Decision evaluation in complex risk network systems (DecernsSDSS) demo and Black River case study

The selection of metrics for ecosystem restoration programs is critical for improving the quality of monitoring programs and characterizing project success. Moreover it is oftentimes very difficult to balance the importance of multiple ecological, social, and economical metrics. Metric selection process is a complex and must simultaneously take into account monitoring data, environmental models, socio-economic considerations, and stakeholder interests. We propose multicriteria decision analysis (MCDA) methods, broadly defined, for the selection of optimal sets of metrics to enhance evaluation of ecosystem restoration alternatives. Two MCDA methods, a multiattribute utility analysis (MAUT), and a probabilistic multicriteria acceptability analysis (ProMAA), are applied and compared for a hypothetical case study of a river restoration involving multiple stakeholders. Overall, the MCDA results in a systematic, unbiased, and transparent solution, informing restoration alternatives evaluation. The two methods provide comparable results in terms of selected metrics. However, because ProMAA can consider probability distributions for weights and utility values of metrics for each criteria, it is suggested as the best option if data uncertainty is high. Despite the increase in complexity in the metric selection process, MCDA improves upon the current ad-hoc decision practice based on the consultations with stakeholders and experts, and encourages transparent and quantitative aggregation of data and judgement, increasing the transparency of decision making in restoration projects. We believe that MCDA can enhance the overall sustainability of ecosystem by enhancing both ecological and societal needs.

Diagnosing Causes of Water Scarcity in Complex Water Resources Systems and Identifying Risk Management Actions

From the water management perspective, water scarcity is an unacceptable risk of facing water shortages to serve water demands in the near future. Water scarcity may be temporary and related to drought conditions or other accidental situation, or may be permanent and due to deeper causes such as excessive demand growth, lack of infrastructure for water storage or transport, or constraints in water management. Diagnosing the causes of water scarcity in complex water resources systems is a precondition to adopt effective drought risk management actions. In this paper we present four indices which have been developed to evaluate water scarcity. We propose a methodology for interpretation of index values that can lead to conclusions about the reliability and vulnerability of systems to water scarcity, as well as to diagnose their possible causes and to propose solutions. The described methodology was applied to the Ebro river basin, identifying existing and expected problems and possible solutions. System diagnostics, based exclusively on the analysis of index values, were compared with the known reality as perceived by system managers, validating the conclusions in all cases

Membrane Systems Working with the PFactor: Best Strategy to Solve Complex Problems.

A membrane system is a massive parallel system, which is inspired by the living cells when processing information. As a part of unconventional computing, membrane systems are proven to be effective in solving complex problems. A new factor is introduced. This factor can decide whether a technique is worthwhile being used or not. The use of this factor provides the best chances for selecting the strategy for the rules application phase. Referring to the “best” is in reference to the one that reduces execution time within the membrane system. A pre-analysis of the membrane system determines the P-factor, which in return advises the optimal strategy to use. In particular, this paper compares the use of two strategies based on the P-factor and provides results upon the application of them. The paper concludes that the P-factor is an effective indicator for choosing the right strategy to implement the rules application phase in membrane systems.

Evaluating alternative industrial network organizations and information systems

Purpose – The purpose of this paper is to present a simulation‐based evaluation method for the comparison of different organizational forms and software support levels in the field of supply chain management (SCM). Design/methodology/approach – Apart from widely known logistic performance indicators, the discrete event simulation model considers explicitly coordination cost as stemming from iterative administration procedures. Findings - The method is applied to an exemplary supply chain configuration considering various parameter settings. Curiously, additional coordination cost does not always result in improved logistic performance. Influence factor variations lead to different organizational recommendations. The results confirm the high importance of (up to now) disregarded dimensions when evaluating SCM concepts and IT tools. Research limitations/implications – The model is based on simplified product and network structures. Future research shall include more complex, real world configurations. Practical implications – The developed method is designed for the identification of improvement potential when SCM software is employed. Coordination schemes based only on ERP systems are valid alternatives in industrial practice because significant investment IT can be avoided. Therefore, the evaluation of these coordination procedures, in particular the cost due to iterations, is of high managerial interest and the method provides a comprehensive tool for strategic IT decision making. Originality/value – Reviewed literature is mostly focused on the benefits of SCM software implementations. However, ERP system based supply chain coordination is still widespread industrial practice but associated coordination cost has not been addressed by researchers.

Emotions and the Engineering of Adaptiveness in Complex Systems

A major challenge in the engineering of complex and critical systems is the management of change, both in the system and in its operational environment. Due to the growing of complexity in systems, new approaches on autonomy must be able to detect critical changes and avoid their progress towards undesirable states. We are searching for methods to build systems that can tune the adaptability protocols. New mechanisms that use system-wellness requirements to reduce the influence of the outer domain and transfer the control of uncertainly to the inner one. Under the view of cognitive systems, biological emotions suggests a strategy to configure value-based systems to use semantic self-representations of the state. A method inspired by emotion theories to causally connect to the inner domain of the system and its objectives of wellness, focusing on dynamically adapting the system to avoid the progress of critical states. This method shall endow the system with a transversal mechanism to monitor its inner processes, detecting critical states and managing its adaptivity in order to maintain the wellness goals. The paper describes the current vision produced by this work-in-progress.

Enhancing regression models for complex systems using evolutionary techniques for feature engineering

This work proposes an automatic methodology for modeling complex systems. Our methodology is based on the combination of Grammatical Evolution and classical regression to obtain an optimal set of features that take part of a linear and convex model. This technique provides both Feature Engineering and Symbolic Regression in order to infer accurate models with no effort or designer's expertise requirements. As advanced Cloud services are becoming mainstream, the contribution of data centers in the overall power consumption of modern cities is growing dramatically. These facilities consume from 10 to 100 times more power per square foot than typical office buildings. Modeling the power consumption for these infrastructures is crucial to anticipate the effects of aggressive optimization policies, but accurate and fast power modeling is a complex challenge for high-end servers not yet satisfied by analytical approaches. For this case study, our methodology minimizes error in power prediction. This work has been tested using real Cloud applications resulting on an average error in power estimation of 3.98%. Our work improves the possibilities of deriving Cloud energy efficient policies in Cloud data centers being applicable to other computing environments with similar characteristics.

Mathematical foundations for efficient structural controllability and observability analysis of complex systems

The relationship between structural controllability and observability of complex systems is studied. Algebraic and graph theoretic tools are combined to prove the extent of some controller/observer duality results. Two types of control design problems are addressed and some fundamental theoretical results are provided. In addition new algorithms are presented to compute optimal solutions for monitoring large scale real networks.

3D simulation of complex shading affecting PV systems taking benefit from the power of graphics cards developed for the video game industry

Shading reduces the power output of a photovoltaic (PV) system. The design engineering of PV systems requires modeling and evaluating shading losses. Some PV systems are affected by complex shading scenes whose resulting PV energy losses are very difficult to evaluate with current modeling tools. Several specialized PV design and simulation software include the possibility to evaluate shading losses. They generally possess a Graphical User Interface (GUI) through which the user can draw a 3D shading scene, and then evaluate its corresponding PV energy losses. The complexity of the objects that these tools can handle is relatively limited. We have created a software solution, 3DPV, which allows evaluating the energy losses induced by complex 3D scenes on PV generators. The 3D objects can be imported from specialized 3D modeling software or from a 3D object library. The shadows cast by this 3D scene on the PV generator are then directly evaluated from the Graphics Processing Unit (GPU). Thanks to the recent development of GPUs for the video game industry, the shadows can be evaluated with a very high spatial resolution that reaches well beyond the PV cell level, in very short calculation times. A PV simulation model then translates the geometrical shading into PV energy output losses. 3DPV has been implemented using WebGL, which allows it to run directly from a Web browser, without requiring any local installation from the user. This also allows taken full benefits from the information already available from Internet, such as the 3D object libraries. This contribution describes, step by step, the method that allows 3DPV to evaluate the PV energy losses caused by complex shading. We then illustrate the results of this methodology to several application cases that are encountered in the world of PV systems design. Keywords: 3D, modeling, simulation, GPU, shading, losses, shadow mapping, solar, photovoltaic, PV, WebGL

Emotions and the Engineering of Adaptiveness in Complex Systems

A major challenge in the engineering of complex and critical systems is the management of change, both in the system and in its operational environment. Due to the growing of complexity in systems, new approaches on autonomy must be able to detect critical changes and avoid their progress towards undesirable states. We are searching for methods to build systems that can tune the adaptability protocols. New mechanisms that use system-wellness requirements to reduce the influence of the outer domain and transfer the control of uncertainly to the inner one. Under the view of cognitive systems, biological emotions suggests a strategy to configure value-based systems to use semantic self-representations of the state. A method inspired by emotion theories to causally connect to the inner domain of the system and its objectives of wellness, focusing on dynamically adapting the system to avoid the progress of critical states. This method shall endow the system with a transversal mechanism to monitor its inner processes, detecting critical states and managing its adaptivity in order to maintain the wellness goals. The paper describes the current vision produced by this work-in-progress.

Análisis de sistemas dinámicos y complejos en la Liga Profesional de Balonmano de España = Complex and dynamical systems analysis in Spanish Professional Handball League

El propósito de esta tesis fue estudiar el rendimiento ofensivo de los equipos de balonmano de élite cuando se considera el balonmano como un sistema dinámico complejo no lineal. La perspectiva de análisis dinámica dependiente del tiempo fue adoptada para evaluar el rendimiento de los equipos durante el partido. La muestra general comprendió los 240 partidos jugados en la temporada 2011-2012 de la liga profesional masculina de balonmano de España (Liga ASOBAL). En el análisis posterior solo se consideraron los partidos ajustados (diferencia final de goles ≤ 5; n = 142). El estado del marcador, la localización del partido, el nivel de los oponentes y el periodo de juego fueron incorporados al análisis como variables situacionales. Tres estudios compusieron el núcleo de la tesis. En el primer estudio, analizamos la coordinación entre las series temporales que representan el proceso goleador a lo largo del partido de cada uno de los dos equipos que se enfrentan. Autocorrelaciones, correlaciones cruzadas, doble media móvil y transformada de Hilbert fueron usadas para el análisis. El proceso goleador de los equipos presentó una alta consistencia a lo largo de todos los partidos, así como fuertes modos de coordinación en fase en todos los contextos de juego. Las únicas diferencias se encontraron en relación al periodo de juego. La coordinación en los procesos goleadores de los equipos fue significativamente menor en el 1er y 2º periodo (0–10 min y 10–20 min), mostrando una clara coordinación creciente a medida que el partido avanzaba. Esto sugiere que son los 20 primeros minutos aquellos que rompen los partidos. En el segundo estudio, analizamos los efectos temporales (efecto inmediato, a corto y a medio plazo) de los tiempos muertos en el rendimiento goleador de los equipos. Modelos de regresión lineal múltiple fueron empleados para el análisis. Los resultados mostraron incrementos de 0.59, 1.40 y 1.85 goles para los periodos que comprenden la primera, tercera y quinta posesión de los equipos que pidieron el tiempo muerto. Inversamente, se encontraron efectos significativamente negativos para los equipos rivales, con decrementos de 0.50, 1.43 y 2.05 goles en los mismos periodos respectivamente. La influencia de las variables situacionales solo se registró en ciertos periodos de juego. Finalmente, en el tercer estudio, analizamos los efectos temporales de las exclusiones de los jugadores sobre el rendimiento goleador de los equipos, tanto para los equipos que sufren la exclusión (inferioridad numérica) como para los rivales (superioridad numérica). Se emplearon modelos de regresión lineal múltiple para el análisis. Los resultados mostraron efectos negativos significativos en el número de goles marcados por los equipos con un jugador menos, con decrementos de 0.25, 0.40, 0.61, 0.62 y 0.57 goles para los periodos que comprenden el primer, segundo, tercer, cuarto y quinto minutos previos y posteriores a la exclusión. Para los rivales, los resultados mostraron efectos positivos significativos, con incrementos de la misma magnitud en los mismos periodos. Esta tendencia no se vio afectada por el estado del marcador, localización del partido, nivel de los oponentes o periodo de juego. Los incrementos goleadores fueron menores de lo que se podría esperar de una superioridad numérica de 2 minutos. Diferentes teorías psicológicas como la paralización ante situaciones de presión donde se espera un gran rendimiento pueden ayudar a explicar este hecho. Los últimos capítulos de la tesis enumeran las conclusiones principales y presentan diferentes aplicaciones prácticas que surgen de los tres estudios. Por último, se presentan las limitaciones y futuras líneas de investigación. ABSTRACT The purpose of this thesis was to investigate the offensive performance of elite handball teams when considering handball as a complex non-linear dynamical system. The time-dependent dynamic approach was adopted to assess teams’ performance during the game. The overall sample comprised the 240 games played in the season 2011-2012 of men’s Spanish Professional Handball League (ASOBAL League). In the subsequent analyses, only close games (final goal-difference ≤ 5; n = 142) were considered. Match status, game location, quality of opposition, and game period situational variables were incorporated into the analysis. Three studies composed the core of the thesis. In the first study, we analyzed the game-scoring coordination between the time series representing the scoring processes of the two opposing teams throughout the game. Autocorrelation, cross-correlation, double moving average, and Hilbert transform were used for analysis. The scoring processes of the teams presented a high consistency across all the games as well as strong in-phase modes of coordination in all the game contexts. The only differences were found when controlling for the game period. The coordination in the scoring processes of the teams was significantly lower for the 1st and 2nd period (0–10 min and 10–20 min), showing a clear increasing coordination behavior as the game progressed. This suggests that the first 20 minutes are those that break the game-scoring. In the second study, we analyzed the temporal effects (immediate effect, short-term effect, and medium-term effect) of team timeouts on teams’ scoring performance. Multiple linear regression models were used for the analysis. The results showed increments of 0.59, 1.40 and 1.85 goals for the periods within the first, third and fifth timeout ball possessions for the teams that requested the timeout. Conversely, significant negative effects on goals scored were found for the opponent teams, with decrements of 0.59, 1.43 and 2.04 goals for the same periods, respectively. The influence of situational variables on the scoring performance was only registered in certain game periods. Finally, in the third study, we analyzed the players’ exclusions temporal effects on teams’ scoring performance, for the teams that suffer the exclusion (numerical inferiority) and for the opponents (numerical superiority). Multiple linear regression models were used for the analysis. The results showed significant negative effects on the number of goals scored for the teams with one less player, with decrements of 0.25, 0.40, 0.61, 0.62, and 0.57 goals for the periods within the previous and post one, two, three, four and five minutes of play. For the opponent teams, the results showed positive effects, with increments of the same magnitude in the same game periods. This trend was not affected by match status, game location, quality of opposition, or game period. The scoring increments were smaller than might be expected from a 2-minute numerical playing superiority. Psychological theories such as choking under pressure situations where good performance is expected could contribute to explain this finding. The final chapters of the thesis enumerate the main conclusions and underline the main practical applications that arise from the three studies. Lastly, limitations and future research directions are described.

Chromatin-bound PCNA complex formation triggered by DNA damage occurs independent of the ATM gene product in human cells

Proliferating cell nuclear antigen (PCNA), a processivity factor for DNA polymerases δ and ɛ, is involved in DNA replication as well as in diverse DNA repair pathways. In quiescent cells, UV light-induced bulky DNA damage triggers the transition of PCNA from a soluble to an insoluble chromatin-bound form, which is intimately associated with the repair synthesis by polymerases δ and ɛ. In this study, we investigated the efficiency of PCNA complex formation in response to ionizing radiation-induced DNA strand breaks in normal and radiation-sensitive Ataxia telangiectasia (AT) cells by immunofluorescence and western blot techniques. Exposure of normal cells to γ-rays rapidly triggered the formation of PCNA foci in a dose-dependent manner in the nuclei and the PCNA foci (40–45%) co-localized with sites of repair synthesis detected by bromodeoxyuridine labeling. The chromatin-bound PCNA gradually declined with increasing post-irradiation times and almost reached the level of unirradiated cells by 6 h. The PCNA foci formed after γ-irradiation was resistant to high salt extraction and the chromatin association of PCNA was lost after DNase I digestion. Interestingly, two radiosensitive primary fibroblast cell lines, derived from AT patients harboring homozygous mutations in the ATM gene, displayed an efficient PCNA redistribution after γ-irradiation. We also analyzed the PCNA complex induced by a radiomimetic agent, Bleomycin (BLM), which produces predominantly single- and double-strand DNA breaks. The efficiency and the time course of PCNA complex induced by BLM were identical in both normal and AT cells. Our study demonstrates for the first time that the ATM gene product is not required for PCNA complex assembly in response to DNA strand breaks. Additionally, we observed an increased interaction of PCNA with the Ku70 and Ku80 heterodimer after DNA damage, suggestive of a role for PCNA in the non-homologous end-joining repair pathway of DNA strand breaks.

Complex dynamics of multilocus systems subjected to cyclical selection.

Earlier we have shown that oscillations with a long period ("supercycles") may arise in two-locus systems experiencing cyclical selection with a short period. However, this mode of complex limiting behavior appeared to be possible for narrow ranges of parameters. Here we demonstrate that a multilocus system subjected to stabilizing selection with cyclically moving optimum can generate ubiquitous complex limiting behavior including supercycles, T-cycles, and chaotic-like phenomena. This mode of multilocus dynamics far exceeds the potential attainable under ordinary selection models resulting in simple behavior. It may represent a novel evolutionary mechanism increasing genetic diversity over long-term time periods.

Proteolysis of major histocompatibility complex class II-associated invariant chain is regulated by the alternatively spliced gene product, p41.

Invariant chain (Ii) is an intracellular type II transmembrane glycoprotein that is associated with major histocompatibility complex class II molecules during biosynthesis. Ii exists in two alternatively spliced forms, p31 and p41. Both p31 and p41 facilitate folding of class II molecules, promote egress from the endoplasmic reticulum, prevent premature peptide binding, and enhance localization to proteolytic endosomal compartments that are thought to be the sites for Ii degradation, antigen processing, and class II-peptide association. In spite of the dramatic and apparently equivalent effects that p31 and p41 have on class II biosynthesis, the ability of invariant chain to enhance antigen presentation to T cells is mostly restricted to p41. Here we show that degradation of Ii leads to the generation of a 12-kDa amino-terminal fragment that in p41-positive, but not in p31-positive, cells remains associated with class II molecules for an extended time. Interestingly, we find that coexpression of the two isoforms results in a change in the pattern of p31 degradation such that endosomal processing of p31 also leads to extended association of a similar 12-kDa fragment with class II molecules. These data raise the possibility that p41 may have the ability to impart its pattern of proteolytic processing on p31 molecules expressed in the same cells. This would enable a small number of p41 molecules to modify the post-translational transport and/or processing of an entire cohort of class II-Ii complexes in a manner that could account for the unique ability of p41 to enhance antigen presentation.

Characterization of the VHL tumor suppressor gene product: localization, complex formation, and the effect of natural inactivating mutations.

The human VHL tumor suppressor gene has been implicated in the inherited disorder von Hippel-Lindau disease and in sporadic renal carcinoma. The homologous rat gene encodes a 185-amino acid protein that is 88% sequence identical to the aligned 213-amino acid human VHL gene product. When expressed in COS-7 cells, both the human and the rat VHL proteins showed predominant nuclear, nuclear and cytosolic, or predominant cytosolic VHL staining by immunofluorescence. A complicated pattern of cellular proteins was seen that could be specifically coimmunoprecipitated with the introduced VHL protein. A complex containing VHL and proteins of apparent molecular masses 16 and 9 kDa was the most consistently observed. Certain naturally occurring VHL missense mutations demonstrated either complete or partial loss of the p16-p9 complex. Thus, the VHL tumor suppressor gene product is a nuclear protein, perhaps capable of specifically translocating between the nucleus and the cytosol. It is likely that VHL executes its functions via formation of specific multiprotein complexes. Identification of these VHL-associated proteins will likely clarify the physiology of this tumor suppressor gene.

The glucocorticoid receptor type II complex is a target of the HIV-1 vpr gene product.

The vpr gene of human immunodeficiency virus type 1 (HIV-1) encodes a 15-kDa virion-associated protein that functions as a regulator of cellular processes linked to the HIV life cycle. We report the interaction of a 41-kDa cytosolic viral protein R interacting protein 1 (Rip-1) with Vpr in vitro. Rip-1 displays a wide tissue distribution, including relevant targets of HIV infection. Vpr protein induced nuclear translocation of Rip-1, as did glucocorticoid receptor (GR)-II-stimulating steroids. Importantly, Vpr and Rip-1 coimmunoprecipitated with the human GR as part of an activated receptor complex. Vpr complementation of a vpr mutant virus was also mimicked by GR-II-stimulating steroids. Vpr and GR-II actions were inhibited by mifepristone, a GR-II pathway inhibitor. Together these data directly link the activity of the vpr gene product to the glucocorticoid steroid pathway and provide a biochemical mechanism for the cellular and viral activity of Vpr, as well as suggest that a unique class of antivirals, which includes mifepristone (RU486), may influence HIV-1 replication.