| 1. |
- Weinstein, John N., et al.
(author)
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The cancer genome atlas pan-cancer analysis project
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Research review (peer-reviewed)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Campo, E, et al.
(author)
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The International Consensus Classification of Mature Lymphoid Neoplasms: a report from the Clinical Advisory Committee
- 2022
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In: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 140:11, s. 1229-1253
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Journal article (peer-reviewed)abstract
- Since the publication of the Revised European-American Classification of Lymphoid Neoplasms in 1994, subsequent updates of the classification of lymphoid neoplasms have been generated through iterative international efforts to achieve broad consensus among hematopathologists, geneticists, molecular scientists, and clinicians. Significant progress has recently been made in the characterization of malignancies of the immune system, with many new insights provided by genomic studies. They have led to this proposal. We have followed the same process that was successfully used for the third and fourth editions of the World Health Organization Classification of Hematologic Neoplasms. The definition, recommended studies, and criteria for the diagnosis of many entities have been extensively refined. Some categories considered provisional have now been upgraded to definite entities. Terminology for some diseases has been revised to adapt nomenclature to the current knowledge of their biology, but these modifications have been restricted to well-justified situations. Major findings from recent genomic studies have impacted the conceptual framework and diagnostic criteria for many disease entities. These changes will have an impact on optimal clinical management. The conclusions of this work are summarized in this report as the proposed International Consensus Classification of mature lymphoid, histiocytic, and dendritic cell tumors.
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| 5. |
- Niinemets, Ue., et al.
(author)
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Estimations of isoprenoid emission capacity from enclosure studies: measurements, data processing, quality and standardized measurement protocols
- 2011
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In: Biogeosciences. - : Copernicus GmbH. - 1726-4189. ; 8:8, s. 2209-2246
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Journal article (peer-reviewed)abstract
- The capacity for volatile isoprenoid production under standardized environmental conditions at a certain time (E-S, the emission factor) is a key characteristic in constructing isoprenoid emission inventories. However, there is large variation in published E-S estimates for any given species partly driven by dynamic modifications in E-S due to acclimation and stress responses. Here we review additional sources of variation in E-S estimates that are due to measurement and analytical techniques and calculation and averaging procedures, and demonstrate that estimations of E-S critically depend on applied experimental protocols and on data processing and reporting. A great variety of experimental setups has been used in the past, contributing to study-to-study variations in E-S estimates. We suggest that past experimental data should be distributed into broad quality classes depending on whether the data can or cannot be considered quantitative based on rigorous experimental standards. Apart from analytical issues, the accuracy of E-S values is strongly driven by extrapolation and integration errors introduced during data processing. Additional sources of error, especially in meta-database construction, can further arise from inconsistent use of units and expression bases of E-S. We propose a standardized experimental protocol for BVOC estimations and highlight basic meta-information that we strongly recommend to report with any E-S measurement. We conclude that standardization of experimental and calculation protocols and critical examination of past reports is essential for development of accurate emission factor databases.
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| 6. |
- Staudt, A, et al.
(author)
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beta(1)-Adrenoceptor antibodies induce positive inotropic response in isolated cardiomyocytes.
- 2001
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In: European journal of pharmacology. - 0014-2999. ; 423:2-3, s. 115-9
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Journal article (peer-reviewed)abstract
- beta(1)-Adrenoceptor autoantibodies are present in approximately 30% of patients suffering from dilated cardiomyopathy. The inotropic effects mediated by these antibodies remain to be studied. Monoclonal antibodies were raised against a peptide corresponding to the second extracellular loop of the human beta(1)-adrenoceptor in balb/C mouse (n=6), and were characterized by enzyme immunoassay after purification by protein A. Purified immunoglobulin G from non-immunized animals (controls) did not influence Ca(2+) transient and cell shortening of rat cardiomyocytes measured by confocal-laser-scanning-microscopy. beta(1)-adrenoceptor antibodies caused a dose-related increase in Ca(2+) transient (dilution 1:2: +35.3+/-5.1%), and in cell shortening (dilution 1:2: +40.5+/-6.3%) (P<0.01 vs. controls). The effect of the beta(1)-adrenoceptor antibodies was blocked by the antigenic peptide and by the antagonist metoprolol. In addition, beta(1)-adrenoceptor antibodies induced a dose-dependent increase of the cyclic adenosine monophosphate. The inotropic response induced by isoproterenol was attenuated by the beta(1)-adrenoceptor antibody. beta(1)-adrenoceptor antibodies as partial agonists induce a specific positive inotropic effect via the protein-kinase-A-cascade.
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| 7. |
- Breznau, Nate, et al.
(author)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
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In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
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Journal article (peer-reviewed)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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