Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.

Robust effect sizes and their confidence intervals for group difference between trajectories in hierarchical linear growth model

Hierarchical linear growth model (HLGM), as a flexible and powerful analytic method, has played an increased important role in psychology, public health and medical sciences in recent decades. Mostly, researchers who conduct HLGM are interested in the treatment effect on individual trajectories, which can be indicated by the cross-level interaction effects. However, the statistical hypothesis test for the effect of cross-level interaction in HLGM only show us whether there is a significant group difference in the average rate of change, rate of acceleration or higher polynomial effect; it fails to convey information about the magnitude of the difference between the group trajectories at specific time point. Thus, reporting and interpreting effect sizes have been increased emphases in HLGM in recent years, due to the limitations and increased criticisms for statistical hypothesis testing. However, most researchers fail to report these model-implied effect sizes for group trajectories comparison and their corresponding confidence intervals in HLGM analysis, since lack of appropriate and standard functions to estimate effect sizes associated with the model-implied difference between grouping trajectories in HLGM, and also lack of computing packages in the popular statistical software to automatically calculate them. ^ The present project is the first to establish the appropriate computing functions to assess the standard difference between grouping trajectories in HLGM. We proposed the two functions to estimate effect sizes on model-based grouping trajectories difference at specific time, we also suggested the robust effect sizes to reduce the bias of estimated effect sizes. Then, we applied the proposed functions to estimate the population effect sizes (d ) and robust effect sizes (du) on the cross-level interaction in HLGM by using the three simulated datasets, and also we compared the three methods of constructing confidence intervals around d and du recommended the best one for application. At the end, we constructed 95% confidence intervals with the suitable method for the effect sizes what we obtained with the three simulated datasets. ^ The effect sizes between grouping trajectories for the three simulated longitudinal datasets indicated that even though the statistical hypothesis test shows no significant difference between grouping trajectories, effect sizes between these grouping trajectories can still be large at some time points. Therefore, effect sizes between grouping trajectories in HLGM analysis provide us additional and meaningful information to assess group effect on individual trajectories. In addition, we also compared the three methods to construct 95% confident intervals around corresponding effect sizes in this project, which handled with the uncertainty of effect sizes to population parameter. We suggested the noncentral t-distribution based method when the assumptions held, and the bootstrap bias-corrected and accelerated method when the assumptions are not met.^

Agglomeration and firm-level productivity : a Bayesian spatial approach

This paper estimates the impact of industrial agglomeration on firm-level productivity in Chinese manufacturing sectors. To account for spatial autocorrelation across regions, we formulate a hierarchical spatial model at the firm level and develop a Bayesian estimation algorithm. A Bayesian instrumental-variables approach is used to address endogeneity bias of agglomeration. Robust to these potential biases, we find that agglomeration of the same industry (i.e. localization) has a productivity-boosting effect, but agglomeration of urban population (i.e. urbanization) has no such effects. Additionally, the localization effects increase with educational levels of employees and the share of intermediate inputs in gross output. These results may suggest that agglomeration externalities occur through knowledge spillovers and input sharing among firms producing similar manufactures.

Forward Stagewise Naive Bayes

The naïve Bayes approach is a simple but often satisfactory method for supervised classification. In this paper, we focus on the naïve Bayes model and propose the application of regularization techniques to learn a naïve Bayes classifier. The main contribution of the paper is a stagewise version of the selective naïve Bayes, which can be considered a regularized version of the naïve Bayes model. We call it forward stagewise naïve Bayes. For comparison’s sake, we also introduce an explicitly regularized formulation of the naïve Bayes model, where conditional independence (absence of arcs) is promoted via an L 1/L 2-group penalty on the parameters that define the conditional probability distributions. Although already published in the literature, this idea has only been applied for continuous predictors. We extend this formulation to discrete predictors and propose a modification that yields an adaptive penalization. We show that, whereas the L 1/L 2 group penalty formulation only discards irrelevant predictors, the forward stagewise naïve Bayes can discard both irrelevant and redundant predictors, which are known to be harmful for the naïve Bayes classifier. Both approaches, however, usually improve the classical naïve Bayes model’s accuracy.

TRHIOS: Trust and reputation in hierarchical and quality-oriented societies

In this paper we present TRHIOS: a Trust and Reputation system for HIerarchical and quality-Oriented Societies. We focus our work on hierarchical medical organizations. The model estimates the reputation of an individual, RTRHIOS, taking into account information from three trust dimensions: the hierarchy of the system; the source of information; and the quality of the results. Besides the concrete reputation value, it is important to know how reliable that value is; for each of the three dimensions we calculate the reliability of the assessed reputations; and aggregating them, the reliability of the reputation of an individual. The modular approach followed in the definition of the different types of reputations provides the system with a high flexibility that allows adapting the model to the peculiarities of each society.

A hierarchical strategy for real-time tracking on-board UAVs

In this paper, we present a real-time tracking strategy based on direct methods for tracking tasks on-board UAVs, that is able to overcome problems posed by the challenging conditions of the task: e.g. constant vibrations, fast 3D changes, and limited capacity on-board. The vast majority of approaches make use of feature-based methods to track objects. Nonetheless, in this paper we show that although some of these feature-based solutions are faster, direct methods can be more robust under fast 3D motions (fast changes in position), some changes in appearance, constant vibrations (without requiring any specific hardware or software for video stabilization), and situations where part of the object to track is out the field of view of the camera. The performance of the proposed strategy is evaluated with images from real-flight tests using different evaluation mechanisms (e.g. accurate position estimation using a Vicon sytem). Results show that our tracking strategy performs better than well known feature-based algorithms and well known configurations of direct methods, and that the recovered data is robust enough for vision-in-the-loop tasks.

Hierarchical boundary elements

In this paper we show the possibility of applying adaptive procedures as an alternative to the well-known philosophy of standard Boundary Elements. The three characteristic steps of adaptive procedures, i.e. hierarchical shape functions families, indicator criteria, and a posteriori estimation, can be defined in order to govern an automatic refinement and stopping of the solution process. A computer program to treat potential problems, called QUEIMADA, has been developed to show the capabilities of the new idea.

Linear Bayes policy for learning in contextual-bandits

Machine and Statistical Learning techniques are used in almost all online advertisement systems. The problem of discovering which content is more demanded (e.g. receive more clicks) can be modeled as a multi-armed bandit problem. Contextual bandits (i.e., bandits with covariates, side information or associative reinforcement learning) associate, to each specific content, several features that define the “context” in which it appears (e.g. user, web page, time, region). This problem can be studied in the stochastic/statistical setting by means of the conditional probability paradigm using the Bayes’ theorem. However, for very large contextual information and/or real-time constraints, the exact calculation of the Bayes’ rule is computationally infeasible. In this article, we present a method that is able to handle large contextual information for learning in contextual-bandits problems. This method was tested in the Challenge on Yahoo! dataset at ICML2012’s Workshop “new Challenges for Exploration & Exploitation 3”, obtaining the second place. Its basic exploration policy is deterministic in the sense that for the same input data (as a time-series) the same results are obtained. We address the deterministic exploration vs. exploitation issue, explaining the way in which the proposed method deterministically finds an effective dynamic trade-off based solely in the input-data, in contrast to other methods that use a random number generator.

Polypropylene/glass fiber hierarchical composites incorporating inorganic fullerene-like nanoparticles for advanced technological applications

Novel isotactic polypropylene (iPP)/glass fiber (GF) laminates reinforced with inorganic fullerene-like tungsten disulfide (IF-WS2) nanoparticles as environmentally friendly fillers have been successfully fabricated by simple melt-blending and fiber impregnation in a hot-press without the addition of any compatibilizer. The influence of IF-WS2 concentration on the morphology, viscosity. and thermal and mechanical behavior of the hierarchical composites has been investigated. Results revealed an unprecedented 62 °C increase in the degradation temperature of iPP/GF upon addition of only 4.0 wt % IF-WS2. The coexistence of both micro- and nanoscale fillers resulted in synergistic effects on enhancing the stiffness, strength, crystallinity, thermal stability, glass transition (Tg) and heat distortion temperature (HDT) of the matrix. The approach used in this work is an efficient, versatile, scalable and economic strategy to improve the mechanical and thermal behavior of GF-reinforced thermoplastics with a view to extend their use in advanced technological applications. This new type of composite materials shows great potential to improve the efficiency and sustainability of many forms of transport.

A Hierarchical Tracking Strategy for Vision-Based Applications On-Board UAVs

In this paper, we apply a hierarchical tracking strategy of planar objects (or that can be assumed to be planar) that is based on direct methods for vision-based applications on-board UAVs. The use of this tracking strategy allows to achieve the tasks at real-time frame rates and to overcome problems posed by the challenging conditions of the tasks: e.g. constant vibrations, fast 3D changes, or limited capacity on-board. The vast majority of approaches make use of feature-based methods to track objects. Nonetheless, in this paper we show that although some of these feature-based solutions are faster, direct methods can be more robust under fast 3D motions (fast changes in position), some changes in appearance, constant vibrations (without requiring any specific hardware or software for video stabilization), and situations in which part of the object to track is outside of the field of view of the camera. The performance of the proposed tracking strategy on-board UAVs is evaluated with images from realflight tests using manually-generated ground truth information, accurate position estimation using a Vicon system, and also with simulated data from a simulation environment. Results show that the hierarchical tracking strategy performs better than wellknown feature-based algorithms and well-known configurations of direct methods, and that its performance is robust enough for vision-in-the-loop tasks, e.g. for vision-based landing tasks.

Adapting mode switches into the hierarchical scheduling

Mode switches are used to partition the system’s behavior into different modes to reduce the complexity of large embedded systems. Such systems operate in multiple modes in which each one corresponds to a specific application scenario; these are called Multi-Mode Systems (MMS). A different piece of software is normally executed for each mode. At any given time, the system can be in one of the predefined modes and then be switched to another as a result of a certain condition. A mode switch mechanism (or mode change protocol) is used to shift the system from one mode to another at run-time. In this thesis we have used a hierarchical scheduling framework to implement a multi-mode system called Multi-Mode Hierarchical Scheduling Framework (MMHSF). A two-level Hierarchical Scheduling Framework (HSF) has already been implemented in an open source real-time operating system, FreeRTOS, to support temporal isolation among real-time components. The main contribution of this thesis is the extension of the HSF featuring a multimode feature with an emphasis on making minimal changes in the underlying operating system (FreeRTOS) and its HSF implementation. Our implementation uses fixed-priority preemptive scheduling at both local and global scheduling levels and idling periodic servers. It also now supports different modes of the system which can be switched at run-time. Each subsystem and task exhibit different timing attributes according to mode, and upon a Mode Change Request (MCR) the task-set and timing interfaces of the entire system (including subsystems and tasks) undergo a change. A Mode Change Protocol specifies precisely how the system-mode will be changed. However, an application may not only need to change a mode but also a different mode change protocol semantic. For example, the mode change from normal to shutdown can allow all the tasks to be completed before the mode itself is changed, while changing a mode from normal to emergency may require aborting all tasks instantly. In our work, both the system mode and the mode change protocol can be changed at run-time. We have implemented three different mode change protocols to switch from one mode to another: the Suspend/resume protocol, the Abort protocol, and the Complete protocol. These protocols increase the flexibility of the system, allowing users to select the way they want to switch to a new mode. The implementation of MMHSF is tested and evaluated on an AVR-based 32 bit board EVK1100 with an AVR32UC3A0512 micro-controller. We have tested the behavior of each system mode and for each mode change protocol. We also provide the results for the performance measures of all mode change protocols in the thesis. RESUMEN Los conmutadores de modo son usados para particionar el comportamiento del sistema en diferentes modos, reduciendo así la complejidad de grandes sistemas empotrados. Estos sistemas tienen multiples modos de operación, cada uno de ellos correspondiente a distintos escenarios y para distintas aplicaciones; son llamados Sistemas Multimodales (o en inglés “Multi-Mode Systems” o MMS). Normalmente cada modo ejecuta una parte de código distinto. En un momento dado el sistema, que está en un modo concreto, puede ser cambiado a otro modo distinto como resultado de alguna condicion impuesta previamente. Los mecanismos de cambio de modo (o protocolos de cambio de modo) son usados para mover el sistema de un modo a otro durante el tiempo de ejecución. En este trabajo se ha usado un modelo de sistema operativo para implementar un sistema multimodo llamado MMHSF, siglas en inglés correspondientes a (Multi-Mode Hierarchical Scheduling Framework). Este sistema está basado en el HSF (Hierarchical Scheduling Framework), un modelo de sistema operativo con jerarquía de dos niveles, implementado en un sistema operativo en tiempo real de libre distribución llamado FreeRTOS, capaz de permitir el aislamiento temporal entre componentes. La principal contribución de este trabajo es la ampliación del HSF convirtiendolo en un sistema multimodo realizando los cambios mínimos necesarios sobre el sistema operativo FreeRTOS y la implementación ya existente del HSF. Esta implementación usa un sistema de planificación de prioridad fija para ambos niveles de jerarquía, ocupando el tiempo entre tareas con un “modo reposo”. Además el sistema es capaz de cambiar de un modo a otro en tiempo de ejecución. Cada subsistema y tarea son capaces de tener distintos atributos de tiempo (prioridad, periodo y tiempo de ejecución) en función del modo. Bajo una demanda de cambio de modo (Mode Change Request MCR) se puede variar el set de tareas en ejecución, así como los atributos de los servidores y las tareas. Un protocolo de cambio de modo espeficica precisamente cómo será cambiado el sistema de un modo a otro. Sin embargo una aplicación puede requerir no solo un cambio de modo, sino que lo haga de una forma especifica. Por ejemplo, el cambio de modo de “normal” a “apagado” puede permitir a las tareas en ejecución ser finalizadas antes de que se complete la transición, pero sin embargo el cambio de “normal” a “emergencia” puede requerir abortar todas las tareas instantaneamente. En este trabajo ambas características, tanto el modo como el protocolo de cambio, pueden ser cambiadas en tiempo de ejecución, pero deben ser previamente definidas por el desarrollador. Han sido definidos tres protocolos de cambios: el protocolo “suspender/continuar”, protocolo “abortar” y el protocolo “completar”. Estos protocolos incrementan la flexibilidad del sistema, permitiendo al usuario seleccionar de que forma quieren cambiar hacia el nuevo modo. La implementación del MMHSF ha sido testada y evaluada en una placa AVR EVK1100, con un micro-controlador AVR32UC3A0. Se ha comprobado el comportamiento de los distintos modos para los distintos protocolos, definidos previamente. Como resultado se proporcionan las medidades de rendimiento de los distintos protocolos de cambio de modo.

Hierarchical graph maps for visualization of collaborative recommender systems

In this paper we provide a method that allows the visualization of similarity relationships present between items of collaborative filtering recommender systems, as well as the relative importance of each of these. The objective is to offer visual representations of the recommender system?s set of items and of their relationships; these graphs show us where the most representative information can be found and which items are rated in a more similar way by the recommender system?s community of users. The visual representations achieved take the shape of phylogenetic trees, displaying the numerical similarity and the reliability between each pair of items considered to be similar. As a case study we provide the results obtained using the public database Movielens 1M, which contains 3900 movies.