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  • 1
    Publication Date: 2018-03-27
    Description: NAMD goes quantum: an integrative suite for hybrid simulations NAMD goes quantum: an integrative suite for hybrid simulations, Published online: 26 March 2018; doi:10.1038/nmeth.4638 The integration of quantum chemistry and molecular dynamics programs coupled with a graphical user interface provides a streamlined tool for powerful simulations of biomolecular reaction mechanisms.
    Print ISSN: 1548-7091
    Electronic ISSN: 1548-7105
    Topics: Biology , Medicine
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  • 2
    Publication Date: 2015-02-07
    Description: Most undergraduates give high ratings to research experiences. Studies report that these experiences improve participation and persistence, often by strengthening students' views of themselves as scientists. Yet, the evidence for these claims is weak. More than half the 60 studies reviewed rely on self-report surveys or interviews. Rather than introducing new images of science, research experiences may reinforce flawed images especially of research practices and conceptual understanding. The most convincing studies show benefits for mentoring and for communicating the nature of science, but the ideas that students learn are often isolated or fragmented rather than integrated and coherent. Rigorous research is needed to identify ways to design research experiences so that they promote integrated understanding. These studies need powerful and generalizable assessments that can document student progress, help distinguish effective and ineffective aspects of the experiences, and illustrate how students interpret the research experiences they encounter. To create research experiences that meet the needs of interested students and make effective use of scarce resources, we encourage systematic, iterative studies with multiple indicators of success.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Linn, Marcia C -- Palmer, Erin -- Baranger, Anne -- Gerard, Elizabeth -- Stone, Elisa -- New York, N.Y. -- Science. 2015 Feb 6;347(6222):1261757. doi: 10.1126/science.1261757.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, Berkeley, CA, USA. mclinn@berkeley.edu. ; University of California, Berkeley, CA, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25657254" target="_blank"〉PubMed〈/a〉
    Keywords: *Career Choice ; Curriculum ; *Mentors ; Research/*education ; Students
    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
    Publication Date: 2014-10-25
    Description: Cellular circuits sense the environment, process signals, and compute decisions using networks of interacting proteins. To model such a system, the abundance of each activated protein species can be described as a stochastic function of the abundance of other proteins. High-dimensional single-cell technologies, such as mass cytometry, offer an opportunity to characterize signaling circuit-wide. However, the challenge of developing and applying computational approaches to interpret such complex data remains. Here, we developed computational methods, based on established statistical concepts, to characterize signaling network relationships by quantifying the strengths of network edges and deriving signaling response functions. In comparing signaling between naive and antigen-exposed CD4(+) T lymphocytes, we find that although these two cell subtypes had similarly wired networks, naive cells transmitted more information along a key signaling cascade than did antigen-exposed cells. We validated our characterization on mice lacking the extracellular-regulated mitogen-activated protein kinase (MAPK) ERK2, which showed stronger influence of pERK on pS6 (phosphorylated-ribosomal protein S6), in naive cells as compared with antigen-exposed cells, as predicted. We demonstrate that by using cell-to-cell variation inherent in single-cell data, we can derive response functions underlying molecular circuits and drive the understanding of how cells process signals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334155/" 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/PMC4334155/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krishnaswamy, Smita -- Spitzer, Matthew H -- Mingueneau, Michael -- Bendall, Sean C -- Litvin, Oren -- Stone, Erica -- Pe'er, Dana -- Nolan, Garry P -- 1K01DK095008/DK/NIDDK NIH HHS/ -- 1R01CA130826/CA/NCI NIH HHS/ -- 1U54CA121852-01A1/CA/NCI NIH HHS/ -- CA 09-011/CA/NCI NIH HHS/ -- HHSN268201000034C/HV/NHLBI NIH HHS/ -- HHSN272200700038C/PHS HHS/ -- HV-10-05/HV/NHLBI NIH HHS/ -- K01 DK095008/DK/NIDDK NIH HHS/ -- P01 CA034233/CA/NCI NIH HHS/ -- R00 GM104148/GM/NIGMS NIH HHS/ -- R01 CA130826/CA/NCI NIH HHS/ -- S10RR027582-01/RR/NCRR NIH HHS/ -- U19 AI057229/AI/NIAID NIH HHS/ -- U19 AI100627/AI/NIAID NIH HHS/ -- U54 CA149145/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2014 Nov 28;346(6213):1250689. doi: 10.1126/science.1250689. Epub 2014 Oct 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, NY, USA. ; Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. ; Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA. ; Molecular Biology Section, Division of Biological Sciences, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. ; Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, NY, USA. dpeer@biology.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25342659" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CD4-Positive T-Lymphocytes/*immunology ; Computer Simulation ; Image Cytometry ; Male ; Mice ; Mice, Mutant Strains ; Mitogen-Activated Protein Kinase 1/genetics ; Receptors, Antigen, T-Cell/*metabolism ; Ribosomal Protein S6/metabolism ; Signal Transduction ; Single-Cell Analysis/*methods ; Systems Biology/*methods ; eIF-2 Kinase/metabolism
    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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  • 4
    Publication Date: 2018-02-09
    Description: Treatment choices for acute myelogenous leukemia (AML) patients resistant to conventional chemotherapies are limited and novel therapeutic agents are needed. IL3 receptor alpha (IL3Rα, or CD123) is expressed on the majority of AML blasts, and there is evidence that its expression is increased on leukemic relative to normal hematopoietic stem cells, which makes it an attractive target for antibody-based therapy. Here, we report the generation and preclinical characterization of SGN-CD123A, an antibody–drug conjugate using the pyrrolobenzodiazepine dimer (PBD) linker and a humanized CD123 antibody with engineered cysteines for site-specific conjugation. Mechanistically, SGN-CD123A induces activation of DNA damage response pathways, cell-cycle changes, and apoptosis in AML cells. In vitro , SGN-CD123A–mediated potent cytotoxicity of 11/12 CD123 + AML cell lines and 20/23 primary samples from AML patients, including those with unfavorable cytogenetic profiles or FLT3 mutations. In vivo , SGN-CD123A treatment led to AML eradication in a disseminated disease model, remission in a subcutaneous xenograft model, and significant growth delay in a multidrug resistance xenograft model. Moreover, SGN-CD123A also resulted in durable complete remission of a patient-derived xenograft AML model. When combined with a FLT3 inhibitor quizartinib, SGN-CD123A enhanced the activity of quizartinib against two FLT3-mutated xenograft models. Overall, these data demonstrate that SGN-CD123A is a potent antileukemic agent, supporting an ongoing trial to evaluate its safety and efficacy in AML patients (NCT02848248). Mol Cancer Ther; 17(2); 554–64. ©2017 AACR .
    Print ISSN: 1535-7163
    Electronic ISSN: 1538-8514
    Topics: Medicine
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  • 5
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    German Medical Science GMS Publishing House; Düsseldorf
    In:  G-I-N Conference 2012; 20120822-20120825; Berlin; DOCO73 /20120710/
    Publication Date: 2012-07-11
    Keywords: ddc: 610
    Language: English
    Type: conferenceObject
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  • 6
    ISSN: 0197-4556
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters A 178 (1993), S. 105-113 
    ISSN: 0375-9601
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters A 155 (1991), S. 29-42 
    ISSN: 0375-9601
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of neurochemistry 21 (1973), S. 0 
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: —Exhaustive stress in rats is followed by a temporary reduction of hypothalamic norepinephrine (NE) together with a persistent increase in turnover during recovery. To test for persistent alterations of NE storage and metabolism produced by stress, rats were subjected to 3 h of forced running and were then injected intraventricularly with [3H]NE or [3H]dopamine (DA). The hypothalamus was assayed for [3H]NE and its metabolites at various intervals after injection. The effects of stress were compared with those of reserpine (7·5 mg/kg) or α-methyltyrosine (AMT, 300 mg/kg) pretreatment. It was found that the stress-induced reduction of endogenous NE was not accompanied by a change in the accumulation of exogenous [3H]NE either 10 or 30 min after injection, whereas the NE depletions produced by reserpine or AMT were associated with decreased or increased accumulation, respectively. However, stress did produce an increased accumulation of [3H]NE endogenously synthesized from [3H]DA. These results indicate that exhaustive stress does not adversely affect the storage of NE. They also suggest that stores of NE depleted by stress are replenished chiefly with newly synthesized NE and not through an increased uptake and binding or decreased metabolism of extraneuronal NE. The latter factors may play a role in the maintenance of brain NE stores when biosynthesis is low, i.e. after AMT. The major metabolites of exogenous [3H]NE, at 30 min after injection, were identified as conjugates of 3,4-dihydroxyphenylglycol (DOPEG) and 3-methoxy-4-hydroxyphenylglycol (MOPEG) in approximately equal amounts. The finding of high levels of conjugated DOPEG confirms a recent report (Slgden and Eccleston, 1971) that this compound is a major metabolite of brain NE. Reserpine produced marked elevations of both conjugates; AMT slightly reduced each. Prior stress increased only conjugated MOPEG, an observation suggesting that CNS levels of this metabolite may reflect NE released by nervous activity.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1434-6036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract A generalized version of the Nordheim model, appropriate to a metal with an anisotropic electron mean-free-path, is used to derive a lower bound upon the resistivity of a wire of diameterd when scattering from the wire surface is completely diffuse. Measurements of the electrical resistivities of thin tungsten wires are presented and shown to fall below this lower bound. These measurements are therefore inconsistent with the existence of completely diffuse surface scattering. Within the framework of the model, the data determine an amount of specular scattering specified by a specularity parameter of magnitudep≧0.2.
    Type of Medium: Electronic Resource
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