Clinical probability assessment and biochemical markers in the diagnosis of deep vein thrombosis

The combination of pre-test clinical probability assessment and D-dimer test is now widely applied in the diagnostic process of DVT. The general objective of the present investigation was to validate these results in a Swedish routine emergency setting were the prevalence of the disease is high and were the clinical probability assessment was handled by many junior physicians. Furthermore, our aims were to evaluate our D-dimer method and to make comparisons with other D-dimer methods as with a new marker of coagulation, the APC-PCI complex. In addition, a cost effectiveness analysis was made of this diagnostic strategy. Material and methods: 357 outpatients with clinical suspicion of DVT were included in the clinical management study. The diagnostic workup included estimation of pre-test probability, D-dimer determination, objective imaging as well as 3 month clinical follow up of negative patients (Paper I). 350 plasma samples from the management study was used for comparison between two well established D-dimer methods and the APC-PCI complex (Paper II) and 311 plasma samples for the evaluation of two new D-dimer methods (Paper III). Direct and indirect costs were calculated for the tested diagnostic strategy and for two hypothetical strategies. A decision analysis was performed (Paper IV). Results and conclusions: One out of 110 patients categorized as having a low clinical probability in combination with a negative D-dimer test was diagnosed with DVT during follow up. About 30% of the patients do not need further investigation for DVT. The APC-PCI complex perform inferior to the D-dimer methods for the exclusion of DVT but slightly superior when indicating its presence. The AxSYM® and Innovance™ D-dimer assays perform well and in good agreement with the two well established assays with NPV´s of > 98% in the low clinical probability estimate (CP). Objective imaging in all patients was the least cost effective (€581) strategy, D-dimer screening of all patients before CP (€421) and CP in combination with D-Dimer testing only in patients with low CP (€406). Conclusion: the investigated diagnostic strategy is safe, result in more convenient and cost-effective care for patients

What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?

Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame with “regulatory” codons, cognate to the amino acid that is synthesized by the enzymes encoded by the operon. When the amino acid is in short supply, translation of the regulatory codons is slow, which allows transcription to continue into the structural genes of the operon. When amino acid supply is in excess, translation of regulatory codons is rapid, which leads to termination of transcription. We use a discrete master equation approach to formulate a probabilistic model for the positioning of the RNA polymerase and the ribosome in the attenuator leader sequence. The model describes how the current rate of amino acid supply compared to the demand in protein synthesis (signal) determines the expression of the amino acid biosynthetic operon (response). The focus of our analysis is on the sensitivity of operon expression to a change in the amino acid supply. We show that attenuation of transcription can be hyper-sensitive for two main reasons. The first is that its response depends on the outcome of a race between two multi-step mechanisms with synchronized starts: transcription of the leader of the operon, and translation of its regulatory codons. The relative change in the probability that transcription is aborted (attenuated) can therefore be much larger than the relative change in the time it takes for the ribosome to read a regulatory codon. The second is that the general usage frequencies of codons of the type used in attenuation control are small. A small percentage decrease in the rate of supply of the controlled amino acid can therefore lead to a much larger percentage decrease in the rate of reading a regulatory codon. We show that high sensitivity further requires a particular choice of regulatory codon among several synonymous codons for the same amino acid. We demonstrate the importance of a high fraction of regulatory codons in the control region. Finally, our integrated model explains how differences in leader sequence design of the trp and his operons of Escherichia coli and Salmonella typhimurium lead to high basal expression and low sensitivity in the former case, and to large dynamic range and high sensitivity in the latter. The model clarifies how mechanistic and systems biological aspects of the attenuation mechanism contribute to its overall sensitivity. It also explains structural differences between the leader sequences of the trp and his operons in terms of their different functions

Simulated single molecule microscopy with SMeagol

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule microscopy data. Availability and Implementation: SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code, and binaries for recent versions of Mac OS, Windows, and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net.Comment: v2: 14 pages including supplementary text. Pre-copyedited, author-produced version of an application note published in Bioinformatics following peer review. The version of record, and additional supplementary material is available online at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw10

Noise-Induced Min Phenotypes in E. coli

The spatiotemporal oscillations of the Escherichia coli proteins MinD and MinE direct cell division to the region between the chromosomes. Several quantitative models of the Min system have been suggested before, but no one of them accounts for the behavior of all documented mutant phenotypes. We analyzed the stochastic reaction-diffusion kinetics of the Min proteins for several E. coli mutants and compared the results to the corresponding deterministic mean-field description. We found that wild-type (wt) and filamentous (ftsZ( −)) cells are well characterized by the mean-field model, but that a stochastic model is necessary to account for several of the characteristics of the spherical (rodA(−)) and phospathedylethanolamide-deficient (PE(−)) phenotypes. For spherical cells, the mean-field model is bistable, and the system can get trapped in a non-oscillatory state. However, when the intrinsic noise is considered, only the experimentally observed oscillatory behavior remains. The stochastic model also reproduces the change in oscillation directions observed in the spherical phenotype and the occasional gliding of the MinD region along the inner membrane. For the PE(−) mutant, the stochastic model explains the appearance of randomly localized and dense MinD clusters as a nucleation phenomenon, in which the stochastic kinetics at low copy number causes local discharges of the high MinD(ATP) to MinD(ADP) potential. We find that a simple five-reaction model of the Min system can explain all documented Min phenotypes, if stochastic kinetics and three-dimensional diffusion are accounted for. Our results emphasize that local copy number fluctuation may result in phenotypic differences although the total number of molecules of the relevant species is high

Multi-Level Equilibrium Signaling for Molecular Communication

International audienceTwo key challenges in diffusion-based molecular communication are low data rates and accounting for the geometry of the fluid medium in the form of obstacles and the boundary. To reduce the need for the receiver to have knowledge of the geometry of the medium, binary equilibrium signaling has recently been proposed for molecular communication with a passive receiver in bounded channels. In this approach, reversible chemical reactions are introduced at the transmitter and the receiver in order for the system to converge to a known equilibrium state. This provides a means of designing simple detection rules that only depend on the transmitted signal and the volume of the bounded fluid medium. In this paper, we introduce multi-level equilibrium signaling, which allows for higher data rates via higher order modulation. We show that for a wide range of conditions, with appropriate receiver optimization, multi-level equilibrium signaling can outperform conventional concentration shift keying schemes. As such, our approach provides a basis to improve data rates in molecular communications without the need to increase the complexity of the system by exploiting techniques such as multiple information-carrying molecules