amda 2 13 a major update for automated cross platform microarray data analysis

Microarray platforms require analytical pipelines with modules for data pre-processing including data normalization, statistical analysis for identification of differentially expressed genes, cluster analysis, and functional annotation. We previously developed the Automated Microarray Data Analysis (AMDA, version 2.3.5) pipeline to process Affymetrix 3′ IVT GeneChips. The availability of newer technologies that demand open-source tools for microarray data analysis has impelled us to develop an updated multi-platform version, AMDA 2.13. It includes additional quality control metrics, annotation-driven (annotation grade of Affymetrix NetAffx) and signal-driven (Inter-Quartile Range) gene filtering, and approaches to experimental design. To enhance understanding of biological data, differentially expressed genes have been mapped into KEGG pathways. Finally, a more stable and user-friendly interface was designed to integrate the requirements for different platforms. AMDA 2.13 allows the analysis of Affymetrix..

Commentaires topographiques à l'Énéide

Castagnoli Ferdinando. Commentaires topographiques à l'Énéide. In: Comptes rendus des séances de l'Académie des Inscriptions et Belles-Lettres, 127ᵉ année, N. 1, 1983. pp. 202-215

Testudo, tegula deliciaris e il tempio di Giove capitolino

Ferdinando Castagnoli, Testudo, tegula deliciaris e il tempio di Giove capitolino, p. 37-45. Si critica la teoria che il tempio di Giove capitolino avesse un tetto a tre falde. Essa si basa 1) sulla debole indicazione offerta da un frammento di tegola trovata ad Ardea, che deve appartenere a un tetto a più falde (ma non necessariamente al tetto di un tempio; si prende occasione per discutere anche la definizione che è stata proposta di questo tipo di tegola corne tegula deliciaris : è più probabile infatti che si debba parlare di t. angularis ; la t. deliciaris è invece da spiegarsi, in modo simmetricamente opposto alla t. colliciaris, tegola convessa) ; 2) su una interpretazione non corretta di Servio, ad Aen. IX, 446; 3) sullo studio del tipo di tetto a ventaglio documentato dalla architettura sepolcrale etrusca; in questo tipo di tetto sarebbe da riconoscersi la testudo descritta da Servio, ad Aen. I, 505 (è invece più probabile che questo termine indichi una edicola coperta con volta, all'interno della cella).Castagnoli Ferdinando. Testudo, tegula deliciaris e il tempio di Giove capitolino. In: Mélanges de l'École française de Rome. Antiquité, tome 98, n°1. 1986. pp. 37-45

Les sanctuaires du Latium archaïque

Castagnoli Ferdinando. Les sanctuaires du Latium archaïque. In: Comptes rendus des séances de l'Académie des Inscriptions et Belles-Lettres, 121ᵉ année, N. 3, 1977. pp. 460-476

Biomarkers of Primary Resistance to Trastuzumab in HER2-Positive Metastatic Gastric Cancer Patients: the AMNESIA Case-Control Study

Purpose: Refining the selection of HER2-positive metastatic gastric cancer patient candidates for trastuzumab is a challenge of precision oncology. Preclinical studies have suggested several genomic mechanisms of primary resistance, leading to activation of tyrosine kinase receptors other than HER2 or downstream signaling pathways.Experimental Design: We carried out this multicenter, prospective, case-control study to demonstrate the negative predictive impact of a panel of candidate genomic alterations (AMNESIA panel), including EGFR/MET/KRAS/PI3K/PTEN mutations and EGFR/MET/KRAS amplifications. Hypothesizing a prevalence of candidate alterations of 30% and 0% in resistant and sensitive HER2-positive patients, respectively, 20 patients per group were needed.Results: AMNESIA panel alterations were significantly more frequent in resistant (11 of 20, 55%) as compared with sensitive (0% of 17) patients (P < 0.001), and in HER2 IHC 2+ (7 of 13, 53.8%) than 3+ (4 of 24, 16.7%) tumors (P = 0.028). Patients with tumors bearing no candidate alterations had a significantly longer median progression-free [5.2 vs. 2.6 months; HR, 0.34; 95% confidence interval (CI), 0.07-0.48; P = 0.001] and overall survival (16.1 vs. 7.6 months; HR, 0.38; 95% CI, 0.09-0.75; P = 0.015). The predictive accuracy of the AMNESIA panel and HER2 IHC was 76% and 65%, respectively. The predictive accuracy of the combined evaluation of the AMNESIA panel and HER2 IHC was 84%.Conclusions: Our panel of candidate genomic alterations may be clinically useful to predict primary resistance to trastuzumab in patients with HER2-positive metastatic gastric cancer and should be further validated with the aim of molecularly stratifying HER2-addicted cancers for the development of novel treatment strategies. Clin Cancer Res; 1-8. ©2017 AACR