Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

EP-1811: Accuracy of dose calculations on CBCT scans of lung cancer patients using a vendor-specific approach

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Multilinear Wavelets: A Statistical Shape Space for Human Faces

We present a statistical model for $3$D human faces in varying expression, which decomposes the surface of the face using a wavelet transform, and learns many localized, decorrelated multilinear models on the resulting coefficients. Using this model we are able to reconstruct faces from noisy and occluded $3$D face scans, and facial motion sequences. Accurate reconstruction of face shape is important for applications such as tele-presence and gaming. The localized and multi-scale nature of our model allows for recovery of fine-scale detail while retaining robustness to severe noise and occlusion, and is computationally efficient and scalable. We validate these properties experimentally on challenging data in the form of static scans and motion sequences. We show that in comparison to a global multilinear model, our model better preserves fine detail and is computationally faster, while in comparison to a localized PCA model, our model better handles variation in expression, is faster, and allows us to fix identity parameters for a given subject.Comment: 10 pages, 7 figures; accepted to ECCV 201

Robot-Assisted Epiretinal Membrane Peeling: A Prospective Assessment of Pre- and Intra-Operative Times and of Surgeons' Subjective Perceptions.

PURPOSE The Preceyes Surgical System (PSS) is a robotic assistive device that may enhance surgical precision. This study assessed pre- and intra-operative times and surgeons' perceptions of robot-assisted epiretinal membrane peeling (RA-MP). METHODS We analyzed the time requirement of three main tasks: the preparation of the PSS (I), patient preparation (II), and surgery (III). Following surgery, the surgeons were asked questions about their experience. RESULTS RA-MP was performed in nine eyes of nine patients. Task I required an average time of 12.3 min, initially taking 15 min but decreasing to 6 min in the last surgery. Task II showed a mean time of 47.2 (range of 36-65) min. Task III had a mean time of 72.4 (range of 57-100) min. A mean time of 27.9 (range of 9-46) min was necessary for RA-MP. The responses to the questionnaire revealed a trend towards increasing ease and reduced stress as familiarity with the PSS increased. CONCLUSIONS A substantial reduction in pre- and intra-operative times, decreasing to a total of 115 min, was demonstrated. RA-MP was positively anticipated by the surgeons and led to no hand or arm strain while being more complex than manual MP

A machine learning pipeline for discriminant pathways identification

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a machine learning solution for molecular profiling with a recent network comparison method. The pipeline can identify changes occurring between specific sub-modules of networks built in a case-control biomarker study, discriminating key groups of genes whose interactions are modified by an underlying condition. The proposal is independent from the classification algorithm used. Three applications on genomewide data are presented regarding children susceptibility to air pollution and two neurodegenerative diseases: Parkinson's and Alzheimer's. Availability: Details about the software used for the experiments discussed in this paper are provided in the Appendix

Spinor classification of the Weyl tensor in five dimensions

We investigate the spinor classification of the Weyl tensor in five dimensions due to De Smet. We show that a previously overlooked reality condition reduces the number of possible types in the classification. We classify all vacuum solutions belonging to the most special algebraic type. The connection between this spinor and the tensor classification due to Coley, Milson, Pravda and Pravdov\'a is investigated and the relation between most of the types in each of the classifications is given. We show that the black ring is algebraically general in the spinor classification.Comment: 40 page

Skipping orbits and enhanced resistivity in large-diameter InAs/GaSb antidot lattices

We investigated the magnetotransport properties of high-mobility InAs/GaSb antidot lattices. In addition to the usual commensurability features at low magnetic field we found a broad maximum of classical origin around 2.5 T. The latter can be ascribed to a class of rosetta type orbits encircling a single antidot. This is shown by both a simple transport calculation based on a classical Kubo formula and an analysis of the Poincare surface of section at different magnetic field values. At low temperatures we observe weak 1/B-periodic oscillations superimposed on the classical maximum.Comment: 4 pages, 4 Postscript figures, REVTeX, submitted to Phys Rev

Performance evaluation of CHP with heat storage in buildings

Paper presented at the 5th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, South Africa, 1-4 July, 2007.Combined heat and power (CHP) production gains more and more attention. Offices and public buildings often have a large thermal power demand in combination with a fairly large electrical power demand. On the other hand they are seldom occupied by night and in weekends, reducing the actual operational time of the heating system. This in turn brings down the financial benefits of investing in CHP. A second problem is that electrical and thermal demands are often shifted in time. The running time of the engine is again limited this way, as it is often not allowed to deliver electricity to the power grid. A possible solution is using heat storage. This way the CHP-engine can run when the electricity demand is high. In the paper a simulation model of CHP with gas engine and heat storage by means of a hot water vessel is developed. The model is validated through experiments on an engine and a vessel. This model is used to analyze the design, control and performance of cogeneration plants. It is shown that storage is marginal beneficial and the design has to be done with great care.cs201

The Kerr-Newman-Godel Black Hole

By applying a set of Hassan-Sen transformations and string dualities to the Kerr-Godel solution of minimal D=5 supergravity we derive a four parameter family of five dimensional solutions in type II string theory. They describe rotating, charged black holes in a rotating background. For zero background rotation, the solution is D=5 Kerr-Newman; for zero charge it is Kerr-Godel. In a particular extremal limit the solution describes an asymptotically Godel BMPV black hole.Comment: 12 pages, LaTeX, no figures; v2: one reference added, very minor changes; to appear in CQ