PARTICIPANT IMPACTS FROM A PARTICIPATORY WATER MODELING WORKSHOP IN THE SONORA RIVER BASIN, MEXICO

Much of the research in the field of participatory modeling (PM) has focused on the developed world. Few cases are focused on developing regions, and even fewer on Latin American developing countries. The work that has been done in Latin America has often involved water management, often specifically involving water users, and has not focused on the decision making stage of the policy cycle. Little work has been done to measure the effect PM may have on the perceptions and beliefs of decision makers. In fact, throughout the field of PM, very few attempts have been made to quantitatively measure changes in participant beliefs and perceptions following participation. Of the very few exceptions, none have attempted to measure the long-term change in perceptions and beliefs. This research fills that gap. As part of a participatory modeling project in Sonora, Mexico, a region with water quantity and quality problems, I measured the change in beliefs among participants about water models: ability to use and understand them, their usefulness, and their accuracy. I also measured changes in beliefs about climate change, and about water quantity problems, specifically the causes, solutions, and impacts. I also assessed participant satisfaction with the process and outputs from the participatory modeling workshops. Participants were from water agencies, academic institutions, NGOs, and independent consulting firms. Results indicated that participant comfort and self-efficacy with water models, their beliefs in the usefulness of water models, and their beliefs about the impact of water quantity problems changed significantly as a result of the workshops. I present my findings and discuss the results.

High-Level Modeling of Multimodal Interaction Techniques Using NiMMiT

The past few years, multimodal interaction has been gaining importance in virtual environments. Although multimodality renders interacting with an environment more natural and intuitive, the development cycle of such an application is often long and expensive. In our overall field of research, we investigate how modelbased design can facilitate the development process by designing environments through the use of highlevel diagrams. In this scope, we present ‘NiMMiT’, a graphical notation for expressing and evaluating multimodal user interaction; we elaborate on the NiMMiT primitives and demonstrate its use by means of a comprehensive example.

Realistic Single Cell Modeling – from Experiment to Simulation

This tutorial gives a step by step explanation of how one uses experimental data to construct a biologically realistic multicompartmental model. Special emphasis is given on the many ways that this process can be imprecise. The tutorial is intended for both experimentalists who want to get into computer modeling and for computer scientists who use abstract neural network models but are curious about biological realistic modeling. The tutorial is not dependent on the use of a specific simulation engine, but rather covers the kind of data needed for constructing a model, how they are used, and potential pitfalls in the process.

The Advantages of Parametric Modeling for the Reconstruction of Historic Buildings

Consecrated in 1297 as the monastery church of the four years earlier founded St. Catherine’s monastery, the Gothic Church of St. Catherine was largely destroyed in a devastating bombing raid on January 2nd 1945. To counteract the process of disintegration, the departments of geo-information and lower monument protection authority of the City of Nuremburg decided to getting done a three dimensional building model of the Church of St. Catherine’s. A heterogeneous set of data was used for preparation of a parametric architectural model. In effect the modeling of historic buildings can profit from the so called BIM method (Building Information Modeling), as the necessary structuring of the basic data renders it into very sustainable information. The resulting model is perfectly suited to deliver a vivid impression of the interior and exterior of this former mendicant orders’ church to present observers.

Relations between the attentional blink and aspects of psychometric intelligence: A fixed-links modeling approach

The attentional blink phenomenon (AB) represents impaired identification of the second of two targets presented in rapid succession within a stream of stimuli. Despite the well-known association between attentional processes and psychometric intelligence (PI), evidence for a relationship between AB and PI is highly inconsistent. Theory and empirical findings suggest AB to be multifaceted. Hence, relations between AB and PI may be blurred when AB is measured as a single process. Furthermore, different aspects of PI might be differentially related to AB. The present study explored the relationship between processes underlying AB and general PI as well as specific aspects of PI (Reasoning, Speed, Memory, and Creativity) in 201 female students. Fixed-links modeling revealed three processes underlying AB: (1) a U-shaped process positively related to Speed and negatively related to Memory but unrelated to Reasoning, Creativity, and general PI, (2) an increasing process positively related to Reasoning, Speed, Memory, and general PI but not to Creativity, and (3) a decreasing process positively related to general PI and Memory but not to other aspects of PI. Our findings demonstrate that dissociating processes underlying AB and considering specific aspects of PI is required to understand the relationship between AB and PI.

Potentials and constraints of modeling for transdisciplinary co-producing strategies for sustainable water governance

Both climate change and socio-economic development will significantly modify the supply and consumption of water in future. Consequently, regional development has to face aggravation of existing or emergence of new conflicts of interest. In this context, transdisciplinary co-production of knowledge is considered as an important means for coping with these challenges. Accordingly, the MontanAqua project aims at developing strategies for more sustainable water management in the study area Crans-Montana-Sierre (Switzerland) in a transdisciplinary way. It strives for co-producing system, target and transformation knowledge among researchers, policy makers, public administration and civil society organizations. The research process basically consisted of the following steps: First, the current water situation in the study region was investigated. How much water is available? How much water is being used? How are decisions on water distribution and use taken? Second, participatory scenario workshops were conducted in order to identify the stakeholders’ visions of regional development. Third, the water situation in 2050 was simulated by modeling the evolution of water resources and water use and by reflecting on the institutional aspects. These steps laid ground for jointly assessing the consequences of the stakeholders’ visions of development in view of scientific data regarding governance, availability and use of water in the region as well as developing necessary transformation knowledge. During all of these steps researchers have collaborated with stakeholders in the support group RegiEau. The RegiEau group consists of key representatives of owners, managers, users, and pressure groups related to water and landscape: representatives of the communes (mostly the presidents), the canton (administration and parliament), water management associations, agriculture, viticulture, hydropower, tourism, and landscape protection. The aim of the talk is to explore potentials and constraints of scientific modeling of water availability and use within the process of transdisciplinary co-producing strategies for more sustainable water governance.

MODELING SPORADIC TUMOR FORMATION DRIVEN BY TELOMERE DYSFUNCTION IN THE GASTROINTESTINAL TRACT

Colorectal cancer is a complex disease that is thought to arise when cells accumulate mutations that allow for uncontrolled growth. There are several recognized mechanisms for generating such mutations in sporadic colon cancer; one of which is chromosomal instability (CIN). One hypothesized driver of CIN in cancer is the improper repair of dysfunctional telomeres. Telomeres comprise the linear ends of chromosomes and play a dual role in cancer. Its length is maintained by the ribonucleoprotein, telomerase, which is not a normally expressed in somatic cells and as cells divide, telomeres continuously shorten. Critically shortened telomeres are considered dysfunctional as they are recognized as sites of DNA damage and cells respond by entering into replicative senescence or apoptosis, a process that is p53-dependent and the mechanism for telomere-induced tumor suppression. Loss of this checkpoint and improper repair of dysfunctional telomeres can initiate a cycle of fusion, bridge and breakage that can lead to chromosomal changes and genomic instability, a process that can lead to transformation of normal cells to cancer cells. Mouse models of telomere dysfunction are currently based on knocking out the telomerase protein or RNA component; however, the naturally long telomeres of mice require multiple generational crosses of telomerase null mice to achieve critically short telomeres. Shelterin is a complex of six core proteins that bind to telomeres specifically. Pot1a is a highly conserved member of this complex that specifically binds to the telomeric single-stranded 3’ G-rich overhang. Previous work in our lab has shown that Pot1a is essential for chromosomal end protection as deletion of Pot1a in murine embryonic fibroblasts (MEFs) leads to open telomere ends that initiate a DNA damage response mediated by ATR, resulting in p53-dependent cellular senescence. Loss of Pot1a in the background of p53 deficiency results in increased aberrant homologous recombination at telomeres and elevated genomic instability, which allows Pot1a-/-, p53-/- MEFs to form tumors when injected into SCID mice. These phenotypes are similar to those seen in cells with critically shortened telomeres. In this work, we created a mouse model of telomere ysfunction in the gastrointestinal tract through the conditional deletion of Pot1a that recapitulates the microscopic features seen in severe telomere attrition. Combined intestinal loss of Pot1a and p53 lead to formation of invasive adenocarcinomas in the small and large intestines. The tumors formed with long latency, low multiplicity and had complex genomes due to chromosomal instability, features similar to those seen in sporadic human colorectal cancers. Taken together, we have developed a novel mouse model of intestinal tumorigenesis based on genomic instability driven by telomere dysfunction.

A comparison of Markov and generalized linear models of hospital mortality

This paper reports a comparison of three modeling strategies for the analysis of hospital mortality in a sample of general medicine inpatients in a Department of Veterans Affairs medical center. Logistic regression, a Markov chain model, and longitudinal logistic regression were evaluated on predictive performance as measured by the c-index and on accuracy of expected numbers of deaths compared to observed. The logistic regression used patient information collected at admission; the Markov model was comprised of two absorbing states for discharge and death and three transient states reflecting increasing severity of illness as measured by laboratory data collected during the hospital stay; longitudinal regression employed Generalized Estimating Equations (GEE) to model covariance structure for the repeated binary outcome. Results showed that the logistic regression predicted hospital mortality as well as the alternative methods but was limited in scope of application. The Markov chain provides insights into how day to day changes of illness severity lead to discharge or death. The longitudinal logistic regression showed that increasing illness trajectory is associated with hospital mortality. The conclusion is reached that for standard applications in modeling hospital mortality, logistic regression is adequate, but for new challenges facing health services research today, alternative methods are equally predictive, practical, and can provide new insights. ^

Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects

Current models of embryological development focus on intracellular processes such as gene expression and protein networks, rather than on the complex relationship between subcellular processes and the collective cellular organization these processes support. We have explored this collective behavior in the context of neocortical development, by modeling the expansion of a small number of progenitor cells into a laminated cortex with layer and cell type specific projections. The developmental process is steered by a formal language analogous to genomic instructions, and takes place in a physically realistic three-dimensional environment. A common genome inserted into individual cells control their individual behaviors, and thereby gives rise to collective developmental sequences in a biologically plausible manner. The simulation begins with a single progenitor cell containing the artificial genome. This progenitor then gives rise through a lineage of offspring to distinct populations of neuronal precursors that migrate to form the cortical laminae. The precursors differentiate by extending dendrites and axons, which reproduce the experimentally determined branching patterns of a number of different neuronal cell types observed in the cat visual cortex. This result is the first comprehensive demonstration of the principles of self-construction whereby the cortical architecture develops. In addition, our model makes several testable predictions concerning cell migration and branching mechanisms.

Modeling episodic fluid-release events in the ductile carbonates of the Glarus thrust

The exposed Glarus thrust displays midcrustal deformation with tens of kilometers of displacement on an ultrathin layer, the principal slip zone (PSZ). Geological observations indicate that this structure resulted from repeated stick-slip events in the presence of highly overpressured fluids. Here we show that the major characteristics of the Glarus thrust movement (localization, periodicity, and evidence of pressurized fluids) can be reconciled by the coupling of two processes, namely, shear heating and fluid release by carbonate decomposition. During this coupling, slow ductile creep deformation raises the temperature through shear heating and ultimately activates the chemical decomposition of carbonates. The subsequent release of highly overpressurized fluids forms and lubricates the PSZ, allowing a ductile fault to move tens of kilometers on millimeter-thick bands in episodic stick-slip events. This model identifies carbonate decomposition as a key process for motion on the Glarus thrust and explains the source of overpressured fluids accessing the PSZ.

Achieving a more realistic assessment of rockfall hazards by coupling three-dimensional process models and field-based tree-ring data

Sound knowledge of the spatial and temporal patterns of rockfalls is fundamental for the management of this very common hazard in mountain environments. Process-based, three-dimensional simulation models are nowadays capable of reproducing the spatial distribution of rockfall occurrences with reasonable accuracy through the simulation of numerous individual trajectories on highly-resolved digital terrain models. At the same time, however, simulation models typically fail to quantify the ‘real’ frequency of rockfalls (in terms of return intervals). The analysis of impact scars on trees, in contrast, yields real rockfall frequencies, but trees may not be present at the location of interest and rare trajectories may not necessarily be captured due to the limited age of forest stands. In this article, we demonstrate that the coupling of modeling with tree-ring techniques may overcome the limitations inherent to both approaches. Based on the analysis of 64 cells (40 m × 40 m) of a rockfall slope located above a 1631-m long road section in the Swiss Alps, we illustrate results from 488 rockfalls detected in 1260 trees. We illustrate that tree impact data cannot only be used (i) to reconstruct the real frequency of rockfalls for individual cells, but that they also serve (ii) the calibration of the rockfall model Rockyfor3D, as well as (iii) the transformation of simulated trajectories into real frequencies. Calibrated simulation results are in good agreement with real rockfall frequencies and exhibit significant differences in rockfall activity between the cells (zones) along the road section. Real frequencies, expressed as rock passages per meter road section, also enable quantification and direct comparison of the hazard potential between the zones. The contribution provides an approach for hazard zoning procedures that complements traditional methods with a quantification of rockfall frequencies in terms of return intervals through a systematic inclusion of impact records in trees.

Benchmark problems for reactive transport modeling of the generation and attenuation of acid rock drainage

Acid rock drainage (ARD) is a problem of international relevance with substantial environmental and economic implications. Reactive transport modeling has proven a powerful tool for the process-based assessment of metal release and attenuation at ARD sites. Although a variety of models has been used to investigate ARD, a systematic model intercomparison has not been conducted to date. This contribution presents such a model intercomparison involving three synthetic benchmark problems designed to evaluate model results for the most relevant processes at ARD sites. The first benchmark (ARD-B1) focuses on the oxidation of sulfide minerals in an unsaturated tailing impoundment, affected by the ingress of atmospheric oxygen. ARD-B2 extends the first problem to include pH buffering by primary mineral dissolution and secondary mineral precipitation. The third problem (ARD-B3) in addition considers the kinetic and pH-dependent dissolution of silicate minerals under low pH conditions. The set of benchmarks was solved by four reactive transport codes, namely CrunchFlow, Flotran, HP1, and MIN3P. The results comparison focused on spatial profiles of dissolved concentrations, pH and pE, pore gas composition, and mineral assemblages. In addition, results of transient profiles for selected elements and cumulative mass loadings were considered in the intercomparison. Despite substantial differences in model formulations, very good agreement was obtained between the various codes. Residual deviations between the results are analyzed and discussed in terms of their implications for capturing system evolution and long-term mass loading predictions.

The Process-Outcome Mindfulness Effects in Trainees (PrOMET) study: protocol of a pragmatic randomized controlled trial

Background Mindfulness has its origins in an Eastern Buddhist tradition that is over 2500 years old and can be defined as a specific form of attention that is non-judgmental, purposeful, and focused on the present moment. It has been well established in cognitive-behavior therapy in the last decades, while it has been investigated in manualized group settings such as mindfulness-based stress reduction and mindfulness-based cognitive therapy. However, there is scarce research evidence on the effects of mindfulness as a treatment element in individual therapy. Consequently, the demand to investigate mindfulness under effectiveness conditions in trainee therapists has been highlighted. Methods/Design To fill in this research gap, we designed the PrOMET Study. In our study, we will investigate the effects of brief, audiotape-presented, session-introducing interventions with mindfulness elements conducted by trainee therapists and their patients at the beginning of individual therapy sessions in a prospective, randomized, controlled design under naturalistic conditions with a total of 30 trainee therapists and 150 patients with depression and anxiety disorders in a large outpatient training center. We hypothesize that the primary outcomes of the session-introducing intervention with mindfulness elements will be positive effects on therapeutic alliance (Working Alliance Inventory) and general clinical symptomatology (Brief Symptom Checklist) in contrast to the session-introducing progressive muscle relaxation and treatment-as-usual control conditions. Treatment duration is 25 therapy sessions. Therapeutic alliance will be assessed on a session-to-session basis. Clinical symptomatology will be assessed at baseline, session 5, 15 and 25. We will conduct multilevel modeling to address the nested data structure. The secondary outcome measures include depression, anxiety, interpersonal functioning, mindful awareness, and mindfulness during the sessions. Discussion The study results could provide important practical implications because they could inform ideas on how to improve the clinical training of psychotherapists that could be implemented very easily; this is because there is no need for complex infrastructures or additional time concerning these brief session-introducing interventions with mindfulness elements that are directly implemented in the treatment sessions.

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

Effects of Surface Forcing on Interannual Variability of the Fall Phytoplankton Bloom in the Gulf of Maine Revealed Using a Process-Oriented Model

SeaWiFS (Sea-viewing Wide Field-of-view Sensor) chlorophyll data revealed strong interannual variability in fall phytoplankton dynamics in the Gulf of Maine, with 3 general features in any one year: (1) rapid chlorophyll increases in response to storm events in fall; (2) gradual chlorophyll increases in response to seasonal wind-and cooling-induced mixing that gradually deepens the mixed layer; and (3) the absence of any observable fall bloom. We applied a mixed-layer box model and a 1-dimensional physical-biological numerical model to examine the influence of physical forcing (surface wind, heat flux, and freshening) on the mixed-layer dynamics and its impact on the entrainment of deep-water nutrients and thus on the appearance of fall bloom. The model results suggest that during early fall, the surface mixed-layer depth is controlled by both wind-and cooling-induced mixing. Strong interannual variability in mixed-layer depth has a direct impact on short-and long-term vertical nutrient fluxes and thus the fall bloom. Phytoplankton concentrations over time are sensitive to initial pre-bloom profiles of nutrients. The strength of the initial stratification can affect the modeled phytoplankton concentration, while the timing of intermittent freshening events is related to the significant interannual variability of fall blooms.