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  • Analytical Chemistry and Spectroscopy  (509)
  • Mutation  (131)
  • Wiley-Blackwell  (509)
  • American Association for the Advancement of Science (AAAS)  (131)
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  • 2010-2014  (120)
  • 1980-1984  (520)
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  • Wiley-Blackwell  (509)
  • American Association for the Advancement of Science (AAAS)  (131)
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  • American Institute of Physics
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  • 1
    Publication Date: 2011-07-19
    Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding Sites, Antibody ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Heavy Chains/chemistry ; Immunoglobulin Light Chains/chemistry ; Molecular Mimicry ; Molecular Sequence Data ; Mutation ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2013-10-05
    Description: Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947637/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947637/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khurana, Ekta -- Fu, Yao -- Colonna, Vincenza -- Mu, Xinmeng Jasmine -- Kang, Hyun Min -- Lappalainen, Tuuli -- Sboner, Andrea -- Lochovsky, Lucas -- Chen, Jieming -- Harmanci, Arif -- Das, Jishnu -- Abyzov, Alexej -- Balasubramanian, Suganthi -- Beal, Kathryn -- Chakravarty, Dimple -- Challis, Daniel -- Chen, Yuan -- Clarke, Declan -- Clarke, Laura -- Cunningham, Fiona -- Evani, Uday S -- Flicek, Paul -- Fragoza, Robert -- Garrison, Erik -- Gibbs, Richard -- Gumus, Zeynep H -- Herrero, Javier -- Kitabayashi, Naoki -- Kong, Yong -- Lage, Kasper -- Liluashvili, Vaja -- Lipkin, Steven M -- MacArthur, Daniel G -- Marth, Gabor -- Muzny, Donna -- Pers, Tune H -- Ritchie, Graham R S -- Rosenfeld, Jeffrey A -- Sisu, Cristina -- Wei, Xiaomu -- Wilson, Michael -- Xue, Yali -- Yu, Fuli -- 1000 Genomes Project Consortium -- Dermitzakis, Emmanouil T -- Yu, Haiyuan -- Rubin, Mark A -- Tyler-Smith, Chris -- Gerstein, Mark -- 085532/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 095908/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- CA167824/CA/NCI NIH HHS/ -- G12 MD007579/MD/NIMHD NIH HHS/ -- G12 RR003050/RR/NCRR NIH HHS/ -- GM104424/GM/NIGMS NIH HHS/ -- HG005718/HG/NHGRI NIH HHS/ -- HG007000/HG/NHGRI NIH HHS/ -- P20 MD006899/MD/NIMHD NIH HHS/ -- R01 CA166661/CA/NCI NIH HHS/ -- R01 HG002898/HG/NHGRI NIH HHS/ -- R01CA152057/CA/NCI NIH HHS/ -- R01HG4719/HG/NHGRI NIH HHS/ -- U01 CA111275/CA/NCI NIH HHS/ -- U01 HG005718/HG/NHGRI NIH HHS/ -- U01HG6513/HG/NHGRI NIH HHS/ -- U41 HG007000/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- UL1 TR000457/TR/NCATS NIH HHS/ -- WT085532/Wellcome Trust/United Kingdom -- WT095908/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092746" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites/genetics ; *Genetic Variation ; Genome, Human ; Genomics ; Humans ; Kruppel-Like Transcription Factors/metabolism ; Molecular Sequence Annotation/*methods ; Mutation ; Neoplasms/*genetics ; Polymorphism, Single Nucleotide ; Population/genetics ; RNA, Untranslated/genetics ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    ISSN: 1052-9306
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As part of a study to make a comparative analysis of selected halogenated compounds in man and the environmental media, a quantitative gas chromatographic mass spectrometric analysis of the levels of the halogenated compounds found in the breath, blood and urine of an exposed population (Old Love Canal area, Niagara, New York) and their immediate environment (air and water) was undertaken. In addition, levels of halogenated hydrocarbons in air samples taken in the general Buffalo, Niagara Falls area were determined.
    Additional Material: 8 Ill.
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  • 4
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effects of protonation and hydrogen bonding in linear Schiff bases obtained from n-butylamine with butyraldehyde, crotonaldehyde, sorbaldehyde and all-trans-retinal were studied by means of 15N and 13C NMR. The protonation-induced chemical shifts (Δδ) are an order of magnitude larger for 15N than for 13C. For 15N, this effect was found to increase with the extent of conjugation, culminating in the retinylideneimine (Δδ = -146 ppm), which constitutes a model for the study of the structure of the Schiff base linkage in visual pigments and related systems. Theoretical calculations of protonation-induced Δδ values based on MINDO/ 3 are in agreement with experimental results.
    Additional Material: 4 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 16 (1981), S. 123-125 
    ISSN: 0030-4921
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two NQR lines were observed for 35Cl in 2,5-dichloro-4-nitroaniline at room temperature, using a self-quenched super-regenerative spectrometer. Analysis of the Zeeman effect on the two lines using a cylindrical single crystal reveals that the crystal belongs to the monoclinic system. The principal field gradient Z axes enclose an angle of 35° and 28° in the cases of the low and high frequency resonance lines, respectively. The b axis is parallel to 81°, 280°. The unit cell contains either two or a multiple of two molecules. The molecules in the crystal can be arranged into two sets, with the molecular planes in each set being parallel among each other. The angle subtended between the two planes is 159° and each of the planes is inclined to the b axis at an angle of 79.5°. There is an in-plane bending of the two C—Cl bonds by 5.5°. The ionic, single bond and double bond characters of the C—Cl bonds for both chlorines are almost equal, and are in the ratio 24:73:3.
    Additional Material: 3 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    Journal of Raman Spectroscopy 9 (1980), S. 230-238 
    ISSN: 0377-0486
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The IR spectra (1400 cm-1 to 160 cm-1) of the gases at ambient temperature and the Raman spectra (below 1400 cm-1) of the liquids near -196°C are reported for CF3OF and CF3OCl. All fundamentals are assigned under Cs symmetry and the results of a normal coordinate analysis are presented. The assignments of Smardzewski and Fox are adopted with one exception for both CF3OF and CF3OCl: the CF3 rock of A″ symmetry is assigned near 430 cm-1 and the two bands between 200 cm-1 and 300 cm-1 are assigned to an A′ fundamental, involving CF3 rocking and COX bending and a Δν=2 transition in the CF3 torsion. An extra band at 548 cm-1 in the Raman spectrum of liquid CF3 COl near -196°C is assigned to a CF3OCl⃛Cl2 complex. The values of the force constants d(OX) for CF3OX molecules are suggested to be near those for X2O molecules. More than half the normal modes of A′ symmetry show extensive mixing of symmetry coordinates. In some of these cases the symmetry coordinate for which the normal mode is named is the largest but not the dominant contributor to the potential energy distribution, while in others this symmetry coordinate is not even the largest contributor to the potential energy distribution. No normal modes of A′ symmetry are present in which ν(CO), δs(CF3), δ(COX), or δ(CF3) symmetry coordinates are dominant, and the mode conventionally labeled as v(CO) should be labeled as νs(CF3). For the remaining A′ normal modes and all the A″ normal modes, the symmetry coordinate for which the normal mode is named is dominant in the potential energy distribution.
    Additional Material: 3 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    Chichester [u.a.] : Wiley-Blackwell
    Journal of Raman Spectroscopy 14 (1983), S. 144-149 
    ISSN: 0377-0486
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: Raman spectra of thallous carbonate have been studied to c. 52 kbar and mid-IR spectra to 36 kbar. Details of the assignment have also been established using single-crystal IR reflectance and Raman spectroscopy. Phase transitions were found near 13 and 38 kbar on the basis of the Raman evidence, thus supporting the earlier conclusions of Meisalo and Kalliomaki based on x-ray powder and optical results. Analysis of possible space group relations between phases III (ambient) and IV showed that IV must be orthorhombic and adopt one of the D2hn groups, where n = 17, 19, 21, 25 or 28. Structural relationships between the phases are discussed.
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  • 8
    Publication Date: 2010-01-16
    Description: Artemisinin is a plant natural product produced by Artemisia annua and the active ingredient in the most effective treatment for malaria. Efforts to eradicate malaria are increasing demand for an affordable, high-quality, robust supply of artemisinin. We performed deep sequencing on the transcriptome of A. annua to identify genes and markers for fast-track breeding. Extensive genetic variation enabled us to build a detailed genetic map with nine linkage groups. Replicated field trials resulted in a quantitative trait loci (QTL) map that accounts for a significant amount of the variation in key traits controlling artemisinin yield. Enrichment for positive QTLs in parents of new high-yielding hybrids confirms that the knowledge and tools to convert A. annua into a robust crop are now available.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graham, Ian A -- Besser, Katrin -- Blumer, Susan -- Branigan, Caroline A -- Czechowski, Tomasz -- Elias, Luisa -- Guterman, Inna -- Harvey, David -- Isaac, Peter G -- Khan, Awais M -- Larson, Tony R -- Li, Yi -- Pawson, Tanya -- Penfield, Teresa -- Rae, Anne M -- Rathbone, Deborah A -- Reid, Sonja -- Ross, Joe -- Smallwood, Margaret F -- Segura, Vincent -- Townsend, Theresa -- Vyas, Darshna -- Winzer, Thilo -- Bowles, Dianna -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):328-31. doi: 10.1126/science.1182612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK. iag1@york.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075252" target="_blank"〉PubMed〈/a〉
    Keywords: Antimalarials/*metabolism ; Artemisia/*genetics/*metabolism ; Artemisinins/*metabolism ; *Chromosome Mapping ; Crosses, Genetic ; DNA, Complementary ; Gene Expression Profiling ; *Genes, Plant ; Genetic Association Studies ; Humans ; Malaria/drug therapy ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2010-04-24
    Description: We generated a high-resolution whole-genome sequence and individually deleted 5100 genes in Sigma1278b, a Saccharomyces cerevisiae strain closely related to reference strain S288c. Similar to the variation between human individuals, Sigma1278b and S288c average 3.2 single-nucleotide polymorphisms per kilobase. A genome-wide comparison of deletion mutant phenotypes identified a subset of genes that were conditionally essential by strain, including 44 essential genes unique to Sigma1278b and 13 unique to S288c. Genetic analysis indicates the conditional phenotype was most often governed by complex genetic interactions, depending on multiple background-specific modifiers. Our comprehensive analysis suggests that the presence of a complex set of modifiers will often underlie the phenotypic differences between individuals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dowell, Robin D -- Ryan, Owen -- Jansen, An -- Cheung, Doris -- Agarwala, Sudeep -- Danford, Timothy -- Bernstein, Douglas A -- Rolfe, P Alexander -- Heisler, Lawrence E -- Chin, Brian -- Nislow, Corey -- Giaever, Guri -- Phillips, Patrick C -- Fink, Gerald R -- Gifford, David K -- Boone, Charles -- DK076284/DK/NIDDK NIH HHS/ -- GM035010/GM/NIGMS NIH HHS/ -- GM069676/GM/NIGMS NIH HHS/ -- P01 NS055923/NS/NINDS NIH HHS/ -- R01 GM035010/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):469. doi: 10.1126/science.1189015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413493" target="_blank"〉PubMed〈/a〉
    Keywords: Crosses, Genetic ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; *Genes, Essential ; *Genes, Fungal ; Genetic Variation ; Genome, Fungal ; Genotype ; Mutation ; Phenotype ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2012-04-21
    Description: Salicylate, a plant product, has been in medicinal use since ancient times. More recently, it has been replaced by synthetic derivatives such as aspirin and salsalate, both of which are rapidly broken down to salicylate in vivo. At concentrations reached in plasma after administration of salsalate or of aspirin at high doses, salicylate activates adenosine monophosphate-activated protein kinase (AMPK), a central regulator of cell growth and metabolism. Salicylate binds at the same site as the synthetic activator A-769662 to cause allosteric activation and inhibition of dephosphorylation of the activating phosphorylation site, threonine-172. In AMPK knockout mice, effects of salicylate to increase fat utilization and to lower plasma fatty acids in vivo were lost. Our results suggest that AMPK activation could explain some beneficial effects of salsalate and aspirin in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawley, Simon A -- Fullerton, Morgan D -- Ross, Fiona A -- Schertzer, Jonathan D -- Chevtzoff, Cyrille -- Walker, Katherine J -- Peggie, Mark W -- Zibrova, Darya -- Green, Kevin A -- Mustard, Kirsty J -- Kemp, Bruce E -- Sakamoto, Kei -- Steinberg, Gregory R -- Hardie, D Grahame -- 080982/Wellcome Trust/United Kingdom -- 097726/Wellcome Trust/United Kingdom -- MC_U127088492/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 May 18;336(6083):918-22. doi: 10.1126/science.1215327. Epub 2012 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517326" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases/genetics/*metabolism ; Amino Acid Substitution ; Animals ; Aspirin/pharmacology ; Binding Sites ; Carbohydrate Metabolism/drug effects ; Cell Line ; Enzyme Activation ; Enzyme Activators/pharmacology ; HEK293 Cells ; Humans ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism ; Mice ; Mice, Knockout ; Mutation ; Oxygen Consumption/drug effects ; Phosphorylation ; Pyrones/pharmacology ; Rats ; Salicylates/blood/*metabolism/*pharmacology ; Thiophenes/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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