Probabilities of spurious connections in gene networks: Application to expression time series

Motivation: The reconstruction of gene networks from gene expression microarrays is gaining popularity as methods improve and as more data become available. The reliability of such networks could be judged by the probability that a connection between genes is spurious, resulting from chance fluctuations rather than from a true biological relationship. Results: Unlike the false discovery rate and positive false discovery rate, the decisive false discovery rate (dFDR) is exactly equal to a conditional probability without assuming independence or the randomness of hypothesis truth values. This property is useful not only in the common application to the detection of differential gene expression, but also in determining the probability of a spurious connection in a reconstructed gene network. Estimators of the dFDR can estimate each of three probabilities: 1. The probability that two genes that appear to be associated with each other lack such association. 2. The probability that a time ordering observed for two associated genes is misleading. 3. The probability that a time ordering observed for two genes is misleading, either because they are not associated or because they are associated without a lag in time. The first probability applies to both static and dynamic gene networks, and the other two only apply to dynamic gene networks. Availability: Cross-platform software for network reconstruction, probability estimation, and plotting is free from http://www.davidbickel.com as R functions and a Java application.Comment: Like q-bio.GN/0404032, this was rejected in March 2004 because it was submitted to the math archive. The only modification is a corrected reference to q-bio.GN/0404032, which was not modified at al

Magma and fluid migration at Yellowstone Caldera in the last three decades inferred from InSAR, leveling and gravity measurements

We studied the Yellowstone caldera geological unrest between 1977 and 2010 by investigating temporal changes in differential Interferometric Synthetic Aperture Radar (InSAR), precise spirit leveling and gravity measurements. The analysis of the 1992–2010 displacement time series, retrieved by applying the SBAS InSAR technique, allowed the identification of three areas of deformation: (i) the Mallard Lake (ML) and Sour Creek (SC) resurgent domes, (ii) a region close to the Northern Caldera Rim (NCR), and (iii) the eastern Snake River Plain (SRP). While the eastern SRP shows a signal related to tectonic deformation, the other two regions are influenced by the caldera unrest. We removed the tectonic signal from the InSAR displacements, and we modeled the InSAR, leveling, and gravity measurements to retrieve the best fitting source parameters. Our findings confirmed the existence of different distinct sources, beneath the brittle-ductile transition zone, which have been intermittently active during the last three decades. Moreover, we interpreted our results in the light of existing seismic tomography studies. Concerning the SC dome, we highlighted the role of hydrothermal fluids as the driving force behind the 1977–1983 uplift; since 1983–1993 the deformation source transformed into a deeper one with a higher magmatic component. Furthermore, our results support the magmatic nature of the deformation source beneath ML dome for the overall investigated period. Finally, the uplift at NCR is interpreted as magma accumulation, while its subsidence could either be the result of fluids migration outside the caldera or the gravitational adjustment of the source from a spherical to a sill-like geometr

DInSAR deformation time series for monitoring urban areas: The impact of the second generation SAR systems

We investigate the capability improvement of the DInSAR techniques to map deformation phenomena affecting urban areas, by performing a comparative analysis of the deformation time series retrieved by applying the full resolution Small BAseline Subset (SBAS) DInSAR technique to selected sequences of SAR data acquired by the ENVISAT, RADARSAT-1 and COSMO-SkyMed (CSK) SAR data. The presented study, focused on the city of Napoli (Italy), allows us to quantify the dramatic increase of the DInSAR coherent pixel density achieved by exploiting the high resolution X-Band CSK SAR images with respect to the RADARSAT-1 and ENVISAT products, respectively; this permits us to analyze nearly all the structures located within the investigated urbanized area and, in many cases, also portions of a same building. © 2012 IEEE

Discerning the relationship between geminiviral infection and vesicle trafficking using virus induced gene silencing

Tomato yellow leaf curl disease is one of the most important threats to tomato crops worldwide. One of its causal agents, Tomato yellow leaf curl Sardinian virus (TYLCSV) is a monopartite member of the genus Begomovirus from the family Geminiviridae. Due to the few proteins encoded by their viral genome, geminiviruses rely heavily on host cellular machineries and interact with a wide range of plant proteins to complete all processes required for infection, such as viral replication, movement and suppression or evasion of plant defence mechanisms. The identification of the host proteins involved in viral infection will be an important step towards the understanding of the mechanisms underlying this process. In our laboratory, transgenic Nicotiana benthamiana plants containing a green fluorescent protein (GFP) expression cassette flanked by two direct repeats of the intergenic region of TYLCSV have been constructed (2IR plants). When these plants are infected with TYLCSV, an overexpression of the reporter gene is observed in those cells where the virus is actively replicating. These plants have been used together with virus induced gene silencing (VIGS) in an effort to identify host genes involved in the infection process using a reverse genetics approach. Using this combined technique our group has identified two genes δ-COP and ARF 1, involved in retrograde vesicle trafficking, which are essential for the infectious process. We are currently assaying genes codifying proteins involved in different pathways of the vesicle trafficking system: Sar1b, γ subunit of AP1, Sec24, SYT1 and two that encode the heavy chain of triskelion proteins. Their effect over viral infection will be presented and discussedUniversidad de Málaga. Campues de Excelencia Internacional Andalucía Tech

Identifying the function of vesicle trafficking in geminiviral infection using virus induced gene silencing

Tomato yellow leaf curl Sardinian virus (TYLCSV) is one of the causal agent of the tomato yel-low leaf curl disease, one of the most important threats to tomato crops worldwide. TYLCSV is a monopartite member of the genus Begomovirus from the family Geminiviridae. To carry out a full infection, geminiviruses need to move inside the infected cell and from one cell to an-other for which they depend on diverse cellular factors. While cell-to-cell movement has been described to occur through plasmodesmata, the way in which geminiviruses move inside the host cells is yet unknown. The identification of the host proteins involved in viral infection will be an important step to-wards the understanding of the mechanisms underlying this process. In our laboratory, trans-genic Nicotianabenthamiana plants containing a green fluorescent protein (GFP) expression cassette flanked by two direct repeats of the intergenic region of TYLCSV have been construct-ed (2IR plants). When these plants are infected with TYLCSV, an overexpression of the reporter gene is observed in those cells where the virus replicates. These plants have been used to-gether with virus induced gene silencing (VIGS) in an effort to identify host genes involved in the infection process using a reverse genetics approach. Using this combined technique our group has identified two genes δ-COP and ARF 1, involved in retrograde vesicle trafficking, which are essential for the infectious process. We are current-ly assaying genes codifying proteins involved in different pathways of the vesicle trafficking system: Sar1b, γ subunit of AP1, Sec24, SYT1 and two that encode the heavy chain of triskelion proteins. Their effect over virus infection will be presented and discussed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Deriving High-Precision Radial Velocities

This chapter describes briefly the key aspects behind the derivation of precise radial velocities. I start by defining radial velocity precision in the context of astrophysics in general and exoplanet searches in particular. Next I discuss the different basic elements that constitute a spectrograph, and how these elements and overall technical choices impact on the derived radial velocity precision. Then I go on to discuss the different wavelength calibration and radial velocity calculation techniques, and how these are intimately related to the spectrograph's properties. I conclude by presenting some interesting examples of planets detected through radial velocity, and some of the new-generation instruments that will push the precision limit further.Comment: Lecture presented at the IVth Azores International Advanced School in Space Sciences on "Asteroseismology and Exoplanets: Listening to the Stars and Searching for New Worlds" (arXiv:1709.00645), which took place in Horta, Azores Islands, Portugal in July 201

Leaning Tower of Pisa — Updated Information

The paper is aimed at giving information on the present situation of the Leaning Tower of Pisa and on the activities undertaken for its safeguard by the International Committee appointed in May 1990 by the Italian Government. After a brief review of the subsoil conditions of the structural features and of the observed movements of the Tower, the activities undertaken by the Committee are also summarized

Integrating Superconductive and Optical Circuits

We have integrated on oxidized silicon wafers superconductive films and Josephson junctions along with sol-gel optical channel waveguides. The fabrication process is carried out in two steps that result to be solid and non-invasive. It is demonstrated that 660 nm light, coupled from an optical fibre into the channel sol-gel waveguide, can be directed toward superconducting tunnel junctions whose current-voltage characteristics are affected by the presence of the radiation. The dependence of the change in the superconducting energy gap under optical pumping is discussed in terms of a non-equilibrium superconductivity model.Comment: Document composed of 7 pages of text and 3 figure