Abstract:
:We describe several algorithms with winning performance in the Dialogue for Reverse Engineering Assessments and Methods (DREAM2) Reverse Engineering Competition 2007. After the gold standards for the challenges were released, the performance of the algorithms could be thoroughly evaluated under different parameters or alternative ways of solving systems of equations. For the analysis of Challenge 4, the "In-silico" challenges, we employed methods to explicitly deal with perturbation data and time-series data. We show that original methods used to produce winning submissions could easily be altered to substantially improve performance. For Challenge 5, the genome-scale Escherichia coli network, we evaluated a variety of measures of association. These data are troublesome, and no good solutions could be produced, either by us or by any other teams. Our best results were obtained when analyzing subdatasets instead of considering the dataset as a whole.
journal_name
Ann N Y Acad Scijournal_title
Annals of the New York Academy of Sciencesauthors
Scheinine A,Mentzen WI,Fotia G,Pieroni E,Maggio F,Mancosu G,de la Fuente Adoi
10.1111/j.1749-6632.2008.04100.xsubject
Has Abstractpub_date
2009-03-01 00:00:00pages
287-301eissn
0077-8923issn
1749-6632pii
NYAS04100journal_volume
1158pub_type
杂志文章abstract::Biologics are playing an increasingly significant role in the practice of modern medicine and surgery in general and orthopedics in particular. Cell-based approaches are among the most important and widely used modalities in orthopedic biologics, with mesenchymal stem cells and other multi/pluripotent cells undergoing...
journal_title:Annals of the New York Academy of Sciences
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abstract::Approximately 90% of all cancer deaths arise from metastasis formation. Hence, understanding the molecular mechanisms underlying tumor progression, local invasion, and the formation of tumor metastases represents one of the great challenges in exploratory cancer research. Recent experimental results indicate that chan...
journal_title:Annals of the New York Academy of Sciences
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abstract::Scant empirical attention has been devoted to understanding endings in youth mentoring relationships, despite the frequency with which they occur. This study examined data from a mixed-methods study of mentoring relationship endings in which youth mentees, the youth's parents or guardians, mentors, and program staff w...
journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章
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abstract::The ability to recognize and discriminate conspecific faces and facial expressions has played a critical role in the evolution of social communication. Darwin was one of the first to speculate that human and nonhuman primate facial expressions share similar mechanisms for production and functions in expressing emotion...
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journal_title:Annals of the New York Academy of Sciences
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abstract::Dr. Josep Font (Barcelona, 1953-2006) devoted his professional career to the care of patients with systemic autoimmune diseases (SAD). In 1995, he created the Department of Autoimmune Diseases at the Hospital Clinic in Barcelona, a pioneering unit in Europe specifically dedicated to the clinical management of these pa...
journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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abstract::CISD2, the causative gene for Wolfram syndrome 2 (WFS2), is an evolutionarily conserved novel gene. Recently, we have demonstrated that CISD2 is involved in mammalian lifespan control; this work also establishes WFS2 as a mitochondria-mediated disorder and effectively links CISD2 gene function, mitochondrial integrity...
journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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更新日期:1987-01-01 00:00:00
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journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章,评审
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更新日期:2012-09-01 00:00:00
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journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
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更新日期:1994-09-15 00:00:00
abstract::We have previously described proopiomelanocortin (POMC) gene-expression in human normal cultured dermal fibroblasts, and its dose- and time-dependent modulation by transforming growth factor-beta (TGF-beta) and tumor necrosis factor-alpha (TNF-alpha). The aim of the work described here was to investigate POMC-derived ...
journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章
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journal_title:Annals of the New York Academy of Sciences
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更新日期:2004-06-01 00:00:00
abstract::The intracellular bacterium, Ehrlichia ruminantium, is the causative agent of heartwater, a tick-borne disease of livestock. Because vaccines need to incorporate components from several virulent isolates, it is essential to have information on the extent of genetic variation among isolates. We therefore amplified and ...
journal_title:Annals of the New York Academy of Sciences
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更新日期:2005-12-01 00:00:00
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journal_title:Annals of the New York Academy of Sciences
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更新日期:2005-11-01 00:00:00
abstract::In thalassemia, iron overload is the joint outcome of excessive iron absorption and transfusional siderosis. While iron absorption is limited by a physiologic ceiling of about 3 mg/d, plasma iron turnover in thalassemia may be 10 to 15 times normal, caused by the wasteful, ineffective erythropoiesis of an enormously e...
journal_title:Annals of the New York Academy of Sciences
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更新日期:1998-06-30 00:00:00
abstract::The cell nucleus is a prominent target of autoantibodies in systemic autoimmune disorders. Approximately 2% of the population in Europe and North America suffers from systemic rheumatic diseases, such as rheumatoid arthritis, systemic lupus erythematosus (SLE), and scleroderma. The molecular mechanisms of systemic aut...
journal_title:Annals of the New York Academy of Sciences
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更新日期:2005-06-01 00:00:00
abstract::Epigenetic modification of CpG islands (CGIs) in promoter regions is an important regulatory mechanism of gene expression in eukaryotic cells. Hypermethylation of CGIs may silence a gene, whereas hypomethylation of previously methylated CGIs allows gene expression. The pattern of methylation is cell-type-specific and ...
journal_title:Annals of the New York Academy of Sciences
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journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章
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更新日期:1987-01-01 00:00:00
abstract::We have developed a rabbit model of in utero exposure to intravenous injections of cocaine given twice daily to dams from gestational days 8-29. At the doses employed (4 mg/kg, injected twice daily), no differences were found in the body weight gain of dams, time to delivery, litter size, and body weight or other phys...
journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章
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更新日期:1998-06-21 00:00:00
abstract::The purpose of this paper is to review the advances in electromagnetic levitation techniques as tools for determination of the thermophysical properties of molten metals under standard gravity and microgravity conditions. We show that a combination of containerless processing and microgravity offers the exclusive poss...
journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章
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更新日期:2002-10-01 00:00:00
abstract::Management of gastroesophageal junction (GEJ) adenocarcinoma is a controversial topic. The rising incidence of this cancer requires a clear consensus to ensure proper management. Application of oncological principles for tumors of the esophagus or stomach is not possible because of comparative differences in the biolo...
journal_title:Annals of the New York Academy of Sciences
pub_type: 杂志文章,评审
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更新日期:2018-12-01 00:00:00