Blocking Gibbs sampling in the mixed inheritance model using graph theory

International audienc

The Effect of Pupil Size on Stimulation of the Melanopsin Containing Retinal Ganglion Cells, as Evaluated by Monochromatic Pupillometry

Purpose: To evaluate the influence of the size of the light exposed pupil in one eye on the pupillary light reflex of the other eye. Method: Using a monochromatic pupillometer, the left eye in each of 10 healthy subjects was exposed to 20 s of monochromatic light of luminance 300 cd/m2, first red (660 nm) and in a following session, blue (470 nm) light. The consensual pupillary diameter in the right eye was continuously measured before, during, and after light exposure. Subsequently, Tropicamide 1% or Pilocarpine 2% was instilled into the left eye and when the pupil was either maximally dilated or contracted, the entire sequence of red and blue light exposure repeated. After at least 3 days, when the effect of the eye drop had subsided, the entire experiment was repeated, this time employing the other substance. Results: Prior dilatation of the left pupil augmented the post light contraction to blue (p < 0.0001), but not to red light. The contraction during light exposure did not change. Prior contraction of the left pupil decreased the post-stimulus contraction to blue light (p < 0.04). Conclusion: The size of the light exposed pupil influences the magnitude of the response to blue, but not to red light. Prior dilatation may therefore prove useful, when the response to blue light – as a marker of melanopsin containing retinal ganglion cell function – is of interest, especially when this response is weak

State of the art and challenges in sequence based T-cell epitope prediction

Sequence based T-cell epitope predictions have improved immensely in the last decade. From predictions of peptide binding to major histocompatibility complex molecules with moderate accuracy, limited allele coverage, and no good estimates of the other events in the antigen-processing pathway, the field has evolved significantly. Methods have now been developed that produce highly accurate binding predictions for many alleles and integrate both proteasomal cleavage and transport events. Moreover have so-called pan-specific methods been developed, which allow for prediction of peptide binding to MHC alleles characterized by limited or no peptide binding data. Most of the developed methods are publicly available, and have proven to be very useful as a shortcut in epitope discovery. Here, we will go through some of the history of sequence-based predictions of helper as well as cytotoxic T cell epitopes. We will focus on some of the most accurate methods and their basic background

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server i