gebhart/patrepeval huggingface dataset:
Tumor-specific, hypomodified phenylalanyl-tRNA is utilized in translation in preference to the fully modified isoacceptor of normal cells. (1985)

Phenylalanine transfer RNA (tRNAPhe) of mammalian tissues contains the hypermodified guanine derivative Y (Wye) adjacent to the 3'-end of the anticodon and two O-methylated bases in the 5' portion of the anticodon loop. These positions are hypomodified in a variety of tumor cells including a mouse neuroblastoma. The normal and tumor-specific Phe-tRNAPhe iso-acceptors were prepared from mouse liver and mouse neuroblastoma cells and compared for their activity in incorporating phenylalanine into each phenylalanine site of rabbit globin in a reticulocyte cell-free protein synthesizing system. The hypomodified Phe-tRNAPhe of neuroblastoma cells is generally preferred to the fully modified tRNAPhe of liver in globin synthesis by about 15%. This preference is the same in the translation of both phenylalanine codons, UUC and UUU, but the ratios of incorporation by the Phe-tRNAPhe species vary from site to site within a 2-fold range. Only 2 of 16 phenylalanine residues are donated preferentially by the fully modified Phe-tRNAPhe. One such residue occurs in beta-42, the second of two tandem phenylalanine residues (both encoded by UUC), while the hypomodified isoacceptor is preferred in translation of the first residue. This result indicates that the translation of tandem residues is particularly affected by the tRNAs available. Since the tumor-specific hypomodified Phe-tRNAPhe is generally utilized preferntially, it appears that the bulky Y base and/or other modifications of normal tRNAPhe may modulate protein synthesis and that tumor cells may achieve a growth advantage if their tRNAPhe is hypomodified.
1,3‐Dipolare Additionen an 7‐Methylthieno[2,3‐c]pyridin‐1,1‐dioxid (1980)

1,3‐Dipolar Additions to 7‐Methylthieno[2,3‐ c ]pyridine 1,1‐dioxide 1,3‐Dipolar additions of diazomethane, diazoethane, ethyl diazoacetate, phenyldiazomethane and phenyl azide to 7‐methylthieno[2,3‐ c ]pyridine 1,1‐dioxide have been examined. The structures of the primary products e.g. 2, 8, 18, 25 have been established and their behaviour towards elevated temperatures and/or basic conditions was investigated. Under these conditions the primary products lost SO 2 or N 2 to yield e.g. 4 , 11 , 19 , 21 , 23 , 27 , 28 .
Recombinant Gene Expression and 1H NMR Characteristics of the Kringle (2 + 3) Supermodule:  Spectroscopic/Functional Individuality of Plasminogen Kringle Domains (1996)

The plasminogen kringle 2 (K2HPg) and kringle 3 (K3HPg) modules occur in tandem within the polypeptide segment that affords the heavy chain of plasmin. The K2HPg and K3HPg are unique among the plasminogen kringle domains in that they also are linked to each other via the Cys169-Cys297 (Cys4 of K2HPg to Cys43 of K3HPg, kringle numbering convention) disulfide bridge, thus generating a K2HPg-K3HPg "supermodule". The kringle (2 + 3) sequence of human plasminogen (r-EE[K2HPgK3HPg]DS) was expressed in Escherichia coli, using an expression vector containing the phage T5 promoter/operator N250PSN250P29 and the codons for an N-terminal hexahistidine tag to ensure the isolation of the recombinant protein by affinity chromatography on Ni(2+)-nitrilotriacetic acid/agarose under denaturing and reducing conditions. Kringle (2 + 3) was refolded in the presence of glutathione redox buffer. By taking advantage of the lysine affinity of kringle 2, the protein was purified by affinity chromatography on lysine-Bio-Gel. Recombinant kringle (2 + 3) was identified by amino acid composition, N-terminal sequence and mass determination. The 1H NMR spectrum shows that the intact r-K2HPgK3HPg is properly folded. By reference to spectra of the individual kringles, r-K2HPg and r-K3HPg, resonances of the K2HPg and K3HPg components in the spectrum of the intact r-K2HPgK3HPg can be readily distinguished. The strictly conserved Leu46 residue (kringle residue number convention) yields delta-methyl signals that are characteristic for K2HPg and K3HPg, exhibiting chemical shifts of -0.87 and -0.94 ppm, respectively, which are distinct from those of K1HPg, K4HPg, and K5HPg, (-1.04 to -1.05 ppm). Thus, the high-field Leu46 signals from K2HPg and K3HPg are well resolved from those of other kringles and can be identified unambiguously in spectra of the K1HPgK2HPgK3HPg elastolytic fragment of plasminogen as well as in spectra of Glu-plasminogen. Overall, r-K2HPgK3HPg exhibits broader resonance line widths than does the K1HPg component, consistent with a lesser mobility of the K2HPgK3HPg segment within the K1HPgK2HPgK3HPg fragment, a reflection of the extra structural constraint imposed by the disulfide bridge linking K2HPg to K3HPg. The ligand 6-aminohexanoic acid (6-AHA), which is known to interact with r-K2HPg but not with r-K3HPg, selectively perturbs K2 aromatic signals in the intact r-K2HPgK3HPg spectrum while leaving K3 resonances largely unaffected. Association constant (K(a)) values for 6-AHA determined from 1H NMR ligand titration experiments yield K(a) approximately 2.2 +/- 0.3 mM(-1) for the intact r-K2HPgK3HPg, comparable to K(a) approximately 2.3 +/- 0.2 mM(-1) determined for the isolated r-K2HPg, which demonstrates that the interactions of 6-AHA with the K2HPg ligand-binding site are not significantly affected by the neighboring K3HPg domain within the intact r-K2HPgK3HPg supermodule.
Efficient preparation of N.alpha.-formylamino acid tert-butyl esters (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEfficient preparation of N.alpha.-formylamino acid tert-butyl estersMichinori Waki and Johannes MeienhoferCite this: J. Org. Chem. 1977, 42, 11, 2019–2020Publication Date (Print):May 1, 1977Publication History Published online1 May 2002Published inissue 1 May 1977https://pubs.acs.org/doi/10.1021/jo00431a046https://doi.org/10.1021/jo00431a046research-articleACS PublicationsRequest reuse permissionsArticle Views1142Altmetric-Citations108LEARN 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
Novel retinoic acid receptor ligands in Xenopus embryos. (1996)

Retinoids are a large family of natural and synthetic compounds related to vitamin A that have pleiotropic effects on body physiology, reproduction, immunity, and embryonic development. The diverse activities of retinoids are primarily mediated by two families of nuclear retinoic acid receptors, the RARs and RXRs. Retinoic acids are thought to be the only natural ligands for these receptors and are widely assumed to be the active principle of vitamin A. However, during an unbiased, bioactivity-guided fractionation of Xenopus embryos, we were unable to detect significant levels of all-trans or 9-cis retinoic acids. Instead, we found that the major bioactive retinoid in the Xenopus egg and early embryo is 4-oxoretinaldehyde, which is capable of binding to and transactivating RARs. In addition to its inherent activity, 4-oxoretinaldehyde appears to be a metabolic precursor of two other RAR ligands, 4-oxoretinoic acid and 4-oxoretinol. The remarkable increase in activity of retinaldehyde and retinol as a consequence of 4-oxo derivatization suggests that this metabolic step could serve a critical regulatory function during embryogenesis.
Metal–Organic Frameworks: Opportunities for Catalysis (2009)

The role of metal-organic frameworks (MOFs) in the field of catalysis is discussed, and special focus is placed on their assets and limits in light of current challenges in catalysis and green chemistry. Their structural and dynamic features are presented in terms of catalytic functions along with how MOFs can be designed to bridge the gap between zeolites and enzymes. The contributions of MOFs to the field of catalysis are comprehensively reviewed and a list of catalytic candidates is given. The subject is presented from a multidisciplinary point of view covering solid-state chemistry, materials science, and catalysis.
Novel Approaches to Cardiac Valve Repair (2004)

I n Part I of this article, several aspects of valve structure and function and their possible clinical relevance were discussed. We now review the clinical evolution and application for various forms of valve repair and outline some of the factors relating to the timing and choice of particular types of repair or replacement and, whenever appropriate, repair versus replacement. In addition, future prospects of valve repair based on understanding of the sophisticated function and structure of valves and the possible future contribution of tissue engineering are discussed.
The lytic enzyme of the pneumococcal phage Dp‐1: a chimeric lysin of intergeneric origin (1997)

We have localized, cloned and characterized the genes coding for the lytic system of the pneumococcal phage Dp-1. The lytic enzyme of this phage (Pal), previously identified as an N-acetyl-muramoyl-L-alanine amidase, shows a modular organization similar to that described for the lytic enzymes of Streptococcus pneumoniae and its bacteriophages. The construction of chimeric enzymes between pneumococcus and bacteria (or phages) that belong to different Gram-positive families has shown that the interchange of functional domains switches enzyme specificity. Interestingly, Pal appears to be a natural chimeric enzyme of intergeneric origin, that is the N-terminal domain was highly similar to that of the murein hydrolase coded by a gene found in the phage BK5-T that infects Lactococcus lactis, whereas the C-terminal domain was homologous to those found in the lytic enzymes of the pneumococcal system that is responsible for the binding to the choline residues present in the cell wall substrate. Biochemical analysis of Pal revealed that this enzyme shares important properties with those of the major LytA101 autolysin found in an atypical, clinical pneumococcal isolate. These peculiar characteristics have been ascribed to a modified C-terminal domain. The natural chimeric enzyme described here provides further support for the theory of modular evolution of proteins and its characteristics also furnish interesting clues on the molecular mechanisms involved in the more invasive types of atypical pneumococci.
Imaging of primary and metastatic liver cancer with 131I monoclonal and polyclonal antibodies against alphafetoprotein. (1987)

Thirteen patients with a history of confirmed liver carcinoma were given either I131 goat polyclonal or murine monoclonal antibodies against alpha-fetoprotein (AFP), and then scanned with a gamma camera. In order to reduce background, nontarget activity, especially in the liver, blood pool, and reticuloendothelial system, 99mTc imaging agents were used for tumor image enhancement by computer-assisted subtraction. A sensitivity of 91% for the primary site, 50% for the lungs (33% for the chest area), and 75% for the abdomen and pelvis was achieved, with a specificity of 100%, 94%, and 100% for these sites, respectively. The accuracy was determined to be 93% for the liver, 86% for the lungs (77% for the chest), and 85% for the abdominal and pelvic area, resulting in an overall accuracy rate for imaging primary and metastatic hepatocellular cancer of 84% (90% if bone metastases are excluded). In two of the 13 patients, lesions that had been missed by conventional liver scintigraphy and transmission computed tomography (CT) were first shown by radioimmunodetection (RAID).
A METHOD FOR ESTIMATING PEANUT MATURITY (1979)

ABSTRACT Over the years, peanut maturity estimations have been based largely on subjective measurements. This paper reports a 3‐yr study of an objective method based on the tight transmittance measurement of a methanolic extract of freshly‐dug peanut pods which is both rapid and simple in operation and adaptable for field use. Results in 1975, 1976 and 1977 showed that the light transmittance of the methanolic extract correlated with the age of peanuts and dollar return per acre. Data also indicated that solar radiation, particularly during the fist 75 days of growth, may affect peanut maturity.
Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis (2004)

The microbial community structure of pig manure slurry (PMS) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (SSU) rDNA partial sequences. Based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the Bacteria, Archaea and Eukarya lineages, respectively. Only 36% of the bacterial phylotypes were closely related (>or=97% similarity) to any previously known sequence in databases. The bacterial groups most often represented in terms of phylotype and clone abundance were the Eubacterium (22% of total sequences), the Clostridium (15% of sequences), the Bacillus-Lactobacillus-Streptococcus subdivision (20% of sequences), theMycoplasma and relatives (10% of sequences) and the Flexibacter-Cytophaga-Bacteroides (20% of sequences). The global microbial community structure and phylotype diversity show a close relationship to the pig gastrointestinal tract ecosystem whereas phylotypes from the Acholeplasma-Anaeroplasma and the Clostridium purinolyticum groups appear to be better represented in manure. Archaeal diversity was dominated by three phylotypes clustering with a group of uncultured microorganisms of unknown activity and only distantly related to the Thermoplasmales and relatives. Other Archaea were methanogenic H2/CO2 utilisers. No known acetoclastic Archaea methanogen was found. Eukaryotic diversity was represented by a pluricellular nematode, two Alveolata, a Blastocystis and an Entamoebidae. Manure slurry physico-chemical characteristics were analysed. Possible inhibitory effects of acetate, sulphide and ammonia concentrations on the microbial anaerobic ecosystem are discussed.
Structural Basis for the Proinflammatory Cytokine Activity of High Mobility Group Box 1 (2003)

High mobility group box 1 (HMGB), a ubiquitous DNA-binding protein, has been implicated as a proinflammatory cytokine and late mediator of lethal endotoxemia. HMGB1 is released by activated macrophages. It amplifies and extends the inflammatory response by inducing cytokine release and mediating acute lung injury, anorexia, and the inflammatory response to tissue necrosis. The kinetics of HMGB1 release provide a wide therapeutic window for endotoxemia because extracellular levels of HMGB1 begin to increase 12 to 24 h after exposure to inflammatory stimuli. Here, we demonstrate that a DNA-binding domain of HMGB1, the B box, recapitulates the cytokine activity of full length HMGB1 and efficiently activates macrophages to release tumor necrosis factor (TNF) and other proinflammatory cytokines. Truncation of the B box revealed that the TNF-stimulating activity localizes to 20 amino acids (HMGB1 amino acids 89 to 108). Passive immunization of mice with antibodies raised against B box conferred significant protection against lethal endotoxemia or sepsis, induced by cecal perforation. These results indicate that a proinflammatory domain of HMGB1 maps to the highly conserved DNA-binding B box, making this primary sequence a suitable target in the design of therapeutics.
Controlling the influence of Auger recombination on the performance of quantum-dot light-emitting diodes (2013)

Development of light-emitting diodes (LEDs) based on colloidal quantum dots is driven by attractive properties of these fluorophores such as spectrally narrow, tunable emission and facile processibility via solution-based methods. A current obstacle towards improved LED performance is an incomplete understanding of the roles of extrinsic factors, such as non-radiative recombination at surface defects, versus intrinsic processes, such as multicarrier Auger recombination or electron-hole separation due to applied electric field. Here we address this problem with studies that correlate the excited state dynamics of structurally engineered quantum dots with their emissive performance within LEDs. We find that because of significant charging of quantum dots with extra electrons, Auger recombination greatly impacts both LED efficiency and the onset of efficiency roll-off at high currents. Further, we demonstrate two specific approaches for mitigating this problem using heterostructured quantum dots, either by suppressing Auger decay through the introduction of an intermediate alloyed layer, or by using an additional shell that impedes electron transfer into the quantum dot to help balance electron and hole injection.
Correlation between phosphorylation of the chemotaxis protein CheY and its activity at the flagellar motor (1992)

Phosphorylation of the chemotaxis protein CheY by its kinase CheA appears to play a central role in the process of signal transduction in bacterial chemotaxis. It is presumed that the role is activation of CheY which results in clockwise (CW) flagellar rotation. The aim of this study was to determine whether this activity of CheY indeed depends on the protein being phosphorylated. Since the phosphorylation of CheY can be detected only in vitro, we studied the ability of CheY to cause CW rotation in an in vitro system, consisting of cytoplasm-free envelopes of Salmonella typhimurium or Escherichia coli having functional flagella. Envelopes containing just buffer rotated only counterclockwise. Inclusion of CheY caused 14% of the rotating envelopes to go CW. This fraction of CW-rotating envelopes was not altered when the phosphate potential in the envelopes was lowered by inclusion of ADP together with CheY in them, indicating that CheY has a certain degree of activity even without being phosphorylated. Attempts to increase the activity of CheY in the envelopes by phosphorylation were not successful. However, when CheY was inserted into partially-lysed cells (semienvelopes) under phosphorylating conditions, the number of CW-rotating cells increased 3-fold. This corresponds to more than a 100-fold increase in the activity of a single CheY molecule upon phosphorylation. It is concluded that nonphosphorylated CheY can interact with the flagellar switch and cause CW rotation, but that this activity is increased by at least 2 orders of magnitude by phosphorylation. This increase in activity requires additional cytoplasmic constituents, the identity of which is not yet known.
Isotropic Atomic Layer Etching of ZnO Using Acetylacetone and O2 Plasma (2018)

Atomic layer etching (ALE) provides Ångström-level control over material removal and holds potential for addressing the challenges in nanomanufacturing faced by conventional etching techniques. Recent research has led to the development of two main classes of ALE: ion-driven plasma processes yielding anisotropic (or directional) etch profiles and thermally driven processes for isotropic material removal. In this work, we extend the possibilities to obtain isotropic etching by introducing a plasma-based ALE process for ZnO which is radical-driven and utilizes acetylacetone (Hacac) and O<sub>2</sub> plasma as reactants. In situ spectroscopic ellipsometry measurements indicate self-limiting half-reactions with etch rates ranging from 0.5 to 1.3 Å/cycle at temperatures between 100 and 250 °C. The ALE process was demonstrated on planar and three-dimensional substrates consisting of a regular array of semiconductor nanowires (NWs) conformally covered using atomic layer deposition of ZnO. Transmission electron microscopy studies conducted on the ZnO-covered NWs before and after ALE proved the isotropic nature and the damage-free characteristics of the process. In situ infrared spectroscopy measurements were used to elucidate the self-limiting nature of the ALE half-reactions and the reaction mechanism. During the Hacac etching reaction that is assumed to produce Zn(acac)<sub>2</sub>, carbonaceous species adsorbed on the ZnO surface are suggested as the cause of the self-limiting behavior. The subsequent O<sub>2</sub> plasma step resets the surface for the next ALE cycle. High etch selectivities (∼80:1) over SiO<sub>2</sub> and HfO<sub>2</sub> were demonstrated. Preliminary results indicate that the etching process can be extended to other oxides such as Al<sub>2</sub>O<sub>3</sub>.
A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity (2010)

Dicer is a central enzyme in microRNA (miRNA) processing. We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. In contrast to other miRNAs, miR-451 levels were refractory to dicer loss of function but were reduced in MZago2 (maternal-zygotic) mutants. We found that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutants showed delayed erythropoiesis that could be rescued by wild-type Ago2 or miR-451-duplex but not by catalytically dead Ago2. Changing the secondary structure of Dicer-dependent miRNAs to mimic that of pre-miR-451 restored miRNA function and rescued developmental defects in MZdicer mutants, indicating that the pre-miRNA secondary structure determines the processing pathway in vivo. We propose that Ago2-mediated cleavage of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs independently of Dicer.
RECRUITMENT (2001)

Children's Healthcare of Atlanta at Scottish Rite, Atlanta, GA Address reprint requests to Susan E. Osborne, MSN, RNC, Children's Healthcare of Atlanta at Scottish Rite, 1001 Johnson Ferry Road NE, Atlanta, GA 30342-1600. E-mail: [email protected]