Showing papers by "Ensenada Center for Scientific Research and Higher Education published in 2019"
University of Georgia1, University of California, San Diego2, Cornell University3, Auburn University4, University of Tennessee5, Columbia University6, Spanish National Research Council7, Ensenada Center for Scientific Research and Higher Education8, University of Wisconsin-Madison9, Marshfield Clinic10, University of Alaska Fairbanks11, Louisiana State University12
TL;DR: The approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples, and reduces buy-in costs because relatively few oligonucleotides are needed to produce a large number of indexed libraries.
Abstract: Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in (i.e., getting the smallest possible amount of data from a run); and (3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: (1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and (2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
199 citations
Marine Biological Association of the United Kingdom1, Woods Hole Oceanographic Institution2, University of California, Davis3, University of Concepción4, Duke University5, University of Mississippi6, Gordon and Betty Moore Foundation7, Yokohama National University8, National Museum of Natural History9, University of Colorado Boulder10, National Institute of Oceanography, India11, Ensenada Center for Scientific Research and Higher Education12, University of California, Riverside13, University of North Carolina at Chapel Hill14, Acadia University15, Hebrew University of Jerusalem16, Marine Biological Laboratory17
TL;DR: The state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles are presented.
Abstract: Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.
166 citations
University of Georgia1, Health Science University2, University of California, San Diego3, Spanish National Research Council4, Ensenada Center for Scientific Research and Higher Education5, University of Wisconsin-Madison6, Marshfield Clinic7, University of Alaska Fairbanks8, Houston Museum of Natural Science9
TL;DR: This approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples, and reduces buy-in costs because relatively few oligonucleotides are needed to produce a large number of indexed libraries.
Abstract: Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing NGS for the first time); 2) buy-in (i.e., getting the smallest possible amount of data from a run); and 3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: 1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and 2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
109 citations
TL;DR: A configurable, reliable, and confidential distributed data storage scheme with the ability to process encrypted data and control results of computations, and introduces AR-RRNS method for error detection, correction, and controlling computational results.
87 citations
Centre national de la recherche scientifique1, Memorial University of Newfoundland2, University of California, San Diego3, Rutgers University4, University of Cyprus5, University of Washington6, University of Western Australia7, World Meteorological Organization8, Finnish Meteorological Institute9, Oceanic Platform of the Canary Islands10, Oregon State University11, Woods Hole Oceanographic Institution12, University of Bergen13, University of Perpignan14, British Antarctic Survey15, Jet Propulsion Laboratory16, United States Naval Research Laboratory17, Pierre-and-Marie-Curie University18, Bermuda Institute of Ocean Sciences19, Dalhousie University20, Texas A&M University21, University of Georgia22, National Oceanography Centre23, Hebrew University of Jerusalem24, National Oceanic and Atmospheric Administration25, Fisheries and Oceans Canada26, Massachusetts Institute of Technology27, Scottish Association for Marine Science28, Korean Ocean Research and Development Institute29, University of Tokyo30, National Taiwan University31, University of Victoria32, Council for Scientific and Industrial Research33, Institut de recherche pour le développement34, University of Puerto Rico at Mayagüez35, Superior National School of Advanced Techniques36, National Institute of Water and Atmospheric Research37, Marine Institute of Memorial University of Newfoundland38, Hobart Corporation39, Ensenada Center for Scientific Research and Higher Education40, Korea University41, NATO42, Royal Dutch Shell43, University of New South Wales44, Spanish National Research Council45, Commonwealth Scientific and Industrial Research Organisation46, University of Gothenburg47, California Institute of Technology48, University of British Columbia49, University of the Virgin Islands50
TL;DR: OceanGliders as mentioned in this paper is an active coordination and enhancement of global glider activity, which brings together marine scientists and engineers operating gliders around the world to observe the long-term physical, biogeochemical and biological ocean processes and phenomena that are relevant for societal applications.
Abstract: The OceanGliders program started in 2016 to support active coordination and enhancement of global glider activity. OceanGliders contributes to the international efforts of the Global Ocean Observation System (GOOS) for Climate, Ocean Health and Operational Services. It brings together marine scientists and engineers operating gliders around the world: (1) to observe the long-term physical, biogeochemical, and biological ocean processes and phenomena that are relevant for societal applications; and, (2) to contribute to the GOOS through real-time and delayed mode data dissemination. The OceanGliders program is distributed across national and regional observing systems and significantly contributes to integrated, multi-scale and multi-platform sampling strategies. OceanGliders shares best practices, requirements, and scientific knowledge needed for glider operations, data collection and analysis. It also monitors global glider activity and supports the dissemination of glider data through regional and global databases, in real-time and delayed modes, facilitating data access to the wider community. OceanGliders currently supports national, regional and global initiatives to maintian and expand the capabilities and application of gliders to meet key global challenges such as improved measurement of ocean boundary currents, water transformation and storm forecast.
83 citations
Ensenada Center for Scientific Research and Higher Education1, University of Southern California2, University of Western Australia3, University of Technology, Sydney4, James Hutton Institute5, Xiamen University6, Scripps Research Institute7, University of Las Palmas de Gran Canaria8, Edith Cowan University9, Spanish National Research Council10
TL;DR: It is shown that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a–based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism, suggesting that proteorodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean.
Abstract: All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to that of chlorophyll-a. We further show that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a–based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism. This suggests that proteorhodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean.
74 citations
TL;DR: This paper proposes an integral analysis framework related to comprehensive security analysis, cost and performance, and the algorithm and implementation for chaos-based image cryptosystems as an effective approach to improve security.
Abstract: Currently, chaos-based cryptosystems are being proposed in the literature to provide confidentiality for digital images, since the diffusion effect in the Advance Encryption Standard (AES) algorithm is weak. Security is the most important challenge to assess in cryptosystems according to the National Institute of Standard and Technology (NIST), then cost and performance, and finally algorithm and implementation. Recent chaos-based image encryption algorithms present basic security analysis, which could make them insecure for some applications. In this paper, we suggest an integral analysis framework related to comprehensive security analysis, cost and performance, and the algorithm and implementation for chaos-based image cryptosystems. The proposed guideline based on 20 analysis points can assist new cryptographic designers to present an integral analysis of new algorithms. Future comparisons of new schemes can be more consistent in terms of security and efficiency. In addition, we present aspects regarding digital chaos implementation, chaos validation, and key definition to improve the security of the overall cryptosystem. The suggested guideline does not guarantee security, and it does not intend to limit the liberty to implement new analysis. However, it provides for the first time in the literature a solid basis about integral analysis for chaos-based image cryptosystems as an effective approach to improve security.
73 citations
TL;DR: The strain TE3, identified as Bacillus subtilis TE3 and its antifungal metabolites are promising effective treatment to control the causal agent of the wheat spot blotch and resulted in a significant reduction of that disease.
57 citations
TL;DR: Experimental results showed that Ca-alginate-PEGMA/A.
54 citations
TL;DR: Light is shed on the role of Ngraph in the ORR, and the CNx buckypaper is demonstrated to be an efficient 3D electrode for electrocatalytic applications, demonstrating an attractive alternative for wastewater remediation through the on-site generation of H2O2.
Abstract: Herein, a series of N-doped carbon nanotube (CNx) samples were obtained by modifying the synthesis temperature. Consequently, the proportion of graphitic nitrogen (Ngraph) in the samples was systematically increased as a function of temperature. This allowed evaluation of the role of the CNx graphitic nitrogen in the oxygen reduction reaction (ORR). A correlation between the Ngraph content and the ORR onset potential was observed, which shifted to more positive potentials with an increase in kinetic current density (jk); this showed that Ngraph played a significant catalytic role in the ORR. The samples with high Ngraph content favored the two-electron pathway for the ORR not only in basic media (pH = 13) but also in neutral media (pH = 7), representing an attractive alternative for wastewater remediation through the on-site generation of H2O2. The energetic calculations showed that the formation of H2O2 must be favorable in the presence of graphitic nitrogen sites. Finally, the performance of the buckypaper arrangement was evaluated, and the CNx buckypaper showed a higher cathodic current peak as compared to CNx traditional ink dispersions. Overall, this study not only sheds light on the role of Ngraph in the ORR, but also demonstrates that CNx buckypaper is an efficient 3D electrode for electrocatalytic applications.
50 citations
TL;DR: A comprehensive security analysis from a cryptographic point of view is presented for hardware implementation such as key space analysis, key sensitivity, floating frequency, histograms, autocorrelation, correlation, entropy, and performance.
Abstract: This paper presents a pseudorandom number generator (PRNG) based on enhanced Henon map (EHM) and its implementation in software and hardware for chaos-based cryptosystems with high processing such as image or video encryption. The proposed EHM presents better statistical properties and higher key sensitivity in comparison with classic Henon map (CHM) by means of numerical tests such as bifurcation diagrams, largest Lyapunov exponent, Gottwald-Melbourne test, and histograms. The proposed 8-bit PRNG-EHM algorithm is implemented in MATLAB (software) and in FPGA technology (hardware) for experimental results. In hardware implementation, we use VHDL language and the Altera DE2-115 FPGA board with RS-232 serial port communication for data extraction, which are analyzed with MATLAB. In both software and hardware level, the proposed PRNG-EHM passes the randomness NIST 800-22 statistical tests. For first time in literature, a comprehensive security analysis from a cryptographic point of view is presented for hardware implementation such as key space analysis, key sensitivity, floating frequency, histograms, autocorrelation, correlation, entropy, and performance. Comparisons of proposed PRNG-EHM with recent similar schemes show main advantages in security capabilities for cryptographic applications. According with the results, the proposed scheme can be used in chaos-based cryptographic applications at software or hardware implementation.
TL;DR: It was found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001), highlighting the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.
Abstract: Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.
TL;DR: It is estimated that the cost of the environmental damages a dam can cause in the lower part of basin almost doubles the purported benefits of emission reductions from hydroelectric generation.
Abstract: We tested how sediment trapping by hydroelectric dams affects tropical estuaries by comparing two dammed and two undammed rivers on Mexico’s Pacific coast. We found that dams demonstrably affected the stability and productivity of the estuaries. The two rivers dammed for hydroelectricity had a rapid coastal recession (between 7.9 and 21.5 ha year−1) in what should otherwise be an accretional coastline. The economic consequences of this dam-induced coastal erosion include loss of habitat for fisheries, loss of coastal protection, release of carbon sequestered in coastal sediments, loss of biodiversity, and the decline of estuarine livelihoods. We estimate that the cost of the environmental damages a dam can cause in the lower part of basin almost doubles the purported benefits of emission reductions from hydroelectric generation.
TL;DR: A thermal evaluation of an absorber-partitioned air channel solar chimney (SC-AP) to determine its feasibility as a building ventilation system in a warm-humid weather is presented in this article.
TL;DR: In this paper, a transient numerical simulation of a solar chimney system (SC), considering convective and radiative gains/losses to the exterior environment, in the warmest day of Madrid, Spain is presented.
TL;DR: In this article, the authors present an overview of transient mathematical models for solar chimneys with/without a phase change material (PCM) in a double-channel solar chimney.
University of California, Irvine1, San Diego State University2, Agricultural Research Service3, Ensenada Center for Scientific Research and Higher Education4, University of Córdoba (Spain)5, Southern California Coastal Water Research Project6, United States Environmental Protection Agency7, Research Triangle Park8
TL;DR: The sediment budget of the Los Laureles Canyon watershed is quantified using the AnnAGNPS model and field measurements of channel geometry to identify priority locations for sediment control measures, and can be used to identify tradeoffs between sediment control and runoff production.
Abstract: Urbanization can increase sheet, rill, gully, and channel erosion. We quantified the sediment budget of the Los Laureles Canyon watershed (LLCW), which is a mixed rural-urbanizing catchment in Northwestern Mexico, using the AnnAGNPS model and field measurements of channel geometry. The model was calibrated with five years of observed runoff and sediment loads and used to evaluate sediment reduction under a mitigation scenario involving paving roads in hotspots of erosion. Calibrated runoff and sediment load had a mean-percent-bias of 28.4 and − 8.1, and root-mean-square errors of 85% and 41% of the mean, respectively. Suspended sediment concentration (SSC) collected at different locations during one storm-event correlated with modeled SSC at those locations, which suggests that the model represented spatial variation in sediment production. Simulated gully erosion represents 16%–37% of hillslope sediment production, and 50% of the hillslope sediment load is produced by only 23% of the watershed area. The model identifies priority locations for sediment control measures, and can be used to identify tradeoffs between sediment control and runoff production. Paving roads in priority areas would reduce total sediment yield by 30%, but may increase peak discharge moderately (1.6%–21%) at the outlet.
TL;DR: This article presents a new design of an ultra-wideband conformal antenna for Unmanned Aerial Vehicle (UAV) applications which is a low-profile structure which is very suitable to diminish aerial vehicle drag problem.
Abstract: This paper was supported by the Mexican Council for Science and Technology (CONACyT), under Grant no. 2016-01-1680.
TL;DR: Quantitatively, FarmerKeeper could successfully support children with autism when attending to neurofeedback training sessions by possibly improving their attention and reducing their anxiety, and qualitatively, it outperforms a commercial BCI video game used for neurofeedbacks.
Abstract: BCI video games are making brain training increasingly popular and available; yet scientific evidence to support its efficacy is lacking. Real-life descriptions of BCI video games deployments in concrete scenarios are urgently needed. In this paper, we report a use case of the development and pilot-testing of a BCI video game designed to support children with autism when attending to Neurofeedback training sessions, called FarmerKeeper. Caring for children with autism may impose new cognitive, motor, behavioral, and attention challenges that current solutions targeted for other populations may not address. The goal of the game is to maintain children’s attention above a threshold to control a runner who is seeking for lost farm animals. FarmerKeeper uses a consumer-grade BCI headset to read user’s attention. We evaluated FarmerKeeper’s usability and user experience through a 4-weeks deployment study with 12 children with autism. Our quantitative results show FarmerKeeper outperforms a commercial BCI video game used for neurofeedback training, and qualitatively, FarmerKeeper could successfully support children with autism when attending to neurofeedback training sessions by possibly improving their attention and reducing their anxiety. We close reflecting on our design aspects and discussing directions for future work.
TL;DR: In this article, the authors present the studies related to the numerical thermal modeling of both, conventional solar chimneys and solar chimney with phase change materials (PCM), focusing on two research areas: Computational Fluid Dynamics (CFD) and Global Energy Balance (GEB).
TL;DR: In this article, the Yucatan Channel and the Straits of Florida were studied for four years (September 2012 to August 2016) of simultaneous current observations across the Yuncatan Channel.
Abstract: Four years (September 2012 to August 2016) of simultaneous current observations across the Yucatan Channel (~21.5°N) and the Straits of Florida (~81°W) have permitted us to investigate the ...
TL;DR: A software tool has been developed for supporting visual network analysis in a user-friendly way; providing several functionalities such as peptide retrieval and filtering, network construction and visualization, interactive exploration, and exporting data options.
Abstract: Motivation Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized and often dirty with data entry errors. Therefore, there is a need for a unified view that enables a more comprehensive analysis of the information on this topic residing at different sites. Results After collecting web pages from a large variety of bioactive peptide databases, we organized the web content into an integrated graph database (starPepDB) that holds a total of 71 310 nodes and 348 505 relationships. In this graph structure, there are 45 120 nodes representing peptides, and the rest of the nodes are connected to peptides for describing metadata. Additionally, to facilitate a better understanding of the integrated data, a software tool (starPep toolbox) has been developed for supporting visual network analysis in a user-friendly way; providing several functionalities such as peptide retrieval and filtering, network construction and visualization, interactive exploration and exporting data options. Availability and implementation Both starPepDB and starPep toolbox are freely available at http://mobiosd-hub.com/starpep/. Supplementary information Supplementary data are available at Bioinformatics online.
TL;DR: In this paper, 2D-ordered plasmonic nanoarrays with different morphologies, as nanoprism, nanoparticle, nanohole and semi-nanoshell arrays, are realized by nanosphere lithography, combining metal depositions, reactive ion etching and thermal treatments.
TL;DR: An in silico pipeline to identify small-molecule inhibitors of the E6-E6AP interaction is proposed and the identified molecules represent a new starting point in the development of anti-HPV drugs.
Abstract: High-risk strains of human papillomavirus (HPV) have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. Although prophylactic HPV vaccines have been approved; it is still necessary a drug-based treatment against the infection and its oncogenic effects. The E6 oncoprotein is one of the most studied therapeutic targets of HPV, it has been identified as a key factor in cell immortalization and tumor progression in HPV-positive cells. E6 can promote the degradation of p53, a tumor suppressor protein, through the interaction with the cellular ubiquitin ligase E6AP. Therefore, preventing the formation of the E6-E6AP complex is one of the main strategies to inhibit the viability and proliferation of infected cells. Herein, we propose an in silico pipeline to identify small-molecule inhibitors of the E6-E6AP interaction. Virtual screening was carried out by predicting the ADME properties of the molecules and performing ensemble-based docking simulations to E6 protein followed by binding free energy estimation through MM/PB(GB)SA methods. Finally, the top-three compounds were selected, and their stability in the E6 docked complex and their effect in the inhibition of the E6-E6AP interaction was corroborated by molecular dynamics simulation. Therefore, this pipeline and the identified molecules represent a new starting point in the development of anti-HPV drugs.
TL;DR: The use of brain programming for automating the video tracking design process is described and a comparison with the method of regions with convolutional neural networks is provided to illustrate the benefit of the approach.
Abstract: This work describes the use of brain programming for automating the video tracking design process The challenge is that of creating visual programs that learn to detect a toy dinosaur from a database while tested in a visual-tracking scenario When planning an object tracking system, two sub-tasks need to be approached: detection of moving objects in each frame and correct association of detection to the same object over time Visual attention is a skill performed by the brain whose functionality is to perceive salient visual features The automatic design of visual attention programs through an optimization paradigm is applied to the detection-based tracking of objects in a video from a moving camera A system based on the acquisition and integration steps of the natural dorsal stream was engineered to emulate its selectivity and goal-driven behavior useful to the task of tracking objects This is considered a challenging problem since many difficulties can arise due to abrupt object motion, changing appearance patterns of both the object and the scene, nonrigid structures, object-to-object and object-to-scene occlusions, as well as camera motion, models, and parameters Tracking relies on the quality of the detection process and automatically designing such stage could significantly improve tracking methods Experimental results confirm the validity of our approach using three different kinds of robotic systems Moreover, a comparison with the method of regions with convolutional neural networks is provided to illustrate the benefit of the approach
TL;DR: This study sampled grapevine plants displaying red blotch symptoms in the major wine producing region of Mexico and sequenced the full-length viral genome of 2016 and 2017 representative isolates to gain a deeper insight into the phylogeny of local GRBV isolates.
Abstract: Grapevine red blotch virus (GRBV) (Al Rwahnih et al. 2013) is a member of the recently recognized genus Grablovirus in the family Geminiviridae (Varsani et al. 2017). GRBV is the causal agent of grapevine red blotch disease (Yepes et al. 2018), affecting viticulture in North America and some other regions around the world (reviewed in Sudarshana et al. [2015]). In this study, we sampled grapevine plants displaying red blotch symptoms in the major wine producing region of Mexico: Ensenada, Baja California, in 2016 and 2017. A total of 46 samples from cultivars Vitis vinifera L. ‘Pinot Noir’ and ‘Merlot’ were tested in 2016 by end-point polymerase chain reaction (PCR) using primers GRBV-V2F (5′-ATGGGTTAGGGGATGAGGCT-3′) and GRBV-V1R (5′-CGGCAATGACTCCTGCGGCT-3′). Results showed amplification of the expected 798-bp product from 31 samples. One of these amplicons was cloned, sequenced, and compared with reported sequences through a BLASTn search. The fragment had high nucleotide sequence identity (98%) with GRBV isolate BCRB5 from Canada (GenBank accession no. KX234092). The presence of GRBV was corroborated using the AmplifyRP Acceler8 kit (Agdia, Elkhart, IN), which detects the GRBV genome by isothermal recombinase polymerase amplification (RPA). In 2017 symptomatic V. vinifera ‘Nebbiolo’ plants were tested by multiplex PCR to amplify a region of the replicase-associated protein (Rep) gene with primers Repfor/Reprev (expected product 318 bp) and a fragment from the coat protein (CP) gene with primers CPfor/CPrev (expected product 257 bp) (Krenz et al. 2014). Amplicons from a positive sample were cleaned using a GenJet PCR purification kit (Thermo Fisher Scientific, Waltham, MA) and analyzed by Sanger sequencing. Both Rep and CP fragments shared >99% nucleotide sequence identity with GRBV isolates ONRB7 (KY316025) and ONRB4 (KY316022) from Canada (Poojari et al. 2017). To gain a deeper insight into the phylogeny of local GRBV isolates, we sequenced the full-length viral genome of 2016 and 2017 representative isolates. Each genome was amplified by high-fidelity PCR in two fragments, combining primers CPfor/Reprev (expected product 1.8 kb) and Repfor/CPrev (expected product 1.9 kb). After Sanger sequencing, the genomes were assembled in the GeneStudio sequence analysis software version 2.2.0.0 (GeneStudio, Suwanee, GA). A phylogenetic tree constructed after comparing the local isolates GRBV-Gpe-JGB (MH557096) and GRBV-Gpe-JCT (MH557095) to GRBV isolates from Canada and the United States grouped the Baja Californian isolates with clade 1 isolates. To our best knowledge, this is the first report of GRBV in Mexico.
TL;DR: In this paper, a phase sensitive optical time domain reflectometry (φ-OTDR) system for vibration measurements utilizing a conventional telecom DFB laser self-stabilized through an external PM optical fiber ring resonator was evaluated.
Abstract: We have evaluated the performance of a phase-sensitive optical time domain reflectometry (φ-OTDR) system for vibration measurements utilizing a conventional telecom DFB laser self-stabilized through an external PM optical fiber ring resonator. This low-cost solution is directly compared with the use of a commercial, ultra-narrow linewidth (∼100 Hz) fiber laser implemented into the same setup. Both systems are tested for measurement of the frequency of vibration applied to a fiber at a distance of 3500 m. The obtained SNR value higher than 6 dB demonstrates the ability of the DFB laser to perform distributed measurements of vibrations with frequencies up to 5600 Hz with a spatial resolution of 10 m.
TL;DR: A parallel evolutionary algorithm to efficiently configure and synchronize traffic lights and improve the average speed of buses and other vehicles is introduced and achieves better quality of service when compared with the current reality.
Abstract: This article presents a parallel evolutionary algorithm for public transport optimization by synchronizing traffic lights in the context of Bus Rapid Transit systems. The related optimization problem is NP-hard, so exact computational methods are not useful to solve real-world instances. Our research introduces a parallel evolutionary algorithm to efficiently configure and synchronize traffic lights and improve the average speed of buses and other vehicles. The Bus Rapid Transit on Garzon Avenue (Montevideo, Uruguay) is used as a case study. This is an interesting complex urban scenario due to the number of crossings, streets, and traffic lights in the zone. The experimental analysis compares the numerical results computed by the parallel evolutionary algorithm with a scenario that models the current reality. The results show that the proposed evolutionary algorithm achieves better quality of service when compared with the current reality, improving up to 15.3% the average bus speed and 24.8% the average speed of other vehicles. A multiobjective optimization analysis also demonstrates that additional improvements can be achieved by assigning different priorities to buses and other vehicles. In addition, further improvements can be achieved on a modified scenario simply by deleting a few bus stops and changing some traffic lights rules. The benefits of using a parallel solver are also highlighted, as the parallel version is able to accelerate the execution times up to 26.9x when compared with the sequential version.
TL;DR: Results indicate that the use of these conversational strategies is effective at increasing the interaction between PwD and a SAR, and provide evidence of the importance of incorporating appropriate Conversational strategies in SARs that support interventions for the care and social stimulation of PwDs.
Abstract: Background Socially assistive robots (SARs) have the potential to assist nonpharmacological interventions based on verbal communication to support the care of persons with dementia (PwDs). However, establishing verbal communication with a PwD is challenging. Thus, several authors have proposed strategies to converse with PwDs. While these strategies have proved effective at enhancing communication between PwDs and their caregivers, they have not been used or tested in the domain of human-robot interaction. Objectives This study aimed to assess the effectiveness of incorporating conversational strategies proposed in the literature for caregivers, during PwD-robot interactions. Methods We conducted a total of 23 group sessions based on music and conversation therapy, where a SAR interacted with 12 PwDs (mean = 80.25 years) diagnosed with mild to moderate-stage dementia. Using a single subject research approach, we designed an AB study to assess the effectiveness of the conversational strategies in the PwD-robot interaction. Our analysis focuses on the direct communication between the PwDs and the robot, and the perceived enjoyment of PwDs. Results The number of utterances made from a PwD to the robot increased significantly when the conversational strategies were included in the robot. In addition, PwDs engaged in more sustained conversations. Additionally, PwDs enjoyed conversing with the robot Eva, as much as listening to music. These results indicate that the use of these conversational strategies is -effective at increasing the interaction between PwD and a SAR. Conclusions PwDs who participated in the study engaged and enjoyed the interaction with the SAR. The results provide evidence of the importance of incorporating appropriate conversational strategies in SARs that support interventions for the care and social stimulation of PwDs.
TL;DR: The metamorphic basement of the Merida Andes in western Venezuela is constituted of paragneiss, orthogneiss, amphibolite, and metagranitoid of the Iglesias Complex.
Abstract: The metamorphic basement of the Merida Andes in western Venezuela is constituted of paragneiss, orthogneiss, amphibolite, and metagranitoid of the Iglesias Complex. In this paper, U–Pb zircon geoch...