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  • Wiley  (10)
  • Oxford University Press  (6)
  • American Association for the Advancement of Science (AAAS)  (5)
  • 2010-2014  (15)
  • 1990-1994  (6)
  • 1
    Publication Date: 2013-01-03
    Description: [1]  CMIP5 multimodel ensemble projection of midlatitude storm track changes has been examined. Storm track activity is quantified by temporal variance of meridional wind and sea level pressure (psl), as well as cyclone track statistics. For the Southern Hemisphere (SH), CMIP5 models project clear poleward migration, upward expansion, and intensification of the storm track. For the Northern Hemisphere (NH), the models also project some poleward shift and upward expansion of the storm track in the upper troposphere/lower stratosphere, but mainly weakening of the storm track toward its equatorward flank in the troposphere. Consistent with these, CMIP5 models project significant increase in the frequency of extreme cyclones during the SH cool season, but significant decrease in such events in the NH. Comparisons with CMIP3 projections indicate high degrees of consistency for SH projections, but significant differences are found in the NH. Overall, CMIP5 models project larger decrease in storm track activity in the NH troposphere, especially over North America in winter, where psl variance as well as cyclone frequency and amplitude are all projected to decrease significantly. In terms of climatology, similar to CMIP3, most CMIP5 models simulate storm tracks that are too weak and display equatorward biases in their latitude. These biases have also been related to future projections. In the NH, the strength of a model's climatological storm track is negatively correlated with its projected amplitude change under global warming, while in the SH, models with large equatorward biases in storm track latitude tend to project larger poleward shifts.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2012-07-22
    Description: During V(D)J recombination, the RAG1/2 recombinase is thought to play an active role in transferring newly excised recombination ends from the RAG post-cleavage complex (PCC) to the non-homologous end joining (NHEJ) machinery to promote appropriate antigen receptor gene assembly. However, this transfer mechanism is poorly understood, partly because of the technical difficulty in revealing weak association of coding ends (CEs) with one of the PCCs, coding end complex (CEC). Using fluorescence resonance energy transfer (FRET) and anisotropy measurement, we present here real-time monitoring of the RAG1/2-catalyzed cleavage reaction, and provide unequivocal evidence that CEs are retained within the CEC in the presence of Mg 2+ . By examining the dynamic fluorescence changes during the cleavage reaction, we compared the stability of CEC assembled with core RAG1 paired with full-length RAG2, core RAG2 or a frameshift RAG2 mutant that was speculated to destabilize the PCC, leading to increased aberrant joining. While the latter two CECs exhibit similar stability, the full-length RAG2 renders a less stable CEC unless H3K4me3 peptides are added. Interestingly, the RAG2 mutant appears to modulate the structure of the RAG-12RSS pre-cleavage complex. Thus, the fluorescence-based detection offers a sensitive, quantitative and continuous assessment of pre-cleavage complex assembly and CEC stability.
    Keywords: Recombination
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2014-05-01
    Description: The teicoplanin-associated locus regulator (TcaR) regulates gene expression of proteins on the intercellular adhesion (ica) locus involved in staphylococci poly- N -acetylglucosamine biosynthesis. The absence of TcaR increases poly- N -acetylglucosamine production and promotes biofilm formation. Until recently, the mechanism of multiple antibiotic resistance regulator family protein members, such as TcaR, was restricted to binding double-stranded DNA. However, we recently found that TcaR strongly interacts with single-stranded DNA, which is a new role for this family of proteins. In this study, we report Staphylococcus epidermidis TcaR–single-stranded DNA complex structures. Our model suggests that TcaR and single-stranded DNA form a 6 1 -symmetry polymer composed of TcaR dimers with single-stranded DNA that wraps outside the polymer and 12 nt per TcaR dimer. Single-stranded DNA binding to TcaR involves a large conformational change at the DNA binding lobe. Several point mutations involving the single-stranded DNA binding surface validate interactions between single-stranded DNA and TcaR. Our results extend the novel role of multiple antibiotic resistance regulator family proteins in staphylococci.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2013-12-11
    Description: [1]  Cyclones are responsible for much of the high impact weather in the extratropics, thus how they will change under global warming is of great concern. Several studies have used the multi-model climate simulations conducted under Phase 5 of the Coupled Model Intercomparison Project (CMIP5) to examine such changes. One study suggested that the frequency of strong cyclones is projected to decrease over the North Pacific, while another concluded that this frequency will increase. [2]  A single tracking algorithm has been used to derive cyclone statistics from 23 CMIP5 simulations using two different definitions of cyclones: cyclones as minima in total sea level pressure (SLP), or cyclones as minima in SLP perturbations about a large scale, low frequency background. When cyclones are defined by total SLP, the frequency of deep cyclones over the Pacific is projected to increase, while if cyclones are defined as perturbations, this frequency is projected to decrease. These differences are shown to be due to a projected deepening of the climatological mean Aleutian low. [3]  In view of these results, it is important to critically assess how cyclones should be defined. Preliminary results suggest that among CMIP5 simulations, over the Pacific, both the projected changes in the frequency of high wind events and mean available potential energy are better correlated with the projected changes in the frequency of cyclones defined as perturbations. It is concluded that more research should be done to quantify and understand the impacts of the different definitions of cyclones.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2014-08-27
    Description: : MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models. Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline ( Broudy et al. , 2014 ) and used via graphical user interface. Contact: ovitek@purdue.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 1990-11-16
    Description: Glycosylphosphatidylinositol (GPI) serves as a membrane anchor for a large number of eukaryotic proteins. A genetic approach was used to investigate the biosynthesis of GPI anchor precursors in mammalian cells. T cell hybridoma mutants that cannot synthesize dolichol-phosphate-mannose (Dol-P-Man) also do not express on their surface GPI-anchored proteins such as Thy-1 and Ly-6A. These mutants cannot form mannose-containing GPI precursors. Transfection with the yeast Dol-P-Man synthase gene rescues the synthesis of both Dol-P-Man and mannose-containing GPI precursors, as well as the surface expression of Thy-1 and Ly-6A, suggesting that Dol-P-Man is the donor of at least one mannose residue in the GPI core.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DeGasperi, R -- Thomas, L J -- Sugiyama, E -- Chang, H M -- Beck, P J -- Orlean, P -- Albright, C -- Waneck, G -- Sambrook, J F -- Warren, C D -- AR-03564/AR/NIAMS NIH HHS/ -- HD-16942/HD/NICHD NIH HHS/ -- HD-21087/HD/NICHD NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1990 Nov 16;250(4983):988-91.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Massachusetts General Hospital, Boston 02114.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1978413" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, Ly/metabolism ; Antigens, Surface/metabolism ; Antigens, Thy-1 ; Cell Membrane/physiology ; Dolichol Monophosphate Mannose/metabolism ; *Genes, Fungal ; Glycolipids/*biosynthesis ; Glycosylphosphatidylinositols ; Hybridomas ; Phosphatidylinositols/*biosynthesis ; Rats ; Saccharomyces cerevisiae/genetics ; *Transfection
    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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  • 7
    Publication Date: 1994-04-29
    Description: In a search for genes that regulate circadian rhythms in mammals, the progeny of mice treated with N-ethyl-N-nitrosourea (ENU) were screened for circadian clock mutations. A semidominant mutation, Clock, that lengthens circadian period and abolishes persistence of rhythmicity was identified. Clock segregated as a single gene that mapped to the midportion of mouse chromosome 5, a region syntenic to human chromosome 4. The power of ENU mutagenesis combined with the ability to clone murine genes by map position provides a generally applicable approach to study complex behavior in mammals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839659/" 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/PMC3839659/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vitaterna, M H -- King, D P -- Chang, A M -- Kornhauser, J M -- Lowrey, P L -- McDonald, J D -- Dove, W F -- Pinto, L H -- Turek, F W -- Takahashi, J S -- P30-CA07175/CA/NCI NIH HHS/ -- R01-DK40493/DK/NIDDK NIH HHS/ -- T32 NS071040/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- etc. -- New York, N.Y. -- Science. 1994 Apr 29;264(5159):719-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Physiology, Northwestern University, Evanston, IL 60208.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8171325" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Chromosome Mapping ; Chromosomes, Human, Pair 4 ; Circadian Rhythm/*genetics ; Ethylnitrosourea ; Female ; *Genes ; Genotype ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; *Mutagenesis ; Phenotype
    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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  • 8
    Publication Date: 2012-06-08
    Description: The mammalian intestinal tract is colonized by trillions of beneficial commensal bacteria that are anatomically restricted to specific niches. However, the mechanisms that regulate anatomical containment remain unclear. Here, we show that interleukin-22 (IL-22)-producing innate lymphoid cells (ILCs) are present in intestinal tissues of healthy mammals. Depletion of ILCs resulted in peripheral dissemination of commensal bacteria and systemic inflammation, which was prevented by administration of IL-22. Disseminating bacteria were identified as Alcaligenes species originating from host lymphoid tissues. Alcaligenes was sufficient to promote systemic inflammation after ILC depletion in mice, and Alcaligenes-specific systemic immune responses were associated with Crohn's disease and progressive hepatitis C virus infection in patients. Collectively, these data indicate that ILCs regulate selective containment of lymphoid-resident bacteria to prevent systemic inflammation associated with chronic diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659421/" 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/PMC3659421/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sonnenberg, Gregory F -- Monticelli, Laurel A -- Alenghat, Theresa -- Fung, Thomas C -- Hutnick, Natalie A -- Kunisawa, Jun -- Shibata, Naoko -- Grunberg, Stephanie -- Sinha, Rohini -- Zahm, Adam M -- Tardif, Melanie R -- Sathaliyawala, Taheri -- Kubota, Masaru -- Farber, Donna L -- Collman, Ronald G -- Shaked, Abraham -- Fouser, Lynette A -- Weiner, David B -- Tessier, Philippe A -- Friedman, Joshua R -- Kiyono, Hiroshi -- Bushman, Frederic D -- Chang, Kyong-Mi -- Artis, David -- 2-P30 CA016520/CA/NCI NIH HHS/ -- AI061570/AI/NIAID NIH HHS/ -- AI074878/AI/NIAID NIH HHS/ -- AI083480/AI/NIAID NIH HHS/ -- AI087990/AI/NIAID NIH HHS/ -- AI095466/AI/NIAID NIH HHS/ -- AI095608/AI/NIAID NIH HHS/ -- AI47619/AI/NIAID NIH HHS/ -- K08 DK093784/DK/NIDDK NIH HHS/ -- K08-DK093784/DK/NIDDK NIH HHS/ -- P30 AI 045008/AI/NIAID NIH HHS/ -- P30DK50306/DK/NIDDK NIH HHS/ -- R01 AI061570/AI/NIAID NIH HHS/ -- R01 AI074878/AI/NIAID NIH HHS/ -- R01 AI095466/AI/NIAID NIH HHS/ -- R01 AI102942/AI/NIAID NIH HHS/ -- R21 AI083480/AI/NIAID NIH HHS/ -- R21 AI087990/AI/NIAID NIH HHS/ -- T32 AI007532/AI/NIAID NIH HHS/ -- T32 AI055428/AI/NIAID NIH HHS/ -- T32 RR007063/RR/NCRR NIH HHS/ -- T32-AI007532/AI/NIAID NIH HHS/ -- T32-AI055428/AI/NIAID NIH HHS/ -- T32-RR007063/RR/NCRR NIH HHS/ -- U01 AI095608/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2012 Jun 8;336(6086):1321-5. doi: 10.1126/science.1222551. Epub 2012 Jun 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22674331" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Alcaligenes/immunology/isolation & purification/*physiology ; Animals ; Bacterial Translocation ; Crohn Disease/immunology/microbiology ; Hepatitis C, Chronic/immunology/microbiology ; Humans ; Immunity, Innate ; Inflammation ; Interleukins/administration & dosage/biosynthesis/*immunology ; Intestines/*immunology/microbiology ; Leukocyte L1 Antigen Complex/metabolism ; Liver/microbiology ; Lymph Nodes/immunology ; Lymphocytes/*immunology ; Lymphoid Tissue/*immunology/*microbiology ; Macaca mulatta ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Spleen/microbiology ; Young Adult
    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: 2014-05-31
    Description: A substantial literature shows that U.S. early childhood interventions have important long-term economic benefits. However, there is little evidence on this question for developing countries. We report substantial effects on the earnings of participants in a randomized intervention conducted in 1986-1987 that gave psychosocial stimulation to growth-stunted Jamaican toddlers. The intervention consisted of weekly visits from community health workers over a 2-year period that taught parenting skills and encouraged mothers and children to interact in ways that develop cognitive and socioemotional skills. The authors reinterviewed 105 out of 129 study participants 20 years later and found that the intervention increased earnings by 25%, enough for them to catch up to the earnings of a nonstunted comparison group identified at baseline (65 out of 84 participants).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574862/" 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/PMC4574862/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gertler, Paul -- Heckman, James -- Pinto, Rodrigo -- Zanolini, Arianna -- Vermeersch, Christel -- Walker, Susan -- Chang, Susan M -- Grantham-McGregor, Sally -- R01 HD054702/HD/NICHD NIH HHS/ -- R01HD54702/HD/NICHD NIH HHS/ -- R37 HD065072/HD/NICHD NIH HHS/ -- R37HD065072/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2014 May 30;344(6187):998-1001. doi: 10.1126/science.1251178.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California Berkeley, Berkeley, CA, USA. National Bureau of Economic Research (NBER), Cambridge, MA, USA. gertler@haas.berkeley.edu. ; University of Chicago, Chicago, IL, USA. American Bar Foundation, Chicago, IL, USA. Institute for Fiscal Studies, University College London, London, UK. ; University of Chicago, Chicago, IL, USA. ; The World Bank, Washington, DC, USA. ; The University of The West Indies, Kingston, Jamaica. ; University College London, London, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876490" target="_blank"〉PubMed〈/a〉
    Keywords: *Child Development ; Child, Preschool ; Cognition ; Developing Countries/*statistics & numerical data ; Early Intervention (Education)/*statistics & numerical data ; Emotions ; Employment/*economics/trends ; Female ; Humans ; Infant ; Jamaica ; Male ; Mother-Child Relations/*psychology ; Parenting/psychology ; Psychology ; Salaries and Fringe Benefits/*statistics & numerical data ; Young Adult
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2013-12-18
    Description: Tumor recurrence is a leading cause of cancer mortality. Therapies for recurrent disease may fail, at least in part, because the genomic alterations driving the growth of recurrences are distinct from those in the initial tumor. To explore this hypothesis, we sequenced the exomes of 23 initial low-grade gliomas and recurrent tumors resected from the same patients. In 43% of cases, at least half of the mutations in the initial tumor were undetected at recurrence, including driver mutations in TP53, ATRX, SMARCA4, and BRAF; this suggests that recurrent tumors are often seeded by cells derived from the initial tumor at a very early stage of their evolution. Notably, tumors from 6 of 10 patients treated with the chemotherapeutic drug temozolomide (TMZ) followed an alternative evolutionary path to high-grade glioma. At recurrence, these tumors were hypermutated and harbored driver mutations in the RB (retinoblastoma) and Akt-mTOR (mammalian target of rapamycin) pathways that bore the signature of TMZ-induced mutagenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998672/" 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/PMC3998672/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Brett E -- Mazor, Tali -- Hong, Chibo -- Barnes, Michael -- Aihara, Koki -- McLean, Cory Y -- Fouse, Shaun D -- Yamamoto, Shogo -- Ueda, Hiroki -- Tatsuno, Kenji -- Asthana, Saurabh -- Jalbert, Llewellyn E -- Nelson, Sarah J -- Bollen, Andrew W -- Gustafson, W Clay -- Charron, Elise -- Weiss, William A -- Smirnov, Ivan V -- Song, Jun S -- Olshen, Adam B -- Cha, Soonmee -- Zhao, Yongjun -- Moore, Richard A -- Mungall, Andrew J -- Jones, Steven J M -- Hirst, Martin -- Marra, Marco A -- Saito, Nobuhito -- Aburatani, Hiroyuki -- Mukasa, Akitake -- Berger, Mitchel S -- Chang, Susan M -- Taylor, Barry S -- Costello, Joseph F -- 1T32CA15102201/CA/NCI NIH HHS/ -- K08 NS079485/NS/NINDS NIH HHS/ -- K08NS079485/NS/NINDS NIH HHS/ -- P01CA81403/CA/NCI NIH HHS/ -- P30 CA082103/CA/NCI NIH HHS/ -- P30CA82103/CA/NCI NIH HHS/ -- P50 CA097257/CA/NCI NIH HHS/ -- P50CA097257/CA/NCI NIH HHS/ -- R01 CA163336/CA/NCI NIH HHS/ -- R01 CA169316/CA/NCI NIH HHS/ -- R01CA163336/CA/NCI NIH HHS/ -- R01CA169316-01/CA/NCI NIH HHS/ -- R25NS070680/NS/NINDS NIH HHS/ -- T32 CA128583/CA/NCI NIH HHS/ -- T32GM008568/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jan 10;343(6167):189-93. doi: 10.1126/science.1239947. Epub 2013 Dec 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336570" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Alkylating/*adverse effects/therapeutic use ; Brain/drug effects/pathology ; Brain Neoplasms/*drug therapy/genetics/*pathology ; DNA Helicases/genetics ; DNA Mutational Analysis ; Dacarbazine/adverse effects/*analogs & derivatives/therapeutic use ; Glioma/*drug therapy/genetics/*pathology ; Humans ; Mutagenesis/drug effects ; Neoplasm Grading ; Neoplasm Recurrence, Local/*chemically induced/drug therapy/*genetics ; Nuclear Proteins/genetics ; Proto-Oncogene Proteins B-raf/genetics ; Proto-Oncogene Proteins c-akt/genetics ; TOR Serine-Threonine Kinases/genetics ; Transcription Factors/genetics ; Tumor Suppressor Protein p53/genetics
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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