Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch

Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.Comment: 14 pages, 4 figure

A Novel Two-Channel Continuous-Time Time-Interleaved 3rd-order Sigma- Delta Modulator with Integrator-Sharing Topology

this paper presents a 3rd-order two-path Continuous-Time Time-Interleaved (CTTI) delta-sigma modulator which is implemented in standard 90nm CMOS technology. The architecture uses a novel method to resolve the delayless feedback path issue arising from the sharing of integrators between paths. By exploiting the concept of the time-interleaving techniques and through the use time domain equations, a conventional single path 3rd-order Discrete-Time (DT) ΔΣ modulator is converted into a corresponding two-path Discrete-Time Time-Interleaved (DTTI) counterpart. The equivalent Continuous-Time Time-Interleaved version derived from the DTTI ΔΣ modulator by determining the DT loop filters and converting them to the equivalent Continuous-Time (CT) loop filters through the use of the Impulse Invariant Transformation. Sharing the integrators between two paths of the reported modulator makes it robust to path mismatch effects compared to the typical Time-Interleaved (TI) modulators which have individual integrators in all paths. The modulator achieves a dynamic range of 12 bits with an OverSampling Ratio (OSR) of 16 over a bandwidth of 10MHz and dissipates only 28mW of power from a 1.8-V supply. The clock frequency of the modulator is 320MHz but integrators, quantizers and DACs operate at 160MHz

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

A Kinome RNAi Screen Identified AMPK as Promoting Poxvirus Entry through the Control of Actin Dynamics

Poxviruses include medically important human pathogens, yet little is known about the specific cellular factors essential for their replication. To identify genes essential for poxvirus infection, we used high-throughput RNA interference to screen the Drosophila kinome for factors required for vaccinia infection. We identified seven genes including the three subunits of AMPK as promoting vaccinia infection. AMPK not only facilitated infection in insect cells, but also in mammalian cells. Moreover, we found that AMPK is required for macropinocytosis, a major endocytic entry pathway for vaccinia. Furthermore, we show that AMPK contributes to other virus-independent actin-dependent processes including lamellipodia formation and wound healing, independent of the known AMPK activators LKB1 and CaMKK. Therefore, AMPK plays a highly conserved role in poxvirus infection and actin dynamics independent of its role as an energy regulator

Are Cuckoos Maximizing Egg Mimicry by Selecting Host Individuals with Better Matching Egg Phenotypes?

Background: Avian brood parasites and their hosts are involved in complex offence-defense coevolutionary arms races. The most common pair of reciprocal adaptations in these systems is egg discrimination by hosts and egg mimicry by parasites. As mimicry improves, more advanced host adaptations evolve such as decreased intra- and increased interclutch variation in egg appearance to facilitate detection of parasitic eggs. As interclutch variation increases, parasites able to choose hosts matching best their own egg phenotype should be selected, but this requires that parasites know their own egg phenotype and select host nests correspondingly. Methodology/Principal Findings: We compared egg mimicry of common cuckoo Cuculus canorus eggs in naturally parasitized marsh warbler Acrocephalus palustris nests and their nearest unparasitized conspecific neighbors having similar laying dates and nest-site characteristics. Modeling of avian vision and image analyses revealed no evidence that cuckoos parasitize nests where their eggs better match the host eggs. Cuckoo eggs were as good mimics, in terms of background and spot color, background luminance, spotting pattern and egg size, of host eggs in the nests actually exploited as those in the neighboring unparasitized nests. Conclusions/Significance: We reviewed the evidence for brood parasites selecting better-matching host egg phenotypes from several relevant studies and argue that such selection probably cannot exist in host-parasite systems where hos

Cost of non-persistence with oral bisphosphonates in post-menopausal osteoporosis treatment in France

<p>Abstract</p> <p>Background</p> <p>During the last decade, oral bisphosphonates (BP) became the most widely prescribed pharmacologic class for post-menopausal osteoporosis. However, many surveys revealed the important issue of poor persistence with those drugs resulting in a failure of treatment to reduce fracture risk sufficiently. Using a published Markov model, this study analyses the economic impact of non-persistence with bisphosphonates in the context of the introduction of generics in France.</p> <p>Methods</p> <p>Direct costs of vertebral, hip and wrist fracture were assessed and included in an existing 10-year Markov model developed to analyse consequences of non-persistence. Three alternatives of comparison were set: no treatment, real-world persistence, and ideal persistence. Simulated patients' characteristics matched those from a French observational study and the real-world adherence alternative employed persistence data from published database analysis. The risk of fracture of menopausal women and the risk reduction associated with the drugs were based on results reported in clinical trials. Incremental cost-effectiveness ratios (ICERs) were calculated first between real-world adherence and no treatment alternatives, and second between ideal and real-world persistence alternatives. The cost of non-persistence was defined as the difference between total cost of ideal and real-world persistence alternatives.</p> <p>Results</p> <p>Within fractured women population, mean costs of 10-year management of fracture were significantly different between the three alternatives with €7,239 (± €4,783), €6,711 (± €4,410) and €6,134 (± €3,945) in the no-treatment, the real-world and ideal persistence alternatives, respectively (p < 0.0001). Cost-effectiveness ratio for real-world treatment persistence compared with no-treatment alternative was found dominant and as well, alternative of ideal persistence dominated the former. Each ten percentage point of persistence gain amounted to €58 per patient, and extrapolation resulted in a global annual cost of non-persistence of over €30 million to the French health care system, with a substantial transfer from hospital to pharmacy budgets.</p> <p>Conclusion</p> <p>Within term, improving persistence with oral bisphosphonates should be economically dominant on levels currently known in real-world. Given this potential savings, ambitious adherence-enhancing interventions should be considered in osteoporotic patients.</p

Estimating the Duration of Pertussis Immunity Using Epidemiological Signatures

Case notifications of pertussis have shown an increase in a number of countries with high rates of routine pediatric immunization. This has led to significant public health concerns over a possible pertussis re-emergence. A leading proposed explanation for the observed increase in incidence is the loss of immunity to pertussis, which is known to occur after both natural infection and vaccination. Little is known, however, about the typical duration of immunity and its epidemiological implications. Here, we analyze a simple mathematical model, exploring specifically the inter-epidemic period and fade-out frequency. These predictions are then contrasted with detailed incidence data for England and Wales. We find model output to be most sensitive to assumptions concerning naturally acquired immunity, which allows us to estimate the average duration of immunity. Our results support a period of natural immunity that is, on average, long-lasting (at least 30 years) but inherently variable

Plant communities as a tool in temporary ponds conservation in SW Portugal

Pond conservationTemporary ponds are seasonal wetlands annually subjected to extreme and unstable ecological conditions, neither truly aquatic nor truly terrestrial. This habitat and its flora have been poorly studied and documented because of the ephemeral character of the flora, the changeable annual weather that has a great effect on the small, herbaceous taxa and the declining abundance of temporary ponds. The objectives of this study are: (a) to define plant community diversity in terms of floristic composition of ephemeral wetlands in SW Portugal, (b) to identify temporary pond types according to their vegetation composition and (c) to identify those ponds that configure the European community priority habitat (3170* – Mediterranean temporary ponds). Vegetation sampling was conducted in 29 ponds, identifying 168 species grouped among 15 plant communities. Soil texture, pH, organic C and N content were measured, but only N and percent of clay appear to be related with the distribution of each community type. The results showed that ephemeral wetlands could be classified into four type: vernal pools, marshlands, deep ponds and disturbed wetlands. Vernal pools correspond to the Mediterranean temporary ponds (3170*), protected as priority habitat under the EU Habitats Directive. Submersed Isoetes species (Isoetes setaceum and Isoetes velatum) represents, together with Eryngium corniculatum, the indicator species for vernal pools. We identify also indicator plant communities of this priority habitat, namely I. setaceum and E. corniculatum– Baldellia ranunculoides plant communities. In this region, the conservation of temporary ponds has so far been compatible with traditional agricultural activities, but today these ponds are endangered by the intensification of agriculture and the loss of traditional land use practices and by the development of touris