1,721,009 research outputs found
Advancements in multivariate analysis of variance
Full text linkDespite the progress made in recent years, the field of multivariate analysis of data from designed experiments is still young. Several open questions remain unanswered, and there is a need to make the methodology available to a broader audience. The aim of this special issue was therefore to stimulate and explore advances in methods, applications, and software for multivariate ANOVA.
The collection of papers includes methodical improvements, practical applications, a tutorial, and a software demonstration. Application areas range from spectroscopic control of fermentation processes to metabolomics and gene expressions. Overall, this issue showcases the power and applicability of multivariate ANOVA methods in a wide range of domains
Extension of SO-PLS to multi-way arrays: SO-N-PLS
No full textMulti-way data arrays are becoming more common in several fields of science. For instance, analytical instruments can sometimes collect signals at different modes simultaneously, as e.g. fluorescence and LC/GC-MS. Higher order data can also arise from sensory science, were product scores can be reported as function of sample, judge and attribute. Another example is process monitoring, where several process variables can be measured over time for several batches. In addition, so-called multi-block data sets where several blocks of data explain the same set of samples are becoming more common. Several methods exist for analyzing either multi-way or multi block data, but there has been little attention on methods that combine these two data properties. A common procedure is to "unfold" multi-way arrays in order to obtain two-way data tables on which classical multi-block methods can be applied. However, it is a known fact that unfolding can lead to overfitted models due to increased flexibility in parameter estimation. In this paper we present a novel multi-block regression method that can handle multi-way data blocks. This method is a combination of a multi-block method called Sequential and Orthogonalized-PLS (SO-PLS) and the multi-way version of PLS, N-PLS. The new method is therefore called SO-N-PLS. We have compared the method to Multi-block-PLS (MB-PLS) and SO-PLS on unfolded data. We investigate the hypotheses that SO-N-PLS has better performances on small data sets and noisy data, and that SO-N-PLS models are easier to interpret. The hypotheses are investigated by a simulation study and two real data examples; one dealing with regression and one with classification. The simulation study show that SO-N-PLS predicts better than the unfolded methods when the sample size is small and the data is noisy. This is due to the fact that it filters out the noise better than MB-PLS and SO-PLS. For the real data examples, the differences in prediction are small but the multi-way method allows easier interpretation
MAGE I transcription factors regulate KAP1 and KRAB domain zinc finger transcription factor mediated gene repression.
No full textClass I MAGE proteins (MAGE I) are normally expressed only in developing germ cells but are aberrantly expressed in many cancers. They have been shown to promote tumor survival, aggressive growth, and chemoresistance but the underlying mechanisms and MAGE I functions have not been fully elucidated. KRAB domain zinc finger transcription factors (KZNFs) are the largest group of vertebrate transcription factors and regulate neoplastic transformation, tumor suppression, cellular proliferation, and apoptosis. KZNFs bind the KAP1 protein and direct KAP1 to specific DNA sequences where it suppresses gene expression by inducing localized heterochromatin characterized by histone 3 lysine 9 trimethylation (H3me3K9). Discovery that MAGE I proteins also bind to KAP1 prompted us to investigate whether MAGE I can affect KZNF and KAP1 mediated gene regulation. We found that expression of MAGE I proteins, MAGE-A3 or MAGE-C2, relieved repression of a reporter gene by ZNF382, a KZNF with tumor suppressor activity. ChIP of MAGE I (-) HEK293T cells showed KAP1 and H3me3K9 are normally bound to the ID1 gene, a target of ZNF382, but that binding is greatly reduced in the presence of MAGE I proteins. MAGE I expression relieved KAP1 mediated ID1 repression, causing increased expression of ID1 mRNA and ID1 chromatin relaxation characterized by loss of H3me3K9. MAGE I binding to KAP1 also induced ZNF382 poly-ubiquitination and degradation, consistent with loss of ZNF382 leading to decreased KAP1 binding to ID1. In contrast, MAGE I expression caused increased KAP1 binding to Ki67, another KAP1 target gene, with increased H3me3K9 and decreased Ki67 mRNA expression. Since KZNFs are required to direct KAP1 to specific genes, these results show that MAGE I proteins can differentially regulate members of the KZNF family and KAP1 mediated gene repression
MAGE-I proteins and cancer-pathways: A bidirectional relationship
No full textData emerged from the last 20 years of basic research on tumor antigens positioned the type I MAGE (Melanoma Antigen GEnes – I or MAGE-I) family as cancer driver factors. MAGE-I gene expression is mainly restricted to normal reproductive tissues. However, abnormal re-expression in cancer unbalances the cell status towards enhanced oncogenic activity or reduced tumor suppression. Anomalous MAGE-I gene re-expression in cancer is attributed to altered epigenetic-mediated chromatin silencing. Still, emerging data indicate that MAGE-I can be regulated at protein level. Results from different laboratories suggest that after its anomalous re-expression, specific MAGE-I proteins can be regulated by well-known signaling pathways or key cellular processes that finally potentiate the cancer cell phenotype. Thus, MAGE-I proteins both regulate and are regulated by cancer-related pathways. Here, we present an updated review highlighting the recent findings on the regulation of MAGE-I by oncogenic pathways and the potential consequences in the tumor cell behavior.Fil: Pascucci, Franco Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Escalada, Micaela Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Suberbordes, Melisa del Valle. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Vidal, Candela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Ladelfa, Maria Fatima. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Monte, Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentin
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
MAGE I regulates KAP1 gene binding, trimethylation of histone 3 on lysine 9, and gene repression in HEK293T cells.
No full text<p>MAGE I expression <i>decreases</i> binding of KAP1, H3me3K9, and repression of the <i>ID1</i> tumor suppressor gene (A, B, D). In contrast, MAGE I expression <i>increases</i> binding of KAP1, H3me3K9, and repression of mRNA and protein levels of the <i>Ki67</i> gene (E, F, H, I, J, L). Note MAGE I binds to <i>Ki67</i> gene sites but not <i>ID1</i> gene sites (C, G, K). “M” denotes Mock transfection control. “A3” and “C2” denote MAGE-A3 and MAGE-C2, respectively.</p
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Caffeine-dependent genetic interaction of <i>MAGE</i> with <i>ATM</i>, <i>ATR</i> and <i>Rad51</i>(<i>SpnA</i>).
No full text<p>(A) Representative eye phenotypes of <i>MAGE</i> (<i>EGUF/+; FRT82B sst<sup>RZ</sup>/FRT82B GMR-hid</i>, loss of <i>MAGE</i> in eye cells), <i>ey>ATMi</i> (knockdown of <i>ATM</i> in eye cells), <i>ey>ATMi;MAGE</i> (<i>EGUF/UAS-ATM-RNAi;FRT82B sst<sup>RZ</sup>/FRT82B GMR-hid,</i> loss of <i>MAGE</i> and knockdown of ATM in eye cells) and <i>ey>ATRi;MAGE</i> (<i>EGUF/UAS-ATR-RNAi;FRT82B sst<sup>RZ</sup>/FRT82B GMR-hid,</i> loss of <i>MAGE</i> and knockdown of ATR in eye cells) flies that were reared on either standard media or media containing 2 mM caffeine. The EGUF system carrying the <i>eyeless-Gal4</i> driver was used to drive the UAS-RNAi transgenes in the eye and also makes the eye homozygous for <i>MAGE</i> (<i>sst<sup>RZ</sup>)</i>. Controls for the effects of each eyeless-driven RNAi alone were carried out for <i>ATM</i> and <i>ATR</i> resulting in wild type appearing eyes, but only the results of <i>ATM</i> RNAi are shown here as an example. (B) Representative eye phenotypes of <i>MAGE</i> knockdown (<i>eyeless-Gal4/+;UAS-MAGE-RNAi/UAS-Dicer2,</i> knockdown of <i>MAGE</i> in eye cells) and <i>MAGE Rad51</i> double knockdown (<i>eyeless-Gal4/UAS-SpnA-RNAi;UAS-MAGE-RNAi/UAS-Dicer2</i>, knockdown of <i>MAGE</i> and <i>Rad51</i> in eye cells) flies that were reared on either standard media or media containing 2 mM caffeine.</p
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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