layer header carries the cache handles.
Concurrent infection with Schistosoma mansoni attenuates inflammation induced changes in colonic morphology, cytokine levels, and smooth muscle contractility of trinitrobenzene sulphonic acid induced colitis in rats (2003)

Concurrent infection with S mansoni significantly attenuates TNBS induced colitis in the rat. Inflammation induced disturbances in contractility of longitudinal and circular colonic muscle strips may outlast the inflammatory reaction.
Monomeric state and ligand binding of recombinant GABA transporter from Escherichia coli (2001)

The gamma-aminobutyric acid (GABA) transporter from Escherichia coli was homologously overexpressed and purified to homogeneity with a yield of 1.0 mg per liter culture. The purification procedure consists of a cobalt affinity column, proteolytic cleavage of His- and myc-tags, and size-exclusion chromatography. The purified transporter exists as a monomer in FOS-Choline 12 detergent, with a Stokes radius of 45 A for the protein-detergent complex. In detergent solution the protein binds substrates, as indicated by tryptophan fluorescence quenching. Its dissociation constants (K(d)) for GABA, muscimol and nipecotic acid are 13.8, 13.3 and 27.9 microM, respectively. This protein preparation provides ideal starting materials for future biochemical, biophysical and structural studies of the GABA transporter.
Amino acid sequences of mouse and human epidermal type II keratins of Mr 67,000 provide a systematic basis for the structural and functional diversity of the end domains of keratin intermediate filament subunits. (1985)

From the nucleotide sequences of specific cDNA clones, we present partial amino acid sequences (75-90% of the total) of 67-kDa type II keratin subunits expressed in terminally differentiating mouse and human epidermis. Analysis of the sequence information reveals that their secondary structures conform to the pattern common for all intermediate filament (IF) subunits. Together with the previously published sequence of the mouse 59-kDa type I keratin (Steinert, P. M., Rice, R. H., Roop, D. R., Trus, B. L., and Steven, A. C. (1983) Nature 302, 794-800) these data allow us to make comparisons between two keratins which are coexpressed in an epithelial cell type and which coassemble into the same IF. Moreover, these comparisons suggest a systematic plan for the general organization of the end domains of other keratin subunits. We postulate that each end domain consists of a set of subdomains which are distributed with bilateral symmetry with respect to the central alpha-helical domain. Type II (but not type I) keratins contain short globular sequences, H1 and H2, immediately adjacent to the central domain, that have been conserved in size and sequence and which account for most of the difference in mass between coexpressed type II and type I keratins. These are flanked by subdomains V1 and V2 that are highly variable in both length and sequence, often contain tandem peptide repeats, and are conspicuously rich in glycines and/or serines. At the termini are strongly basic subdomains (N and C, respectively) that are variable in sequence. Among keratins of a given type, their variability in mass appears to reside in the size of their V1 and V2 subdomains. However, coexpressed type I and type II keratins have generally similar V1 and/or V2 sequences. By virtue of the ease with which large portions of these subdomain sequences can be removed from intact keratin IF by limited proteolysis, we hypothesize that they lie on the periphery of the IF where they participate in interactions with other constituents of epithelial cells.
The response of patients with phenylketonuria and elevated serum phenylalanine to treatment with oral sapropterin dihydrochloride (6R‐tetrahydrobiopterin): a phase II, multicentre, open‐label, screening study (2007)

This study aimed to evaluate the response to and safety of an 8-day course of sapropterin dihydrochloride (6R-tetrahydrobiopterin or 6R-BH4) 10 mg/kg per day in patients with phenylketonuria (PKU), who have elevated blood phenylalanine (Phe) levels, and to identify a suitable cohort of patients who would respond to sapropterin dihydrochloride treatment with a reduction in blood Phe level. Eligible patients were aged > or = 8 years, had blood Phe levels > or = 450 micromol/L and were not adhering to a Phe-restricted diet. Suitable patients were identified by a > or = 30% reduction in blood Phe level from baseline to day 8 following sapropterin dihydrochloride treatment. The proportion of patients who met these criteria was calculated for the overall population and by baseline Phe level (< 600, 600 to < 900, 900 to < 1200 and > or = 1200 micromol/L). In total, 485/490 patients completed the study and 20% (96/485) were identified as patients who would respond to sapropterin dihydrochloride. A reduction in Phe level was observed in all subgroups, although response was greater in patients with lower baseline Phe levels. Wide variability in response was seen across all baseline Phe subgroups. The majority of adverse events were mild and all resolved without complications. Sapropterin dihydrochloride was well tolerated and reduced blood Phe levels across all PKU phenotypes tested. Variability in reduction of Phe indicates that the response to sapropterin dihydrochloride cannot be predicted by baseline Phe level.
The anti-recognition function of sialic acids: studies with erythrocytes and macrophages (1984)

Abstract
Interleukin-13 Induces Dramatically Different Transcriptional Programs in Three Human Airway Cell Types (2001)

Interleukin (IL)-13, a cytokine released by T lymphocytes during immediate hypersensitivity responses, is a central mediator of asthma. Because IL-13 induces phenotypic features of asthma in mice deficient in T and B lymphocytes, it is likely that this cytokine contributes to the development of asthma by acting directly on resident airway cells. To analyze the global effects of IL-13 on gene expression in airway cells that could contribute to the phenotypic features of asthma, we used Genechip HuGene FL arrays (Affymetrix, Santa Clara, CA) that contain probes for approximately 6,500 human genes. Despite activating a common signaling pathway, IL-13 induced dramatically different patterns of gene expression in primary cultures of airway epithelial cells, airway smooth muscle cells, and lung fibroblasts, with little overlap among cell types. The most prominent effects of IL-13 were on airway smooth muscle, but several genes induced in airway epithelial cells and fibroblasts are also candidates that may contribute to phenotypic features of asthma. These results suggest that the in vivo response to IL-13 in the airways likely results from a combination of distinct effects on each of several resident airway cell types.
Methylene blue and serotonin toxicity: inhibition of monoamine oxidase A (MAO A) confirms a theoretical prediction (2007)

MB is a potent reversible inhibitor of MAO A with implications for gut uptake of amines when administered orally. At concentrations reported in the literature after intravenous administration, MAO B would be partially inhibited but MAO A would be completely inhibited. This inhibition of MAO A would be expected to lead to perturbations of 5-hydroxytryptamine metabolism and hence account for ST occurring when administered to patients on SSRI treatment.
Quantitative Proteomics of the Archaeon Methanococcus maripaludis Validated by Microarray Analysis and Real Time PCR (2006)

For the archaeon Methanococcus maripaludis, a fully sequenced and annotated model species of hydrogenotrophic methanogen, we report validation of quantitative protein level expression ratios on a proteome-wide basis. Using an approach based on quantitative multidimensional capillary HPLC and quadrupole ion trap mass spectrometry, coverage of gene expression approached that currently achievable with transcription microarrays. Comprehensive mass spectrometry-based proteomics and spotted cDNA arrays were used to compare global protein and mRNA levels in a wild-type (S2) and mutant strain (S40) of M. maripaludis. Using linear regression with 652 expression ratios generated by both the proteomic and microarray methods, a product moment correlation coefficient of 0.24 was observed. The correlation improved to 0.61 if only genes showing significant expression changes were included. A novel two-stage method of outlier detection was used for the protein measurements when Dixon's Q-test by itself failed to give satisfactory results. The log(2) transformations of the number of peptides or isotopic peptide pairs associated with each ORF, divided by the predicted molecular weight, were found to have moderately positive correlations with two bioinformatic predictors of gene expression based on codon bias. We detected peptides derived from 939 proteins or 55% of the genome coding capacity. Of these, 60 were overexpressed, and 34 were underexpressed in the mutant. Of the 1722 ORFs encoded in the genome, 1597 or 93% were probed by cDNA arrays. Of these, 50 were more highly expressed, and 45 showed lower expression levels in the mutant relative to the wild type. 15 ORFs were shown to be overexpressed by both methods, and two ORFs were shown to be overexpressed by proteomics and underexpressed by microarray.
Dengue-2 vaccine: preparation from a small-plaque virus clone (1980)

The S-1 clone of dengue type 2 virus was used for the preparation of a live-attenuated vaccine after passage in DBS-FRhL-2 cell culture. The vaccine virus had a relatively higher replicative capacity at superoptimal temperatures than its precursor virus, S-1, passaged in primary green monkey kidney cells (S-1 PGMK). There was also a tendency for the S-1 vaccine virus to exhibit leakiness at increased temperatures. Another in vitro marker, replication in monkey peripheral blood leukocytes, indicated less host restriction for the S-1 vaccine in comparative assays with S-1 PGMK virus. Mouse virulence appeared to remain stable on passage in DBS-FRhL-2 cells, whereas monkey immunogenicity decreased. Cautious trials of the dengue type 2 S-1 vaccine in humans are indicated.
Distinct perturbation of the translatome by the antidiabetic drug metformin (2012)

Metformin has been reported to lower cancer incidence among type II diabetics. Metformin exhibits antiproliferative and antineoplastic effects associated with inhibition of mammalian target of rapamycin complex 1 (mTORC1), but the mechanisms are poorly understood. We provide a unique genome-wide analysis of translational targets of canonical mTOR inhibitors (rapamycin and PP242) compared with metformin, revealing that metformin controls gene expression at the level of mRNA translation to an extent comparable to that of canonical mTOR inhibitors. Importantly, metformin's antiproliferative activity can be explained by selective translational suppression of mRNAs encoding cell-cycle regulators via the mTORC1/eukaryotic translation initiation factor 4E-binding protein pathway. Thus, metformin selectively inhibits translation of mRNAs encoding proteins that promote neoplastic proliferation, which should facilitate studies on metformin and related biguanides in cancer prevention and treatment.