Realistic mean field forward predictions for the integration of co-registered EEG/fMRI

Brain activity can be measured non-invasively with functional imaging techniques. Each pixel in such an image represents a neural mass of about 105 to 107 neurons. Mean field models (MFMs) approximate their activity by averaging out neural variability while retaining salient underlying features, like neurotransmitter kinetics. However, MFMs incorporating the regional variability, realistic geometry and connectivity of cortex have so far appeared intractable. This lack of biological realism has led to a focus on gross temporal features of the EEG. We address these impediments and showcase a "proof of principle" forward prediction of co-registered EEG/fMRI for a full-size human cortex in a realistic head model with anatomical connectivity, see figure 1. MFMs usually assume homogeneous neural masses, isotropic long-range connectivity and simplistic signal expression to allow rapid computation with partial differential equations. But these approximations are insufficient in particular for the high spatial resolution obtained with fMRI, since different cortical areas vary in their architectonic and dynamical properties, have complex connectivity, and can contribute non-trivially to the measured signal. Our code instead supports the local variation of model parameters and freely chosen connectivity for many thousand triangulation nodes spanning a cortical surface extracted from structural MRI. This allows the introduction of realistic anatomical and physiological parameters for cortical areas and their connectivity, including both intra- and inter-area connections. Proper cortical folding and conduction through a realistic head model is then added to obtain accurate signal expression for a comparison to experimental data. To showcase the synergy of these computational developments, we predict simultaneously EEG and fMRI BOLD responses by adding an established model for neurovascular coupling and convolving "Balloon-Windkessel" hemodynamics. We also incorporate regional connectivity extracted from the CoCoMac database [1]. Importantly, these extensions can be easily adapted according to future insights and data. Furthermore, while our own simulation is based on one specific MFM [2], the computational framework is general and can be applied to models favored by the user. Finally, we provide a brief outlook on improving the integration of multi-modal imaging data through iterative fits of a single underlying MFM in this realistic simulation framework.

An ontology-based approach for data integration in regionally interoperable healthcare systems

In order to best utilize the limited resource of medical resources, and to reduce the cost and improve the quality of medical treatment, we propose to build an interoperable regional healthcare systems among several levels of medical treatment organizations. In this paper, our approaches are as follows:(1) the ontology based approach is introduced as the methodology and technological solution for information integration; (2) the integration framework of data sharing among different organizations are proposed(3)the virtual database to realize data integration of hospital information system is established. Our methods realize the effective management and integration of the medical workflow and the mass information in the interoperable regional healthcare system. Furthermore, this research provides the interoperable regional healthcare system with characteristic of modularization, expansibility and the stability of the system is enhanced by hierarchy structure.

TRY: a global database of plant traits

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Coupling ensemble weather predictions based on TIGGE database with Grid-Xinanjiang model for flood forecast

The incorporation of numerical weather predictions (NWP) into a flood forecasting system can increase forecast lead times from a few hours to a few days. A single NWP forecast from a single forecast centre, however, is insufficient as it involves considerable non-predictable uncertainties and lead to a high number of false alarms. The availability of global ensemble numerical weather prediction systems through the THORPEX Interactive Grand Global Ensemble' (TIGGE) offers a new opportunity for flood forecast. The Grid-Xinanjiang distributed hydrological model, which is based on the Xinanjiang model theory and the topographical information of each grid cell extracted from the Digital Elevation Model (DEM), is coupled with ensemble weather predictions based on the TIGGE database (CMC, CMA, ECWMF, UKMO, NCEP) for flood forecast. This paper presents a case study using the coupled flood forecasting model on the Xixian catchment (a drainage area of 8826 km2) located in Henan province, China. A probabilistic discharge is provided as the end product of flood forecast. Results show that the association of the Grid-Xinanjiang model and the TIGGE database gives a promising tool for an early warning of flood events several days ahead.

Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort

Background Major Depressive Disorder (MDD) is among the most prevalent and disabling medical conditions worldwide. Identification of clinical and biological markers (“biomarkers”) of treatment response could personalize clinical decisions and lead to better outcomes. This paper describes the aims, design, and methods of a discovery study of biomarkers in antidepressant treatment response, conducted by the Canadian Biomarker Integration Network in Depression (CAN-BIND). The CAN-BIND research program investigates and identifies biomarkers that help to predict outcomes in patients with MDD treated with antidepressant medication. The primary objective of this initial study (known as CAN-BIND-1) is to identify individual and integrated neuroimaging, electrophysiological, molecular, and clinical predictors of response to sequential antidepressant monotherapy and adjunctive therapy in MDD. Methods CAN-BIND-1 is a multisite initiative involving 6 academic health centres working collaboratively with other universities and research centres. In the 16-week protocol, patients with MDD are treated with a first-line antidepressant (escitalopram 10–20 mg/d) that, if clinically warranted after eight weeks, is augmented with an evidence-based, add-on medication (aripiprazole 2–10 mg/d). Comprehensive datasets are obtained using clinical rating scales; behavioural, dimensional, and functioning/quality of life measures; neurocognitive testing; genomic, genetic, and proteomic profiling from blood samples; combined structural and functional magnetic resonance imaging; and electroencephalography. De-identified data from all sites are aggregated within a secure neuroinformatics platform for data integration, management, storage, and analyses. Statistical analyses will include multivariate and machine-learning techniques to identify predictors, moderators, and mediators of treatment response. Discussion From June 2013 to February 2015, a cohort of 134 participants (85 outpatients with MDD and 49 healthy participants) has been evaluated at baseline. The clinical characteristics of this cohort are similar to other studies of MDD. Recruitment at all sites is ongoing to a target sample of 290 participants. CAN-BIND will identify biomarkers of treatment response in MDD through extensive clinical, molecular, and imaging assessments, in order to improve treatment practice and clinical outcomes. It will also create an innovative, robust platform and database for future research.

Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

A Framework supporting collaboration on the distributed design of integrated systems

The work described in this thesis aims to support the distributed design of integrated systems and considers specifically the need for collaborative interaction among designers. Particular emphasis was given to issues which were only marginally considered in previous approaches, such as the abstraction of the distribution of design automation resources over the network, the possibility of both synchronous and asynchronous interaction among designers and the support for extensible design data models. Such issues demand a rather complex software infrastructure, as possible solutions must encompass a wide range of software modules: from user interfaces to middleware to databases. To build such structure, several engineering techniques were employed and some original solutions were devised. The core of the proposed solution is based in the joint application of two homonymic technologies: CAD Frameworks and object-oriented frameworks. The former concept was coined in the late 80's within the electronic design automation community and comprehends a layered software environment which aims to support CAD tool developers, CAD administrators/integrators and designers. The latter, developed during the last decade by the software engineering community, is a software architecture model to build extensible and reusable object-oriented software subsystems. In this work, we proposed to create an object-oriented framework which includes extensible sets of design data primitives and design tool building blocks. Such object-oriented framework is included within a CAD Framework, where it plays important roles on typical CAD Framework services such as design data representation and management, versioning, user interfaces, design management and tool integration. The implemented CAD Framework - named Cave2 - followed the classical layered architecture presented by Barnes, Harrison, Newton and Spickelmier, but the possibilities granted by the use of the object-oriented framework foundations allowed a series of improvements which were not available in previous approaches: - object-oriented frameworks are extensible by design, thus this should be also true regarding the implemented sets of design data primitives and design tool building blocks. This means that both the design representation model and the software modules dealing with it can be upgraded or adapted to a particular design methodology, and that such extensions and adaptations will still inherit the architectural and functional aspects implemented in the object-oriented framework foundation; - the design semantics and the design visualization are both part of the object-oriented framework, but in clearly separated models. This allows for different visualization strategies for a given design data set, which gives collaborating parties the flexibility to choose individual visualization settings; - the control of the consistency between semantics and visualization - a particularly important issue in a design environment with multiple views of a single design - is also included in the foundations of the object-oriented framework. Such mechanism is generic enough to be also used by further extensions of the design data model, as it is based on the inversion of control between view and semantics. The view receives the user input and propagates such event to the semantic model, which evaluates if a state change is possible. If positive, it triggers the change of state of both semantics and view. Our approach took advantage of such inversion of control and included an layer between semantics and view to take into account the possibility of multi-view consistency; - to optimize the consistency control mechanism between views and semantics, we propose an event-based approach that captures each discrete interaction of a designer with his/her respective design views. The information about each interaction is encapsulated inside an event object, which may be propagated to the design semantics - and thus to other possible views - according to the consistency policy which is being used. Furthermore, the use of event pools allows for a late synchronization between view and semantics in case of unavailability of a network connection between them; - the use of proxy objects raised significantly the abstraction of the integration of design automation resources, as either remote or local tools and services are accessed through method calls in a local object. The connection to remote tools and services using a look-up protocol also abstracted completely the network location of such resources, allowing for resource addition and removal during runtime; - the implemented CAD Framework is completely based on Java technology, so it relies on the Java Virtual Machine as the layer which grants the independence between the CAD Framework and the operating system. All such improvements contributed to a higher abstraction on the distribution of design automation resources and also introduced a new paradigm for the remote interaction between designers. The resulting CAD Framework is able to support fine-grained collaboration based on events, so every single design update performed by a designer can be propagated to the rest of the design team regardless of their location in the distributed environment. This can increase the group awareness and allow a richer transfer of experiences among them, improving significantly the collaboration potential when compared to previously proposed file-based or record-based approaches. Three different case studies were conducted to validate the proposed approach, each one focusing one a subset of the contributions of this thesis. The first one uses the proxy-based resource distribution architecture to implement a prototyping platform using reconfigurable hardware modules. The second one extends the foundations of the implemented object-oriented framework to support interface-based design. Such extensions - design representation primitives and tool blocks - are used to implement a design entry tool named IBlaDe, which allows the collaborative creation of functional and structural models of integrated systems. The third case study regards the possibility of integration of multimedia metadata to the design data model. Such possibility is explored in the frame of an online educational and training platform.

Using Neo4J geospatial data storage and integration

Online geographic-databases have been growing increasingly as they have become a crucial source of information for both social networks and safety-critical systems. Since the quality of such applications is largely related to the richness and completeness of their data, it becomes imperative to develop adaptable and persistent storage systems, able to make use of several sources of information as well as enabling the fastest possible response from them. This work will create a shared and extensible geographic model, able to retrieve and store information from the major spatial sources available. A geographic-based system also has very high requirements in terms of scalability, computational power and domain complexity, causing several difficulties for a traditional relational database as the number of results increases. NoSQL systems provide valuable advantages for this scenario, in particular graph databases which are capable of modeling vast amounts of inter-connected data while providing a very substantial increase of performance for several spatial requests, such as finding shortestpath routes and performing relationship lookups with high concurrency. In this work, we will analyze the current state of geographic information systems and develop a unified geographic model, named GeoPlace Explorer (GE). GE is able to import and store spatial data from several online sources at a symbolic level in both a relational and a graph databases, where several stress tests were performed in order to find the advantages and disadvantages of each database paradigm.

Multi-objective evolutionary particle swarm optimization in the assessment of the impact of distributed generation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evolutionary dynamics of rRNA gene clusters in cichlid fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Perceptual Information Integration: Hypothetical Role of Astrocytes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Astrocytes and human cognition: Modeling information integration and modulation of neuronal activity

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Contribution of distributed generators to the harmonic distortion in low voltage power network

In the last 20 years immense efforts have been made to utilize renewable energy sources for electric power generation. This paper investigates some aspects of integration of the distributed generators into the low voltage distribution network. An assessment of impact of the distributed generators on the voltage and current harmonic distortion in the low voltage network is performed. Results obtained from a case study, using real-life low voltage network, are presented and discussed.

A multi-objective evaluation of the impact of the penetration of Distributed Generation

This paper proposes a methodology to consider the effects of the integration of DG on planning. Since DG has potential to defer investments in networks, the impact of DG on grid capacity is evaluated. A multi-objective optimization tool based on the meta-heuristic MEPSO is used, supporting an alternative approach to exploiting the Pareto front features. Tests were performed in distinct conditions with two well-known distribution networks: IEEE-34 and IEEE-123. The results combined minimization and maximization in order to produce different Pareto fronts and determine the extent of the impact caused by DG. The analysis provides useful information, such as the identification of futures that should be considered in planning. A future means a set of realizations of all uncertainties. MEPSO also presented a satisfactory performance in obtaining the Pareto fronts. © 2011 IEEE.

A logical approach to the management of object identifiers in non-conventional database management systems

Non-conventional database management systems are used to achieve a better performance when dealing with complex data. One fundamental concept of these systems is object identity (OID), because each object in the database has a unique identifier that is used to access and reference it in relationships to other objects. Two approaches can be used for the implementation of OIDs: physical or logical OIDs. In order to manage complex data, was proposed the Multimedia Data Manager Kernel (NuGeM) that uses a logical technique, named Indirect Mapping. This paper proposes an improvement to the technique used by NuGeM, whose original contribution is management of OIDs with a fewer number of disc accesses and less processing, thus reducing management time from the pages and eliminating the problem with exhaustion of OIDs. Also, the technique presented here can be applied to others OODBMSs. © 2011 IEEE.