Dictionary learning improves subtyping of breast cancer aCGH data

Author(s):  
Salvatore Masecchia ◽  
Annalisa Barla ◽  
Saverio Salzo ◽  
Alessandro Verri
2014 ◽  
Vol 26 (12) ◽  
pp. 2855-2895 ◽  
Author(s):  
Saverio Salzo ◽  
Salvatore Masecchia ◽  
Alessandro Verri ◽  
Annalisa Barla

We present an algorithm for dictionary learning that is based on the alternating proximal algorithm studied by Attouch, Bolte, Redont, and Soubeyran ( 2010 ), coupled with a reliable and efficient dual algorithm for computation of the related proximity operators. This algorithm is suitable for a general dictionary learning model composed of a Bregman-type data fit term that accounts for the goodness of the representation and several convex penalization terms on the coefficients and atoms, explaining the prior knowledge at hand. As Attouch et al. recently proved, an alternating proximal scheme ensures better convergence properties than the simpler alternating minimization. We take care of the issue of inexactness in the computation of the involved proximity operators, giving a sound stopping criterion for the dual inner algorithm, which keeps under control the related errors, unavoidable for such a complex penalty terms, providing ultimately an overall effective procedure. Thanks to the generality of the proposed framework, we give an application in the context of genome-wide data understanding, revising the model proposed by Nowak, Hastie, Pollack, and Tibshirani ( 2011 ). The aim is to extract latent features (atoms) and perform segmentation on array-based comparative genomic hybridization (aCGH) data. We improve several important aspects that increase the quality and interpretability of the results. We show the effectiveness of the proposed model with two experiments on synthetic data, which highlight the enhancements over the original model.


Author(s):  
G. Kasnic ◽  
S. E. Stewart ◽  
C. Urbanski

We have reported the maturation of an intracisternal A-type particle in murine plasma cell tumor cultures and three human tumor cell cultures (rhabdomyosarcoma, lung adenocarcinoma, and osteogenic sarcoma) after IUDR-DMSO activation. In all of these studies the A-type particle seems to develop into a form with an electron dense nucleoid, presumably mature, which is also intracisternal. A similar intracisternal A-type particle has been described in leukemic guinea pigs. Although no biological activity has yet been demonstrated for these particles, on morphologic grounds, and by the manner in which they develop within the cell, they may represent members of the same family of viruses.


Author(s):  
John L. Swedo ◽  
R. W. Talley ◽  
John H. L. Watson

Since the report, which described the ultrastructure of a metastatic nodule of human breast cancer after estrogen therapy, additional ultrastructural observations, including some which are correlative with pertinent findings in the literature concerning mycoplasmas, have been recorded concerning the same subject. Specimen preparation was identical to that in.The mitochondria possessed few cristae, and were deteriorated and vacuolated. They often contained particulates and fibrous structures, sometimes arranged in spindle-shaped bundles, Fig. 1. Another apparent aberration was the occurrence, Fig. 2 (arrows) of linear profiles of what seems to be SER, which lie between layers of RER, and are often recognizably continuous with them.It was noted that the structure of the round bodies, interpreted as within autophagic vacuoles in the previous communication, and of vesicular bodies, described morphologically closely resembled those of some mycoplasmas. Specifically, they simulated or reflected the various stages of replication reported for mycoplasmas grown on solid nutrient. Based on this observation, they are referred to here as “mycoplasma-like” structures, in anticipation of confirmatory evidence from investigations now in progress.


2010 ◽  
Vol 34 (8) ◽  
pp. S49-S49
Author(s):  
Lei Wang ◽  
Xun Zhou ◽  
Lihong Zhou ◽  
Yong Chen ◽  
Xun Zhu ◽  
...  

2010 ◽  
Vol 34 (8) ◽  
pp. S47-S47
Author(s):  
Guopei Zheng ◽  
Sisi Yi ◽  
Yafei Li ◽  
Fangren Kong ◽  
Yanhui Yu ◽  
...  

2001 ◽  
Vol 120 (5) ◽  
pp. A741-A741
Author(s):  
P ANG ◽  
D SCHRAG ◽  
K SCHNEIDER ◽  
K SHANNON ◽  
J JOHNSON ◽  
...  

Ob Gyn News ◽  
2005 ◽  
Vol 40 (8) ◽  
pp. 39
Author(s):  
Bruce Jancin
Keyword(s):  

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