Gravity duals of supersymmetric gauge theories on three-manifolds

We study gravity duals to a broad class of N=2 supersymmetric gauge theories defined on a general class of three-manifold geometries. The gravity backgrounds are based on Euclidean self-dual solutions to four-dimensional gauged supergravity. As well as constructing new examples, we prove in general that for solutions defined on the four-ball the gravitational free energy depends only on the supersymmetric Killing vector, finding a simple closed formula when the solution has U(1) x U(1) symmetry. Our result agrees with the large N limit of the free energy of the dual gauge theory, computed using localization. This constitutes an exact check of the gauge/gravity correspondence for a very broad class of gauge theories with a large N limit, defined on a general class of background three-manifold geometries.Comment: 74 pages, 2 figures; v2: minor change

Assessment of Orchid Surfaces Using Top-Down Contact Angle Mapping

© 2013 IEEE. Top-down contact angle (CA) measurements are used to characterize the green leaves and purple flowers of both old and young the Cattleya warneri orchids. The top-down CA allows the characterization of large surfaces away from the leaf edge, avoiding traditional cutting required for side view CA measurement. This allows large area mapping without damaging leaves making the method amenable to fieldwork and useful in environmental diagnostics. Young leaves are found to be hydrophobic whilst old leaves become practically hydrophilic across their entirety, mostly as a result of continued exposure to changes in the environment over time. The flowers are hydrophobic because of their visual and tactile attractor function for pollinating animals and the self-cleaning of dirt and pathogens. Real-time measurement and mapping of CA of surfaces open a new tool to assess the long-term impact of plant aging, pollution, and more of organisms in the field. The method has clear applications elsewhere such as in industrial probing of surfaces and products

To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts?

Musculoskeletal models are widely used to estimate joint kinematics, intersegmental loads, and muscle and joint contact forces during movement. These estimates can be heavily affected by the soft tissue artefact (STA) when input positional data are obtained using stereophotogrammetry, but this aspect has not yet been fully characterised for muscle and joint forces. This study aims to assess the sensitivity to the STA of three open-source musculoskeletal models, implemented in OpenSim. A baseline dataset of marker trajectories was created for each model from experimental data of one healthy volunteer. Five hundred STA realizations were then statistically generated using a markerdependent model of the pelvis and lower limb artefact and added to the baseline data. The STA's impact on the musculoskeletal model estimates was finally quantified using a Monte Carlo analysis. The modelled STA distributions were in line with the literature. Observed output variations were comparable across the three models, and sensitivity to the STA was evident for most investigated quantities. Shape, magnitude and timing of the joint angle and moment time histories were not significantly affected throughout the entire gait cycle, whereas magnitude variations were observed for muscle and joint forces. Ranges of contact force variations differed between joints, with hip variations up to 1.8 times body weight observed. Variations of more than 30% were observed for some of the muscle forces. In conclusion, musculoskeletal simulations using stereophotogrammetry may be safely run when only interested in overall output patterns. Caution should be paid when more accurate estimated values are needed

MicroRNA-222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells

A number of microRNAs have been shown to regulate skeletal muscle development and differentiation. MicroRNA-222 is downregulated during myogenic differentiation and its overexpression leads to alteration of muscle differentiation process and specialized structures. By using RNA-induced silencing complex (RISC) pulldown followed by RNA sequencing, combined with in silico microRNA target prediction, we have identified two new targets of microRNA-222 involved in the regulation of myogenic differentiation, Ahnak and Rbm24. Specifically, the RNA-binding protein Rbm24 is a major regulator of muscle-specific alternative splicing and its downregulation by microRNA-222 results in defective exon inclusion impairing the production of muscle-specific isoforms of Coro6, Fxr1 and NACA transcripts. Reconstitution of normal levels of Rbm24 in cells overexpressing microRNA-222 rescues muscle-specific splicing. In conclusion, we have identified a new function of microRNA-222 leading to alteration of myogenic differentiation at the level of alternative splicing, and we provide evidence that this effect is mediated by Rbm24 protei

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

Background: The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartments such as nucleus, cytoplasm or organelles. However, many organelles, like mitochondria, have their own internal compartmentalization. Knowing the precise location of a protein inside mitochondria is crucial for its accurate functional characterization. We recently developed DeepMito, a new method based on a 1-Dimensional Convolutional Neural Network (1D-CNN) architecture outperforming other similar approaches available in literature. Results: Here, we explore the adoption of DeepMito for the large-scale annotation of four sub-mitochondrial localizations on mitochondrial proteomes of five different species, including human, mouse, fly, yeast and Arabidopsis thaliana. A significant fraction of the proteins from these organisms lacked experimental information about sub-mitochondrial localization. We adopted DeepMito to fill the gap, providing complete characterization of protein localization at sub-mitochondrial level for each protein of the five proteomes. Moreover, we identified novel mitochondrial proteins fishing on the set of proteins lacking any subcellular localization annotation using available state-of-the-art subcellular localization predictors. We finally performed additional functional characterization of proteins predicted by DeepMito as localized into the four different sub-mitochondrial compartments using both available experimental and predicted GO terms. All data generated in this study were collected into a database called DeepMitoDB (available at http://busca.biocomp.unibo.it/deepmitodb), providing complete functional characterization of 4307 mitochondrial proteins from the five species. Conclusions: DeepMitoDB offers a comprehensive view of mitochondrial proteins, including experimental and predicted fine-grain sub-cellular localization and annotated and predicted functional annotations. The database complements other similar resources providing characterization of new proteins. Furthermore, it is also unique in including localization information at the sub-mitochondrial level. For this reason, we believe that DeepMitoDB can be a valuable resource for mitochondrial research

Huntingtin: A protein with a peculiar solvent accessible surface

Taking advantage of the last cryogenic electron microscopy structure of human hunt-ingtin, we explored with computational methods its physicochemical properties, focusing on the solvent accessible surface of the protein and highlighting a quite interesting mix of hydrophobic and hydrophilic patterns, with the prevalence of the latter ones. We then evaluated the probability of exposed residues to be in contact with other proteins, discovering that they tend to cluster in specific regions of the protein. We then found that the remaining portions of the protein surface can contain calcium-binding sites that we propose here as putative mediators for the protein to interact with membranes. Our findings are justified in relation to the present knowledge of huntingtin functional annotation