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  • 1
    Publication Date: 2012-11-08
    Description: Author(s): P. Zheng, Y. G. Shi, Q. S. Wu, G. Xu, T. Dong, Z. G. Chen, R. H. Yuan, B. Cheng, K. Yamaura, J. L. Luo, and N. L. Wang We present the specific heat, magnetization, optical spectroscopy measurements, and the first-principles calculations on the Weberite structure Ca 2 Os 2 O 7 single-crystal/polycrystalline sample. The Ca 2 Os 2 O 7 shows a Curie-Weiss nature at high temperature and goes into a ferrimagnetic insulating state a... [Phys. Rev. B 86, 195108] Published Wed Nov 07, 2012
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 2
    Publication Date: 2009-09-04
    Description: Differential DNA methylation of the paternal and maternal alleles regulates the parental origin-specific expression of imprinted genes in mammals. The methylation imprints are established in male and female germ cells during gametogenesis, and the de novo DNA methyltransferase DNMT3A and its cofactor DNMT3L are required in this process. However, the mechanisms underlying locus- and parental-specific targeting of the de novo DNA methylation machinery in germline imprinting are poorly understood. Here we show that amine oxidase (flavin-containing) domain 1 (AOF1), a protein related to the lysine demethylase KDM1 (also known as LSD1), functions as a histone H3 lysine 4 (H3K4) demethylase and is required for de novo DNA methylation of some imprinted genes in oocytes. AOF1, now renamed lysine demethylase 1B (KDM1B) following a new nomenclature, is highly expressed in growing oocytes where genomic imprints are established. Targeted disruption of the gene encoding KDM1B had no effect on mouse development and oogenesis. However, oocytes from KDM1B-deficient females showed a substantial increase in H3K4 methylation and failed to set up the DNA methylation marks at four out of seven imprinted genes examined. Embryos derived from these oocytes showed biallelic expression or biallelic suppression of the affected genes and died before mid-gestation. Our results suggest that demethylation of H3K4 is critical for establishing the DNA methylation imprints during oogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ciccone, David N -- Su, Hui -- Hevi, Sarah -- Gay, Frederique -- Lei, Hong -- Bajko, Jeffrey -- Xu, Guoliang -- Li, En -- Chen, Taiping -- England -- Nature. 2009 Sep 17;461(7262):415-8. doi: 10.1038/nature08315. Epub 2009 Sep 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Epigenetics Program, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727073" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; *DNA Methylation ; Embryo Loss/genetics ; Embryo, Mammalian/metabolism ; Female ; Gene Expression Regulation, Developmental ; Genes, Developmental/genetics ; *Genomic Imprinting ; Histones/*metabolism ; Male ; Mice ; *Mothers ; NIH 3T3 Cells ; Oocytes/metabolism ; Oxidoreductases, N-Demethylating/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2009-07-28
    Description: The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590770/" 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/PMC4590770/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Harris H -- Isaacs, Farren J -- Carr, Peter A -- Sun, Zachary Z -- Xu, George -- Forest, Craig R -- Church, George M -- DP5 OD009172/OD/NIH HHS/ -- England -- Nature. 2009 Aug 13;460(7257):894-8. doi: 10.1038/nature08187. Epub 2009 Jul 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. hhwang@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19633652" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Biotechnology/instrumentation/*methods ; Carotenoids/biosynthesis ; Chromosomes, Bacterial/genetics ; DNA/biosynthesis/genetics ; Directed Molecular Evolution/instrumentation/*methods ; Escherichia coli/cytology/*genetics/*metabolism ; Genetic Variation/genetics ; Genome, Bacterial/*genetics ; Pentosephosphates/biosynthesis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-05-25
    Description: CD8(+) T cell responses focus on a small fraction of pathogen- or vaccine-encoded peptides, and for some pathogens, these restricted recognition hierarchies limit the effectiveness of antipathogen immunity. We found that simian immunodeficiency virus (SIV) protein-expressing rhesus cytomegalovirus (RhCMV) vectors elicit SIV-specific CD8(+) T cells that recognize unusual, diverse, and highly promiscuous epitopes, including dominant responses to epitopes restricted by class II major histocompatibility complex (MHC) molecules. Induction of canonical SIV epitope-specific CD8(+) T cell responses is suppressed by the RhCMV-encoded Rh189 gene (corresponding to human CMV US11), and the promiscuous MHC class I- and class II-restricted CD8(+) T cell responses occur only in the absence of the Rh157.5, Rh157.4, and Rh157.6 (human CMV UL128, UL130, and UL131) genes. Thus, CMV vectors can be genetically programmed to achieve distinct patterns of CD8(+) T cell epitope recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816976/" 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/PMC3816976/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hansen, Scott G -- Sacha, Jonah B -- Hughes, Colette M -- Ford, Julia C -- Burwitz, Benjamin J -- Scholz, Isabel -- Gilbride, Roxanne M -- Lewis, Matthew S -- Gilliam, Awbrey N -- Ventura, Abigail B -- Malouli, Daniel -- Xu, Guangwu -- Richards, Rebecca -- Whizin, Nathan -- Reed, Jason S -- Hammond, Katherine B -- Fischer, Miranda -- Turner, John M -- Legasse, Alfred W -- Axthelm, Michael K -- Edlefsen, Paul T -- Nelson, Jay A -- Lifson, Jeffrey D -- Fruh, Klaus -- Picker, Louis J -- P01 AI094417/AI/NIAID NIH HHS/ -- P51 OD 011092/OD/NIH HHS/ -- R01 AI059457/AI/NIAID NIH HHS/ -- R01 AI060392/AI/NIAID NIH HHS/ -- U24 OD010850/OD/NIH HHS/ -- New York, N.Y. -- Science. 2013 May 24;340(6135):1237874. doi: 10.1126/science.1237874.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704576" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CD8-Positive T-Lymphocytes/*immunology ; Cytokines/immunology ; Cytomegalovirus/genetics/*immunology ; Epitopes, T-Lymphocyte/*immunology ; Female ; Genetic Vectors/genetics/*immunology ; Histocompatibility Antigens Class II/immunology ; Humans ; Macaca mulatta ; Male ; Membrane Glycoproteins/genetics ; SAIDS Vaccines/administration & dosage/*immunology ; Viral Envelope Proteins/genetics
    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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  • 5
    Publication Date: 1997-09-26
    Description: DNA-(cytosine-5) methyltransferase (MCMT) methylates newly replicated mammalian DNA, but the factors regulating this activity are unknown. Here, MCMT is shown to bind proliferating cell nuclear antigen (PCNA), an auxiliary factor for DNA replication and repair. Binding of PCNA requires amino acids 163 to 174 of MCMT, occurs in intact cells at foci of newly replicated DNA, and does not alter MCMT activity. A peptide derived from the cell cycle regulator p21(WAF1) can disrupt the MCMT-PCNA interaction, which suggests that p21(WAF1) may regulate methylation by blocking access of MCMT to PCNA. MCMT and p21(WAF1) may be linked in a regulatory pathway, because the extents of their expression are inversely related in both SV40-transformed and nontransformed cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chuang, L S -- Ian, H I -- Koh, T W -- Ng, H H -- Xu, G -- Li, B F -- New York, N.Y. -- Science. 1997 Sep 26;277(5334):1996-2000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemical Carcinogenesis Laboratory, Institute of Molecular and Cell Biology, National University of Singapore, Kent Ridge Crescent, Singapore 119260, Republic of Singapore.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9302295" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Line, Transformed ; Cell Nucleus/metabolism ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclins/chemistry/*metabolism ; DNA (Cytosine-5-)-Methyltransferase/*metabolism ; DNA Damage ; *DNA Methylation ; DNA Repair ; DNA Replication ; Humans ; Molecular Sequence Data ; Peptides/pharmacology ; Proliferating Cell Nuclear Antigen/*metabolism ; Recombinant Fusion Proteins/metabolism/pharmacology ; Tumor Cells, Cultured
    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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  • 6
    Publication Date: 2011-03-23
    Description: Inhibitor of kappaB (IkappaB) kinase (IKK) phosphorylates IkappaB proteins, leading to their degradation and the liberation of nuclear factor kappaB for gene transcription. Here we report the crystal structure of IKKbeta in complex with an inhibitor, at a resolution of 3.6 A. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, alpha-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with IkappaBalpha that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKKbeta dimerization, but dimerization per se is not important for maintaining IKKbeta activity and instead is required for IKKbeta activation. Other IKK family members, IKKalpha, TBK1 and IKK-i, may have a similar trimodular architecture and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081413/" 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/PMC3081413/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Guozhou -- Lo, Yu-Chih -- Li, Qiubai -- Napolitano, Gennaro -- Wu, Xuefeng -- Jiang, Xuliang -- Dreano, Michel -- Karin, Michael -- Wu, Hao -- R01 AI050872/AI/NIAID NIH HHS/ -- R01 AI050872-10/AI/NIAID NIH HHS/ -- R01 AI079260/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Apr 21;472(7343):325-30. doi: 10.1038/nature09853. Epub 2011 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21423167" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Biocatalysis ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; I-kappa B Kinase/*antagonists & inhibitors/*chemistry/metabolism ; Models, Molecular ; Protein Binding ; Protein Multimerization ; Protein Structure, Tertiary ; Substrate Specificity ; Ubiquitin/chemistry ; Xenopus laevis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2015-03-25
    Description: Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671316/" 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/PMC4671316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Guotai -- Chapman, J Ross -- Brandsma, Inger -- Yuan, Jingsong -- Mistrik, Martin -- Bouwman, Peter -- Bartkova, Jirina -- Gogola, Ewa -- Warmerdam, Daniel -- Barazas, Marco -- Jaspers, Janneke E -- Watanabe, Kenji -- Pieterse, Mark -- Kersbergen, Ariena -- Sol, Wendy -- Celie, Patrick H N -- Schouten, Philip C -- van den Broek, Bram -- Salman, Ahmed -- Nieuwland, Marja -- de Rink, Iris -- de Ronde, Jorma -- Jalink, Kees -- Boulton, Simon J -- Chen, Junjie -- van Gent, Dik C -- Bartek, Jiri -- Jonkers, Jos -- Borst, Piet -- Rottenberg, Sven -- 090532/Wellcome Trust/United Kingdom -- 104558/Wellcome Trust/United Kingdom -- P30 CA016672/CA/NCI NIH HHS/ -- Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2015 May 28;521(7553):541-4. doi: 10.1038/nature14328. Epub 2015 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK. ; Department of Genetics, Erasmus, University Medical Center, 3000 CA Rotterdam, The Netherlands. ; Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. ; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic. ; Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark. ; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; Protein Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; Deep Sequencing Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands. ; DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms, Hertfordshire EN6 3LD, UK. ; 1] Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic [2] Danish Cancer Society Research Center, 2100 Copenhagen, Denmark. ; 1] Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands [2] Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laengassstrasse 122, 3012 Bern, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25799992" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors/metabolism ; BRCA1 Protein/deficiency/genetics/metabolism ; Cell Line ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; *DNA Breaks, Double-Stranded ; DNA-Binding Proteins/metabolism ; Drug Resistance, Neoplasm/genetics ; Histones/metabolism ; Humans ; Immunoglobulin Class Switching/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mad2 Proteins/deficiency/genetics/*metabolism ; Mice ; Nuclear Proteins/metabolism ; *Poly(ADP-ribose) Polymerase Inhibitors ; *Recombinational DNA Repair ; Trans-Activators/metabolism ; Ubiquitin-Protein Ligases/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
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  • 8
    Publication Date: 2016-07-28
    Description: Author(s): W. M. Xu, G. R. Hearne, and M. P. Pasternak The magnetic and electrical-transport properties of CuFe O 2 have been studied by temperature-dependent Fe 57 Mössbauer spectroscopy and resistance measurements to near megabar (∼100 GPa) pressures. Previous studies show that CuFe O 2 comprises the following sublattices at P 〉 23 GPa : 1 3 [ Cu ( S = 1 / 2 ) 2 + Fe ( S = 2 … [Phys. Rev. B 94, 035155] Published Wed Jul 27, 2016
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 9
    Publication Date: 2014-03-14
    Description: Author(s): J. D. Rameau, S. Freutel, L. Rettig, I. Avigo, M. Ligges, Y. Yoshida, H. Eisaki, J. Schneeloch, R. D. Zhong, Z. J. Xu, G. D. Gu, P. D. Johnson, and U. Bovensiepen The dressing of quasiparticles in solids is investigated by changes in the electronic structure E(k) driven by femtosecond laser pulses. Employing time- and angle-resolved photoemission on an optimally doped cuprate above Tc, we observe two effects with different characteristic temporal evolutions a... [Phys. Rev. B 89, 115115] Published Thu Mar 13, 2014
    Keywords: Electronic structure and strongly correlated systems
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  • 10
    Publication Date: 2017-07-11
    Description: Author(s): W. M. Xu, G. R. Hearne, S. Layek, D. Levy, J-P. Itié, M. P. Pasternak, G. Kh. Rozenberg, and E. Greenberg X-ray diffraction studies to ∼ 90 GPa at room temperature show that F e 2 Ti O 4 ferrous inverse spinel undergoes the following sequence of structural transitions: cubic ( F d 3 ¯ m ) → ∼ 8 GPa tetragonal ( I 4 1 / a m d ) → ∼ 16 GPa orthorhombic ( C m c m ) → ∼ 55 GPa orthorhombic ( P m m a ) , at the indicated onset transition pressures. Within th... [Phys. Rev. B 96, 045108] Published Mon Jul 10, 2017
    Keywords: Electronic structure and strongly correlated systems
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    Topics: Physics
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