21,392 research outputs found
Entropy of a network ensemble: definitions and applications to genomic data
No full textIn this paper we introduce the framework for the application of statistical mechanics to network theory, with a particular emphasis to the concept of entropy of network ensembles. This formalism provides novel observables and insights for the analysis of high-throughput transcriptomics data, integrated with apriori biological knowledge, embedded in-to available public databases of protein-protein interaction and cell signaling
Systems Biology approaches to cancer: towards new therapeutical strategies and personalized approaches
No full textNetwork approaches are ubiquitous, from social and ecological systems up to complex biological processes. In our recently published work we used the network framework for a Systems Medicine approach to multiple cancer types, in order to highlight similitudes and differences that can be exploited to extend existing therapeutical strategies. These approaches shed new light to oncological processes, but allow also to pose “old” questions (like the search for novel drug targets) in a “new” way
Título: Operum
No full textSign.: a-e\p4\s A-Z\p4\s, 2A-2Z\p4\s, 3A-3Z\p4\s, 4A-4F\p4\sPort. con gravado xilográficoContén: Metamorphoseon libri X
Il ruolo del rumore nei sistemi biologici
No full textDa qualche tempo, la matematica si occupa di questioni che non sono soltanto quelle, tradizionali, che nascono in ambito fisico. In particolare, sempre più determinato ed efficace si va facendo il suo intervento a fianco delle scienze della vita
Explosive percolation in correlation-based networks
No full textWe show briefly the features of a percolation transition related to the networks obtained from a correlation matrix. The most interesting behaviour of this transition, investigated by numerical simulations with different thresholding rules, is that it shows a much faster transition from the disaggregated to the clustered phase, that resembles what has been described as an “explosive” percolation. A comparison with the “classic” random network percolation is shown, together with some applications of these concepts to the networks obtained from real data, that behave differently depending on the data intrinsic structure
Network measures for protein folding state discrimination
No full textProteins fold using a two-state or multi-state kinetic mechanisms, but up to now there is not a first-principle model to explain this different behavior. We exploit the network properties of protein structures by introducing novel observables to address the problem of classifying the different types of folding kinetics. These observables display a plain physical meaning, in terms of vibrational modes, possible configurations compatible with the native protein structure, and folding cooperativity. The relevance of these observables is supported by a classification performance up to 90%, even with simple classifiers such as discriminant analysis
On the cospectrality between graphs and pseudographs
No full textIn this paper we introduce a spectrum-preserving relation between graphs with loops and graphs without loops. Our approach generalizes the spectral results obtained on
stars to a wider class of graphs, namely
stars with or without loops. The proposed equivalence of the two classes of graphs allows to study pseudographs as simple graphs, by extending the techniques developed for simple graphs to pseudographs, without losing information, and it could be relevant for applications of graph theory to complex systems physics and neural networks. Finally, in order to make the demonstrated results easily applicable, we have provided a public Github repository where Python code that allows straightforward implementations of the outcomes is made available
Report on Meteorological Research March 1, 1935 (m-1)
No full textThe object of the report was to elucidate in detail the various features of the research program in meteorology being carried on at the Daniel Guggenheim Airship Institute in Akron, Ohio. Mr. L. J. Fangman, of the U.S. Weather Bureau, was collaborating with the author in carrying out work such as a study of autographic records of the various meteorological elements during frontal passages with a view to the possible prediction of the intensity of the accompanying disturbance as it may affect the operation of aircraft and a study of atmospheric gustiness with a view to finding the dependence between frequency end amplitude of velocity fluctuations and the vertical temperature and velocity gradients
Merging 1D and 3D genomic information: Challenges in modelling and validation
No full textGenome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and structure of DNA and chromatin inside the nucleus of the cell. It is now clear that these mechanisms have a key role in important processes like gene regulation, yet the detailed ways they act simultaneously and, eventually, come to influence each other even across very different length-scales remain largely unexplored. In this paper, we recapitulate some of the main results concerning gene regulatory and physical mechanisms, in relation to the information encoded in the 1D sequence and the 3D folding structure of DNA. In particular, we stress how reciprocal crossfeeding between 1D and 3D models may provide original insight into how these complex processes work and influence each other. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony
(Fourth) Report on Meteorological Activities at the DGAI (8-1-36)(Weather Bureau Copy)
No full textThis report is on the investigations of frontal phenomena at the Daniel Guggenheim Airship Institute in Akron, Ohio from January 1, 1935 through August 1, 1936. The investigation was carried out with the cooperation of the U.S. Bureau of Aeronautics, the U.S. Weather Bureau, the California Institute of Technology, and the Guggenheim Airship Institute. Mr. R.C. Robinson of the Weather Bureau cooperated with the author in carrying out the investigation. The object of the investigation was to determine the intensity of the atmospheric disturbances (i.e. rapidity of wind shift and gustiness) accompanying the passage of cold fronts, along with a study of the characteristics of the air masses involved and other features which might affect the intensity of the disturbance. The report treated thirty cold fronts which passed the station during 1935 to 1936
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