Function-based approach to mixed haptic effects rendering

Commonly, surface and solid haptic effects are defined in such a way that they hardly can be rendered together. We propose a method for defining mixed haptic effects including surface, solid, and force fields. These haptic effects can be applied to virtual scenes containing various objects, including polygon meshes, point clouds, impostors, and layered textures, voxel models as well as function-based shapes. Accordingly, we propose a way how to identify location of the haptic tool in such virtual scenes as well as consistently and seamlessly determine haptic effects when the haptic tool moves in the scenes with objects having different sizes, locations, and mutual penetrations. To provide for an efficient and flexible rendering of haptic effects, we propose to concurrently use explicit, implicit and parametric functions, and algorithmic procedures.     

Estimating the Natural Illumination Conditions from a Single Outdoor Image

Given a single outdoor image, we present a method for estimating the likely illumination conditions of the scene. In particular, we compute the probability distribution over the sun position and visibility. The method relies on a combination of weak cues that can be extracted from different portions of the image: the sky, the vertical surfaces, the ground, and the convex objects in the image. While no single cue can reliably estimate illumination by itself, each one can reinforce the others to yield a more robust estimate. This is combined with a data-driven prior computed over a dataset of 6 million photos. We present quantitative results on a webcam dataset with annotated sun positions, as well as quantitative and qualitative results on consumer-grade photographs downloaded from Internet. Based on the estimated illumination, we show how to realistically insert synthetic 3-D objects into the scene, and how to transfer appearance across images while keeping the illumination consistent.     

An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein

A new approach has been developed to reduce multiple proteinstructures obtained from NMR structure analysis to a smallernumber of representative structures which still reflect thestructural diversity of the data sets. The method, based onthe clustering of similar structures, has been tested in thehomology model building of the structure of Sox-5, a sequence-specificDNA-binding protein belonging to the high mobility group (HMG)nuclear proteins family. Sox (SRY box) genes are the autosomalgenes related to the sex-determining SRY, Y chromosomal gene.The Sox-5 protein, encoded by one of the SRY-related genes,displays a 29% sequence identity with the HMG1 B-box domainwhose structure, determined previously by NMR, has been usedin our study to predict the structure of Sox-5. Two independentensembles of HMG1 structures, each represented by closely relatedcoordinate sets, were used. Nine representative structures forHMG1 were subsequently selected as starting points for the modellingof Sox-5. The model of the protein shows close similarity tothe HMG1 fold, with differences at the secondary structure levellocated mainly in a-helices 1 and 3. A left-handed, three residueper turn polyproline II helix, forming a conserved polyprolineII/-helix supersecondary motif, was identified in the N-terminalregion of Sox-5 and other HMG boxes.     

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model

The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses'' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible–infected–removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth–death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.     

Noise Effect on Ice Surface Softening During Friction

The ice surface softening by friction is investigated considering the additive non-correlated fluctuations of the shear strain and stress, and the temperature. The premelting is construed by the Kelvin–Voigt equation for shear strain and by the relaxation equations of Landau–Khalatnikov type for shear stress and temperature. Taking into account the noises in these equations, the Langevin and Fokker–Planck equations are derived. Their analysis is based on the investigation of extrema of the distribution function, i.e., steady-state values of the shear strain using the Stratonovich interpretation. The phase diagrams are constructed, where the noises intensities and thermostat temperature determine the regions of ice, softened ice and their mixture (stick–slip rubbing). We present that domain of ice friction is bounded by relatively small background sliding block temperatures and fluctuation intensities of the stress and temperature. The ice film softens with growth of the stress noise intensity even at small thermostat temperatures. The friction force time series for all rubbing modes are calculated and compared with experimentally observed ones.     

DNA Comet Giemsa Staining for Conventional Bright-Field Microscopy

This study was undertaken to evaluate the compatibility of Giemsa staining protocol with the comet assay. We showed, for the first time, that DNA comets can be visualized and analyzed using Giemsa staining. We generated DNA damage dose response curves for human peripheral blood lymphocytes exposed to X-ray radiation using the comet assay with either SybrGreen I or Giemsa stain. The dose response curves were fitted by linear regressions (R² > 0.977). The SybrGreen I results showed only ~1.2-fold higher slope coefficient (method sensitivity) compared to the Giemsa results. The unexpectedly high sensitivity of Giemsa staining for the comet assay is due to the Romanowsky-Giemsa effect, the stain photo-stability and the higher resolution of bright-field imaging compared to fluorescence imaging. Our results demonstrate that Giemsa staining can effectively be used for measuring DNA damage by the comet assay. The low cost and availability of Giemsa stain makes this method affordable for any low budget research and will facilitate new applications of the comet assay in biology and medicine.