Efficiency of split-mouth designs

. The purpose of this paper is (1) to investigate the similarity of the amount, distribution, and, severity of periodontal disease of the within-patient experimental units, (2) to estimate the relative efficiencies of split-mouth designs when compared to whole-mouth designs, and (3) to discuss how stratification on initial pocket depth can result in large differences in the power of the test-statistics in the different disease categories. Periodontal disease characteristics are not always homogeneously distributed over the within-patient experimental units and this heterogeneity can reduce the efficiency of split-mouth designs. In particular, if analyses are stratified on initial pocket depth, sites with an initial probing depth deeper than 6 mm may be small in number and asymmetrically distributed when compared to sites with an initial probing depth less than 6 mm. This may result in large differences of the power of the test statistics among the different disease categories and should lead to a careful interpretation of the statistical significance tests. When disease characteristics are symmetrically distributed over the within-patient experimental units and a sufficient number of sites is present per experimental unit, the split-mouth design can provide moderate to large gains in relative efficiency. In the absence of a symmetric disease distribution, wholemouth clinical trials may be preferable.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75701/1/j.1600-051X.1990.tb01060.x.pd

A call for public archives for biological image data

Public data archives are the backbone of modern biological and biomedical research. While archives for biological molecules and structures are well-established, resources for imaging data do not yet cover the full range of spatial and temporal scales or application domains used by the scientific community. In the last few years, the technical barriers to building such resources have been solved and the first examples of scientific outputs from public image data resources, often through linkage to existing molecular resources, have been published. Using the successes of existing biomolecular resources as a guide, we present the rationale and principles for the construction of image data archives and databases that will be the foundation of the next revolution in biological and biomedical informatics and discovery.Comment: 13 pages, 1 figur

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to "epigenetic solitons" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.Comment: Accepted version; Supplementary movies can be found at http://www2.ph.ed.ac.uk/~dmichiel/KnottedSolitons.html and https://www.youtube.com/watch?v=Osghh9nEhe

Rethinking Job References: A Networking Challenge

Can job references play an active role in shaping your career plans? Would you consider your references as part of your personal and professional network? Although most professionals may respond with a resounding “Yes, of course!” to these questions, I realized that many of my students were skeptical about job references. To counter this, and to help improve their chances in the job market, I designed a multistep assignment that expanded students’ understanding of job references and required them to identify persons who were potential job references and members of their career network. This article provides the details for the assignment