Frans Voorbraak

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value

For real-time monitoring of PCR amplification of DNA, quantitative PCR (qPCR) assays use various fluorescent reporters. DNA binding molecules and hybridization reporters (primers and probes) only fluoresce when bound to DNA and result in the non-cumulative increase in observed fluorescence. Hydrolysis reporters (TaqMan probes and QZyme primers) become fluorescent during DNA elongation and the released fluorophore remains fluorescent during further cycles; this results in a cumulative increase in observed fluorescence. Although the quantification threshold is reached at a lower number of cycles when fluorescence accumulates, in qPCR analysis no distinction is made between the two types of data sets. Mathematical modeling shows that ignoring the cumulative nature of the data leaves the estimated PCR efficiency practically unaffected but will lead to at least one cycle underestimation of the quantification cycle (C(q) value), corresponding to a 2-fold overestimation of target quantity. The effect on the target-reference ratio depends on the PCR efficiency of the target and reference amplicons. The leftward shift of the C(q) value is dependent on the PCR efficiency and with sufficiently large C(q) values, this shift is constant. This allows the C(q) to be corrected and unbiased target quantities to be obtained.

The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format

Interpretation of the results of anatomical and embryological studies relies heavily on proper visualization of complex morphogenetic processes and patterns of gene expression in a three-dimensional (3D) context. However, reconstruction of complete 3D datasets is time consuming and often researchers study only a few sections. To help in understanding the resulting 2D data we developed a program (TRACTS) that places such arbitrary histological sections into a high-resolution 3D model of the developing heart. The program places sections correctly, robustly and as precisely as the best of the fits achieved by five morphology experts. Dissemination of 3D data is severely hampered by the 2D medium of print publication. Many insights gained from studying the 3D object are very hard to convey using 2D images and are consequently lost or cannot be verified independently. It is possible to embed 3D objects into a pdf document, which is a format widely used for the distribution of scientific papers. Using the freeware program Adobe Reader to interact with these 3D objects is reasonably straightforward; creating such objects is not. We have developed a protocol that describes, step by step, how 3D objects can be embedded into a pdf document. Both the use of TRACTS and the inclusion of 3D objects in pdf documents can help in the interpretation of 2D and 3D data, and will thus optimize communication on morphological issues in developmental biology.

Tertiary Teledermatology: A Systematic Review

Telemedicine is becoming widely used in healthcare. Dermatology, because of its visual character, is especially suitable for telemedicine applications. Most common is teledermatology between general practitioners and dermatologists (secondary teledermatology). Another form of the teledermatology process is communication among dermatologists (tertiary teledermatology). The objective of this systematic review is to give an overview of studies on tertiary teledermatology with emphasis on the categories of use. A systematic literature search on tertiary teledermatology studies used all databases of the Cochrane Library, MEDLINE (1966-November 2007) and EMBASE (1980-November 2007). Categories of use were identified for all included articles and the modalities of tertiary teledermatology were extracted, together with technology, the setting the outcome measures, and their results. The search resulted in 1,377 publications, of which 11 were included. Four categories of use were found: getting an expert opinion from a specialized, often academic dermatologist (6/11); resident training (2/11); continuing medical education (4/11); and second opinion from a nonspecialized dermatologist (2/11). Three modalities were found: a teledermatology consultation application (7/11), a Web site (2/11), and an e-mail list (1/11). The majority (7/11) used store-and-forward, and 3/11 used store-and-forward and real-time. Outcome measures mentioned were learning effect (6), costs (5), diagnostic accuracy (1), validity (2) and reliability (2), patient and physician satisfaction (1), and efficiency improvement (3). Tertiary teledermatologys main category of use is getting an expert opinion from a specialized, often academic dermatologist. Tertiary teledermatology research is still in early development. Future research should focus on identifying the scale of tertiary teledermatology and on what modality of teledermatology is most suited for what purpose in communication among dermatologists.

More than a decade of developmental gene expression atlases: where are we now?

To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the ‘ideal atlas’. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms.

The Logic of Objective Knowledge and Rational Belief

In this paper, we study the logical relations between different notions of knowledge and belief by means of generalizations of the usual Kripke models for epistemic logic. We argue that the obtained generalized Kripke models might be useful for carefully distinguishing the many different notions of knowledge and belief. We identify the (highly idealized) notions of objective knowledge and rational (introspective) belief, which correspond with fairly standard notions of knowledge and belief, and propose a system OKRIB for combining both notions which differs essentially from some other such proposals found in the literature. We also consider some other notions of knowledge and belief, and study how they relate to objective knowledge and rational belief.

Reasoning with Uncertainty in AI

This paper provides an introduction to the field of reasoning with uncertainty in Artificial Intelligence (AI), with an emphasis on reasoning with numeric uncertainty. The considered formalisms are Probability Theory and some of its generalizations, the Certainty Factor Model, Dempster-Shafer Theory, and Probabilistic Networks.

A pilot study on tertiary teledermatology: feasibility and acceptance of telecommunication among dermatologists

Tertiary teledermatology (TTD), where a general dermatologist consults a specialized dermatologist on difficult cases, is a relatively new telemedicine service. We evaluated TTD in a Dutch university hospital, where 13 general dermatologists used TTD to consult 11 specialized dermatologists and two residents at the university medical centre. We measured the avoided referrals to the university centre, the usability of the system and the user acceptance of it. During a three-month study, general dermatologists consulted via TTD 28 times. In 17 of the consultations (61%), the general dermatologists would have referred their patients to the university centre if teledermatology had not been available. Referral was not necessary after teledermatology for 12 of these 17 consultations (71%). The mean usability score (0–100) of all the users was 80. All dermatologists were satisfied with TTD (mean satisfaction of 7.6 on a 10-point scale) and acceptance was high. The baseline measurements showed that half of tertiary referrals were suitable for TTD. These results suggest that TTD reduces unnecessary physical referrals and that users are satisfied with it. A large-scale evaluation is now required.

A Simplification of the Completeness Proofs for Guaspari and Solovay's R

Alternative proofs for Guaspari and Solovays completeness the- orems for R are presented. R is an extension of the provability logic L and was developed in order to study the formal properties of the provability predicate of PA occurring in sentences that may contain connectives for wit- ness comparison. (The primary example of sentences involving witness com- parison is the Rosser sentence.) In this article the proof of the Kripke model completeness theorems employs tail models, as introduced by Visser, instead of the more usual finite Kripke models. The use of tail models makes it pos- sible to derive arithmetical completeness from Kripke model completeness by literally embedding Kripke models into PA. Our arithmetical completeness theorem differs slightly from the one proved by Guaspari and Solovay, and it also forms a solution to the problem (advanced by Smoryήski) of obtain- ing a completeness result with respect to a variety of orderings.

Modeling length of stay as an optimized two-class prediction problem.

OBJECTIVES To develop a predictive model for the outcome length of stay at the Intensive Care Unit (ICU LOS), including the choice of an optimal dichotomization threshold for this outcome. Reduction of prediction problems of this type of outcome to a two-class problem is a common strategy to identify high-risk patients. METHODS Threshold selection and model development are performed simultaneously. From the range of possible threshold values, the value is chosen for which the corresponding predictive model has maximal precision based on the data. To compare the precision of models for different dichotomizations of the outcome, the MALOR performance statistic is introduced. This statistic is insensitive to the prevalence of positive cases in a two-class prediction problem. RESULTS The procedure is applied to data from cardiac surgery patients to dichotomize the outcome ICU LOS. The class probability tree method is used to develop predictive models. Within our data, the best model precision is found at the threshold of seven days. CONCLUSIONS The presented method extends existing procedures for predictive modeling with optimization of the outcome definition for predictive purposes. The method can be applied to all prediction problems where the outcome variable needs to be dichotomized, and is insensitive to changes in the prevalence of positive cases with different dichotomization thresholds.

A nonmonotonic observation logic

A variant of Reiters default logic is proposed as a logic for reasoning with (defeasible) observations. Traditionally, default rules are assumed to represent generic information and the facts are assumed to represent specific information about the situation, but in this paper, the specific information derives from defeasible observations represented by (normal free) default rules, and the facts represent (hard) background knowledge. Whenever the evidence underlying some observation is more refined than the evidence underlying another observation, this is modelled by means of a priority between the default rules representing the observations. We thus arrive at an interpretation of prioritized normal free default logic as an observation logic, and we propose a semantics for this observation logic. Finally, we discuss how the proposed observation logic relates to the multiple extension problem and the problem of sensor fusion.