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patricia ruiz

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See detailEmbracing Monogenic Parkinson's Disease: The MJFF Global Genetic PD Cohort
Vollstedt, Eva-Juliane; Schaake, Susen; Lohmann, Katja et al

in Movement Disorders (2023), 38(2), 286--303

BACKGROUND: As gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a ... [more ▼]

BACKGROUND: As gene-targeted therapies are increasingly being developed for Parkinson's disease (PD), identifying and characterizing carriers of specific genetic pathogenic variants is imperative. Only a small fraction of the estimated number of subjects with monogenic PD worldwide are currently represented in the literature and availability of clinical data and clinical trial-ready cohorts is limited. OBJECTIVE: The objectives are to (1) establish an international cohort of affected and unaffected individuals with PD-linked variants; (2) provide harmonized and quality-controlled clinical characterization data for each included individual; and (3) further promote collaboration of researchers in the field of monogenic PD. METHODS: We conducted a worldwide, systematic online survey to collect individual-level data on individuals with PD-linked variants in SNCA, LRRK2 VPS35, PRKN, PINK1, DJ-1, as well as selected pathogenic and risk variants in GBA and corresponding demographic, clinical, and genetic data. All registered cases underwent thorough quality checks, and pathogenicity scoring of the variants and genotype-phenotype relationships were analyzed. RESULTS: We collected 3888 variant carriers for our analyses, reported by 92 centers (42 countries) worldwide. Of the included individuals 3185 had a diagnosis of PD (ie, 1306 LRRK2, 115 SNCA, 23 VPS35 429 PRKN, 75 PINK1, 13 DJ-1, and 1224 GBA) and 703 were unaffected (ie, 328 LRRK2, 32 SNCA, 3 VPS35, 1 PRKN, 1 PINK1, and 338 GBA). In total, we identified 269 different pathogenic variants; 1322 individuals in our cohort (34\%) were indicated as not previously published. CONCLUSIONS: Within the MJFF Global Genetic PD Study Group, we (1) established the largest international cohort of affected and unaffected individuals carrying PD-linked variants; (2) provide harmonized and quality-controlled clinical and genetic data for each included individual; (3) promote collaboration in the field of genetic PD with a view toward clinical and genetic stratification of patients for gene-targeted clinical trials. 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. [less ▲]

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See detailSurvey on Broadcast Algorithms for Mobile Ad Hoc Networks
Ruiz, Patricia UL; Bouvry, Pascal UL

in ACM Computing Surveys (2015), 48(1),

Networking at any time and any place paves the way for a large number of possible applications in ad hoc networks, from disaster relief in remote areas to network extension. Thus, for the past decades ... [more ▼]

Networking at any time and any place paves the way for a large number of possible applications in ad hoc networks, from disaster relief in remote areas to network extension. Thus, for the past decades, many works have been proposed trying to make ad hoc networks a reality. The importance of broadcasting in networking and the broadcast nature of the wireless medium have encouraged researchers to join their efforts on designing efficient dissemination algorithms for Mobile Ad Hoc Networks (MANETs). The many different challenges that MANETs face, such as limited network resources, network partitions, or energy restrictions, gave rise to many different approaches to overcome one or more of those problems. Therefore, literature reveals a huge variety of techniques that have been proposed for efficient message dissemination. In this article, we make an in-depth review of the existing state-of-the-art techniques, as well as propose a new taxonomy that provides a global overview of the most relevant existing algorithms. [less ▲]

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See detailFinding a robust configuration for the AEDB information dissemination protocol for mobile ad hoc networks
Ruiz, Patricia; Dorronsoro, Bernabé UL; Talbi, El-Ghazali et al

in Applied Soft Computing (2015), 32

The Adaptive Enhanced Distance Based Broadcasting Protocol, AEDB hereinafter, is an advanced adaptive protocol for information dissemination in mobile ad hoc networks (MANETs). It is based on the Distance ... [more ▼]

The Adaptive Enhanced Distance Based Broadcasting Protocol, AEDB hereinafter, is an advanced adaptive protocol for information dissemination in mobile ad hoc networks (MANETs). It is based on the Distance Based broadcasting protocol, and it acts differently according to local information to minimize the energy and network use, while maximizing the coverage of the broadcasting process. As most of the existing communication protocols, AEDB relies on different thresholds for adapting its behavior to the environment. We propose in this work to look for configurations that induce a stable performance of the protocol in different networks by automatically fine tuning these thresholds thanks to the use of cooperative coevolutionary multi-objective evolutionary algorithms. Finding robust solutions for this problem is important because MANETs have a highly unpredictable and dynamic topology, features that have a strong influence on the performance of the protocol. Consequently, robust solutions that show a good performance under any circumstances are required. In this work, we define different fitness functions that measure robustness of solutions for better guiding the algorithm towards more robust solutions. They are: median, constrained, worst coverage, and worst hypervolume. Results show, that the two worst-case approaches perform better, not only in case of robustness but also in terms of accuracy of the reported AEDB configurations on a large set of networks. [less ▲]

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See detailOptimizing AEDB Broadcasting Protocol with Parallel Multi-objective Cooperative Coevolutionary NSGAII
Dorronsoro, Bernabé UL; Ruiz, Patricia UL; Talbi, El-Ghazali et al

in Optimizing AEDB Broadcasting Protocol with Parallel Multi-objective Cooperative Coevolutionary NSGAII (2014)

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See detailEvolutionary Algorithms for Mobile Ad Hoc Networks
Dorronsoro, Bernabé UL; Ruiz, Patricia UL; Danoy, Grégoire UL et al

Book published by John Wiley & Sons (2014)

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See detailEfficient Communication Protocols for ad hoc Networks
Ruiz Villalobos, Gracia Patricia UL

Doctoral thesis (2013)

Mobile ad hoc networks, also called MANETs, are self-organised networks spontaneously created between neighbouring devices that do not need any infrastructure. The possibility of deploying a communication ... [more ▼]

Mobile ad hoc networks, also called MANETs, are self-organised networks spontaneously created between neighbouring devices that do not need any infrastructure. The possibility of deploying a communication network at any moment and at any place opens a wide range of potential scenarios where the use of an ad hoc network is extremely important and useful. For example, we can imagine an area with no infrastructure, due to a natural disaster (flooding, earthquake, etc.), a war damage or simply a remote location. In such situations, the deployment of an ad hoc network for rescuing or evacuating people is key. %Allowing the communication between groups located in distant areas may be very helpful in critical situations in order to coordinate and reorganise them. However, ad hoc networks are not restricted to safety of disaster situations, they can also be used for gathering sensed data and send it to a remote server, exchanging safety road messages between vehicles or simply for infotainment, etc. Efficient communication protocols are very important for providing good services, but in ad hoc networks is very challenging. It is necessary to deal with packet loss, collisions, mobility, network partitions, fading, energy constraints, obstacles, etc. Due to the intrinsic broadcast nature of wireless medium, dissemination algorithms are one of the most appropriate protocols for communicating devices. Additionally, broadcasting is one of the main low level operation as many applications and even other protocols rely on its service. Therefore, in this thesis, we are proposing two different broadcasting algorithms for efficiently disseminate messages in the network. The first approach relays on an underlying tree topology, while the second is an energy aware algorithm that tries to reduce the energy consumption. In these unpredictable and changeable networks, protocols need to adapt to the current circumstances and this adaptability is usually obtained using thresholds. The values of these thresholds directly influence the behaviour of the algorithm. Finding them is a complex and critical task as protocols are usually very sensitive. We tackle this problem using approximation algorithms or metaheuristics, more specifically, we use a parallel iterative local search and two evolutionary algorithms. In order to ease this process, we have created a modular experimental framework for evaluating, validating and optimising any algorithm in MANETs. [less ▲]

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See detailA Parallel Multi-objective Local Search for AEDB Protocol Tuning
Iturriaga, Santiago; Ruiz, Patricia UL; Nesmachnow, Sergio et al

in IEEE International Parallel and Distributed Processing Simposium (2013)

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See detailOn the Improvement of the Enhanced Distance Based Broadcasting Algorithm
Ruiz, Patricia UL; Bouvry, Pascal UL

in International Journal of Communication Networks and Distributed Systems (2012), 9(3/4), 225-246

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See detailFinding Scalable Configurations for AEDB Broadcasting Protocol using Multi-objective Evolutionary
Ruiz, Patricia UL; Dorronsoro, Bernabe; Bouvry, Pascal UL

in Cluster Computing (2012), 16

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See detailInformation Dissemination in VANETs based upon a Tree Topology
Ruiz, Patricia UL; Dorronsoro, Bernabé UL; Bouvry, Pascal UL et al

in Ad Hoc Networks (2012), 10(1), 111-127

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See detailOptimisation of the enhanced distance based broadcasting protocol for MANETs
Ruiz, Patricia UL; Dorronsoro, Bernabé UL; Valentini, Giorgio et al

in Journal of Supercomputing (2012), 62(3), 1213-1240

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See detailGuidelines for the use and interpretation of assays for monitoring autophagy.
Klionsky, Daniel J.; Abdalla, Fabio C.; Abeliovich, Hagai et al

in Autophagy (2012), 8(4), 445-544

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field ... [more ▼]

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field. [less ▲]

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See detailOptimization and Performance Analysis of the AEDB Broadcasting Algorithm
Ruiz, Patricia UL; Dorronsoro, Bernabé UL; Bouvry, Pascal UL

in IEEE International Workshop on Wireless Mesh and Ad Hoc Networks (2011)

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See detailDistributed Energy Self-Adaptation in ad hoc Networks
Ruiz, Patricia UL; Bouvry, Pascal UL

in IEEE Globecom (2010)

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See detailTowards Connectivity Improvement in VANETs using Bypass Links
Dorronsoro, Bernabé UL; Ruiz, Patricia UL; Danoy, Grégoire UL et al

in Abstract book of 2009 IEEE Congress on Evolutionary Computation (2009)

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See detailUso de Redes Hibridas para la Mejora de la Conectividad en VANETs
Dorronsoro, Bernabé UL; Ruiz, Patricia UL; Danoy, Grégoire UL et al

in Proceedings of national Conference on Metaheuristicas, Algoritmos Evolutivos y Bioinspirados(MAEB'09) (2009)

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See detailToken Traversal Strategies of a Distributed Spanning Forest Algorithm in Mobile Ad hoc - Delay Tolerant Networks
Piyatumrong, Apivadee UL; Ruiz, Patricia UL; Bouvry, Pascal UL et al

in IAIT (2009)

This paper presents three distributed and decentralized strategies used for token traversal in spanning forest over Mobile Ad Hoc Delay Tolerant Networks. Such networks are characterized by behaviors like ... [more ▼]

This paper presents three distributed and decentralized strategies used for token traversal in spanning forest over Mobile Ad Hoc Delay Tolerant Networks. Such networks are characterized by behaviors like disappearance of mobile devices, connection disruptions, network partitioning, etc. Techniques based on tree topologies are well known for increasing the efficiency of network protocols and/or applications, such as Dynamicity Aware - Graph Relabeling System (DA-GRS). One of the main features of these tree based topologies is the existence of a token traversing in every tree. The use of tokens enables the creation and maintenance of spanning trees in dynamic environments. Subsequently, managing tree-based backbones relies heavily on the token behavior. An efficient and optimal token traversal can highly impact the design of the tree and its usage. In this article, we present a comparison of three distributed and decentralized techniques available for token management, which are Randomness, TABU and Depth First Search. [less ▲]

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See detailImproving Inter-cluster Broadcasting in Ad Hoc Networks by Delayed Flooding
Andronache, Adrian UL; Ruiz, Patricia UL; Rothkugel, Steffen UL

in Modelling, Computation and Optimization in Information Systems and Management Sciences, Second International Conference (MCO 2008) (2008)

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See detailBODYF - A Parameterless Broadcasting Protocol over Dynamic Forests
Ruiz, Patricia UL; Khadraoui, Djamel; Andronache, Adrian UL et al

in special session on Parallel and Grid Computing for Optimization as part of The 2008 International Conference High Performance Computing & Simulation (HPCS'08) and in conjunction with The 22nd European Conference on Modeling and Simulation (ECMS 2008) (2008)

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