Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants

The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters 1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery 2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles 8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis 9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.

Automatic multi-resolution shape modeling of multi-organ structures.

Point Distribution Models (PDM) are among the most popular shape description techniques and their usefulness has been demonstrated in a wide variety of medical imaging applications. However, to adequately characterize the underlying modeled population it is essential to have a representative number of training samples, which is not always possible. This problem is especially relevant as the complexity of the modeled structure increases, being the modeling of ensembles of multiple 3D organs one of the most challenging cases. In this paper, we introduce a new GEneralized Multi-resolution PDM (GEM-PDM) in the context of multi-organ analysis able to efficiently characterize the different inter-object relations, as well as the particular locality of each object separately. Importantly, unlike previous approaches, the configuration of the algorithm is automated thanks to a new agglomerative landmark clustering method proposed here, which equally allows us to identify smaller anatomically significant regions within organs. The significant advantage of the GEM-PDM method over two previous approaches (PDM and hierarchical PDM) in terms of shape modeling accuracy and robustness to noise, has been successfully verified for two different databases of sets of multiple organs: six subcortical brain structures, and seven abdominal organs. Finally, we propose the integration of the new shape modeling framework into an active shape-model-based segmentation algorithm. The resulting algorithm, named GEMA, provides a better overall performance than the two classical approaches tested, ASM, and hierarchical ASM, when applied to the segmentation of 3D brain MRI.

Individual and population level effects of partner notification for Chlamydia trachomatis

Partner notification (PN or contact tracing) is an important aspect of treating bacterial sexually transmitted infections (STIs), such as Chlamydia trachomatis. It facilitates the identification of new infected cases that can be treated through individual case management. PN also acts indirectly by limiting onward transmission in the general population. However, the impact of PN, both at the level of individuals and the population, remains unclear. Since it is difficult to study the effects of PN empirically, mathematical and computational models are useful tools for investigating its potential as a public health intervention. To this end, we developed an individual-based modeling framework called Rstisim. It allows the implementation of different models of STI transmission with various levels of complexity and the reconstruction of the complete dynamic sexual partnership network over any time period. A key feature of this framework is that we can trace an individual's partnership history in detail and investigate the outcome of different PN strategies for C. trachomatis. For individual case management, the results suggest that notifying three or more partners from the preceding 18 months yields substantial numbers of new cases. In contrast, the successful treatment of current partners is most important for preventing re-infection of index cases and reducing further transmission of C. trachomatis at the population level. The findings of this study demonstrate the difference between individual and population level outcomes of public health interventions for STIs.

A model of osteoporosis impact in Switzerland 2000-2020

The aim of our study was to develop a modeling framework suitable to quantify the incidence, absolute number and economic impact of osteoporosis-attributable hip, vertebral and distal forearm fractures, with a particular focus on change over time, and with application to the situation in Switzerland from 2000 to 2020. A Markov process model was developed and analyzed by Monte Carlo simulation. A demographic scenario provided by the Swiss Federal Statistical Office and various Swiss and international data sources were used as model inputs. Demographic and epidemiologic input parameters were reproduced correctly, confirming the internal validity of the model. The proportion of the Swiss population aged 50 years or over will rise from 33.3% in 2000 to 41.3% in 2020. At the total population level, osteoporosis-attributable incidence will rise from 1.16 to 1.54 per 1,000 person-years in the case of hip fracture, from 3.28 to 4.18 per 1,000 person-years in the case of radiographic vertebral fracture, and from 0.59 to 0.70 per 1,000 person-years in the case of distal forearm fracture. Osteoporosis-attributable hip fracture numbers will rise from 8,375 to 11,353, vertebral fracture numbers will rise from 23,584 to 30,883, and distal forearm fracture numbers will rise from 4,209 to 5,186. Population-level osteoporosis-related direct medical inpatient costs per year will rise from 713.4 million Swiss francs (CHF) to CHF946.2 million. These figures correspond to 1.6% and 2.2% of Swiss health care expenditures in 2000. The modeling framework described can be applied to a wide variety of settings. It can be used to assess the impact of new prevention, diagnostic and treatment strategies. In Switzerland incidences of osteoporotic hip, vertebral and distal forearm fracture will rise by 33%, 27%, and 19%, respectively, between 2000 and 2020, if current prevention and treatment patterns are maintained. Corresponding absolute fracture numbers will rise by 36%, 31%, and 23%. Related direct medical inpatient costs are predicted to increase by 33%; however, this estimate is subject to uncertainty due to limited availability of input data.

Adaptation options under climate change for multifunctional agriculture: a simulation study for western Switzerland

Besides its primary role in producing food and fiber, agriculture also has relevant effects on several other functions, such as management of renewable natural resources. Climate change (CC) may lead to new trade-offs between agricultural functions or aggravate existing ones, but suitable agricultural management may maintain or even improve the ability of agroecosystems to supply these functions. Hence, it is necessary to identify relevant drivers (e.g., cropping practices, local conditions) and their interactions, and how they affect agricultural functions in a changing climate. The goal of this study was to use a modeling framework to analyze the sensitivity of indicators of three important agricultural functions, namely crop yield (food and fiber production function), soil erosion (soil conservation function), and nutrient leaching (clean water provision function), to a wide range of agricultural practices for current and future climate conditions. In a two-step approach, cropping practices that explain high proportions of variance of the different indicators were first identified by an analysis of variance-based sensitivity analysis. Then, most suitable combinations of practices to achieve best performance with respect to each indicator were extracted, and trade-offs were analyzed. The procedure was applied to a region in western Switzerland, considering two different soil types to test the importance of local environmental constraints. Results show that the sensitivity of crop yield and soil erosion due to management is high, while nutrient leaching mostly depends on soil type. We found that the influence of most agricultural practices does not change significantly with CC; only irrigation becomes more relevant as a consequence of decreasing summer rainfall. Trade-offs were identified when focusing on best performances of each indicator separately, and these were amplified under CC. For adaptation to CC in the selected study region, conservation soil management and the use of cropped grasslands appear to be the most suitable options to avoid trade-offs.

Influence of the background wind on the local soil moisture-precipitation feedback

The importance of soil moisture anomalies on airmass convection over semiarid regions has been recognized in several studies. The underlying mechanisms remain partly unclear. An open question is why wetter soils can result in either an increase or a decrease of precipitation (positive or negative soil moisture–precipitation feedback, respectively). Here an idealized cloud-resolving modeling framework is used to explore the local soil moisture–precipitation feedback. The approach is able to replicate both positive and negative feedback loops, depending on the environmental parameters. The mechanism relies on horizontal soil moisture variations, which may develop and intensify spontaneously. The positive expression of the feedback is associated with the initiation of convection over dry soil patches, but the convective cells then propagate over wet patches where they strengthen and preferentially precipitate. The negative feedback may occur when the wind profile is too weak to support the propagation of convective features from dry to wet areas. Precipitation is then generally weaker and falls preferentially over dry patches. The results highlight the role of the midtropospheric flow in determining the sign of the feedback. A key element of the positive feedback is the exploitation of both low convective inhibition (CIN) over dry patches (for the initiation of convection) and high CAPE over wet patches (for the generation of precipitation).

A glimpse into the future composition of marine phytoplankton communities

It is expected that climate change will have significant impacts on ecosystems. Most model projections agree that the ocean will experience stronger stratification and less nutrient supply from deep waters. These changes will likely affect marine phytoplankton communities and will thus impact on the higher trophic levels of the oceanic food web. The potential consequences of future climate change on marine microbial communities can be investigated and predicted only with the help of mathematical models. Here we present the application of a model that describes aggregate properties of marine phytoplankton communities and captures the effects of a changing environment on their composition and adaptive capacity. Specifically, the model describes the phytoplankton community in terms of total biomass, mean cell size, and functional diversity. The model is applied to two contrasting regions of the Atlantic Ocean (tropical and temperate) and is tested under two emission scenarios: SRES A2 or “business as usual” and SRES B1 or “local utopia.” We find that all three macroecological properties will decline during the next century in both regions, although this effect will be more pronounced in the temperate region. Being consistent with previous model predictions, our results show that a simple trait-based modeling framework represents a valuable tool for investigating how phytoplankton communities may reorganize under a changing climate.

Climatic and anthropogenic changes in Western Switzerland: Impacts on water stress

Recent observed hydro-climatic changes in mountainous areas are of concern as they may directly affect capacity to fulfill water needs. The canton of Vaud in Western Switzerland is an example of such a region as it has experienced water shortage episodes during the past decade. Based on an integrated modeling framework, this study explores how hydro-climatic conditions and water needs could evolve in mountain environments and assesses their potential impacts on water stress by the 2060 horizon. Flows were simulated based on a daily semi-distributed hydrological model. Future changes were derived from Swiss climate scenarios based on two regional climate models. Regarding water needs, the authorities of the canton of Vaud provided a population growth scenario while irrigation and livestock trends followed a business-as-usual scenario. Currently, the canton of Vaud experiences moderate water stress from June to August, except in its Alpine area where no stress is noted. In the 2060 horizon, water needs could exceed 80% of the rivers' available resources in low- to mid-altitude environments in mid-summer. This arises from the combination of drier and warmer climate that leads to longer and more severe low flows, and increasing urban (+ 40%) and irrigation (+ 25%) water needs. Highlighting regional differences supports the development of sustainable development pathways to reduce water tensions. Based on a quantitative assessment, this study also calls for broader impact studies including water quality issues.

Exposure modeling of high-frequency electromagnetic fields

We developed a geospatial model that calculates ambient high-frequency electromagnetic field (HF-EMF) strengths of stationary transmission installations such as mobile phone base stations and broadcast transmitters with high spatial resolution in the order of 1 m. The model considers the location and transmission patterns of the transmitters, the three-dimensional topography, and shielding effects by buildings. The aim of the present study was to assess the suitability of the model for exposure monitoring and for epidemiological research. We modeled time-averaged HF-EMF strengths for an urban area in the city of Basel as well as for a rural area (Bubendorf). To compare modeling with measurements, we selected 20 outdoor measurement sites in Basel and 18 sites in Bubendorf. We calculated Pearson's correlation coefficients between modeling and measurements. Chance-corrected agreement was evaluated by weighted Cohen's kappa statistics for three exposure categories. Correlation between measurements and modeling of the total HF-EMF strength was 0.67 (95% confidence interval (CI): 0.33-0.86) in the city of Basel and 0.77 (95% CI: 0.46-0.91) in the rural area. In both regions, kappa coefficients between measurements and modeling were 0.63 and 0.77 for the total HF-EMF strengths and for all mobile phone frequency bands. First evaluation of our geospatial model yielded substantial agreement between modeling and measurements. However, before the model can be applied for future epidemiologic research, additional validation studies focusing on indoor values are needed to improve model validity.Journal of Exposure Science and Environmental Epidemiology (2008) 18, 183-191; doi:10.1038/sj.jes.7500575; published online 4 April 2007.

An efficient framework for photon Monte Carlo treatment planning

Currently photon Monte Carlo treatment planning (MCTP) for a patient stored in the patient database of a treatment planning system (TPS) can usually only be performed using a cumbersome multi-step procedure where many user interactions are needed. This means automation is needed for usage in clinical routine. In addition, because of the long computing time in MCTP, optimization of the MC calculations is essential. For these purposes a new graphical user interface (GUI)-based photon MC environment has been developed resulting in a very flexible framework. By this means appropriate MC transport methods are assigned to different geometric regions by still benefiting from the features included in the TPS. In order to provide a flexible MC environment, the MC particle transport has been divided into different parts: the source, beam modifiers and the patient. The source part includes the phase-space source, source models and full MC transport through the treatment head. The beam modifier part consists of one module for each beam modifier. To simulate the radiation transport through each individual beam modifier, one out of three full MC transport codes can be selected independently. Additionally, for each beam modifier a simple or an exact geometry can be chosen. Thereby, different complexity levels of radiation transport are applied during the simulation. For the patient dose calculation, two different MC codes are available. A special plug-in in Eclipse providing all necessary information by means of Dicom streams was used to start the developed MC GUI. The implementation of this framework separates the MC transport from the geometry and the modules pass the particles in memory; hence, no files are used as the interface. The implementation is realized for 6 and 15 MV beams of a Varian Clinac 2300 C/D. Several applications demonstrate the usefulness of the framework. Apart from applications dealing with the beam modifiers, two patient cases are shown. Thereby, comparisons are performed between MC calculated dose distributions and those calculated by a pencil beam or the AAA algorithm. Interfacing this flexible and efficient MC environment with Eclipse allows a widespread use for all kinds of investigations from timing and benchmarking studies to clinical patient studies. Additionally, it is possible to add modules keeping the system highly flexible and efficient.

Representation via Probabilities: Models of Probabilistic Modeling

How do probabilistic models represent their targets and how do they allow us to learn about them? The answer to this question depends on a number of details, in particular on the meaning of the probabilities involved. To classify the options, a minimalist conception of representation (Su\'arez 2004) is adopted: Modelers devise substitutes (``sources'') of their targets and investigate them to infer something about the target. Probabilistic models allow us to infer probabilities about the target from probabilities about the source. This leads to a framework in which we can systematically distinguish between different models of probabilistic modeling. I develop a fully Bayesian view of probabilistic modeling, but I argue that, as an alternative, Bayesian degrees of belief about the target may be derived from ontic probabilities about the source. Remarkably, some accounts of ontic probabilities can avoid problems if they are supposed to apply to sources only.

Experimenting and modeling: sharp distinctions, integration or just a mess?

At first sight, experimenting and modeling form two distinct modes of scientific inquiry. This spurs philosophical debates about how the distinction should be drawn (e.g. Morgan 2005, Winsberg 2009, Parker 2009). But much scientific practice casts serious doubts on the idea that the distinction makes much sense. There are two worries. First, the practices of modeling and experimenting are often intertwined in intricate ways because much modeling involves experimenting, and the interpretation of many experiments relies upon models. Second, there are borderline cases that seem to blur the distinction between experiment and model (if there is any). My talk tries to defend the philosophical project of distinguishing models from experiment and to advance the related philosophical debate. I begin with providing a minimalist framework of conceptualizing experimenting and modeling and their mutual relationships. The methods are conceptualized as different types of activities that are characterized by a primary goal, respectively. The minimalist framwork, which should be uncontroversial, suffices to accommodate the first worry. I address the second worry by suggesting several ways how to conceptualize the distinction in a more flexible way. I make a concrete suggestion of how the distinction may be drawn. I use examples from the history of science to argue my case. The talk concentrates and models and experiments, but I will comment on simulations too.