1,721,054 research outputs found
Comment on Size-dependent modifications of the Raman spectrum of rutile TIO2 [Appl. Phys. Lett. 89, 163118 (2006)]
No full textReverse engineering of natural systems by graph theory
Full text linkWith the advent of high-throughput technology, Biological research widened its horizons in terms of biomarkers and mechanisms of action of several diseases and phenotypes. On the other hand, complex diseases, like diabetes, several neurodegenerative pathologies and cancer, are still orphan of a cause and then of a cure. One of the possible reasons is that these are not strictly monogenic diseases since they result from a global interplay between molecular players and master regulators. In this context, where “the whole is something over and above its parts and not just the sum of them all” (Aristotle 384-322 B.C.), is clear that the Cartesian reductionism cannot completely help understand how a disease arises and develops.
Systems Biology comes on the stage here and puts emphasis on whole behavior as being basically indivisible. It sustains the Smuts’s holistic theory according to which whole systems such as cells, tissues, organisms, and populations were proposed to have unique emergent properties and that it was impossible to reassemble the behavior of the whole from the properties of the individual components. Hence, new technologies were necessary to define and understand the behavior of systems. New mathematical models and computational approaches emerged in the past decades. Thereby taking inspiration from the theory of graphs. Aspects of nature that could be explained by the interaction of individual agents were modeled as networks and their properties studied topologically. Speculations on the global structure of biological systems were based on two important assertions: systems have a hierarchical structure, and the structure is held together by numerous linkages to construct very complex networks.
In this work, we retrace this path by first reconstructing and studying a complex molecular system made by gene and microRNA expression profiles in patients affected by colorectal cancer. We show how the study of topological properties of the system helped identifying a tiny subnetwork of master-regulator and effectors that, individually, were associated to poor survival rates when extremely expressed. Group-effects were not captured, until the development of Pyntacle, a cross-platform and open source Python suite of high-performance computing algorithms for the discovery of key-players in networks. Pyntacle is introduced and presented in this work and then used proficiently in two other case studies. The former regards ecological food webs and reports on the
assessment of their nestedness property, which is an indicator of their global robustness and redundancy. The latter is an exploration of the relationships between sex and ageing process in Drosophila melanogaster, which developed into two computational steps: definition of co-expressing modules of genes and identification of sex independent key-players molecules in male and female flies
Synchrotron light characterization of free metal and oxide nanoparticles
No full textThis work presents a pioneering experimental approach to the study of the interaction of free transition metal nano-sized systems with synchrotron radiation. The results of experiments performed on titanium and titanium oxide nanoparticles (clusters) are presented. The choice for these systems was mainly motivated by their strategic character from the point of view of nanostructured materials assembling, as Ti-based nanostructured materials are widely used in several application fields. The details of the developed experimental set-up and conceptual tools are described. The designed experimental set-up enables independent probing of morphology, reactivity and decay dynamics of excited states of the free nanoparticles, and this results to be mandatory for the emerging complexity of the system under study. Characterization of the nanoparticles is presented in the central part of the work. The chemical reactivity to molecular species of free Ti and TiOx nanoparticles is discussed. The reported morphology, structure and decay dynamics of nanoparticles demonstrate the need for a new picture for their description, alternative to the compact spherical shape model usually adopted for cluster spectroscopy experimental results, and nearer to concepts which are more familiar to the aerosol community. The presented results open interesting perspectives in the view of filling the gap between applications of nanostructured materials and their fundamental understanding
"Theoretical dependence of the B1 field amplitude from the radio frequency shield diameter in 1.5 and 3 T birdcage coils"
No full text
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
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