154 documents found, page 1 of 16
A GPU implementation of the analog ensemble method
Crico, Ruben; Charles, Ines; Balsa, Carlos; Rufino, JoséThe Analog Ensemble (AnEn) method can be used to reconstruct incomplete time series using correlated series. Since the AnEn method may use data including several variables through long periods of time, its storage and computational cost may be substantial, slowing down reconstructions. This paper presents a full GPU implementation of the AnEn method, based on PyCUDA, that leads to a significant a cceleration of...
Contributions to accelerating a numerical simulation of free flow parallel to a...
Schepke, Claudio; Spigolon, Roberta A.; Rufino, José; Cristaldo, Cesar F. Da C.; Pizzolato, Glener L.Flow models over flat p orous surfaces have applications in natural processes, such as material, food, chemical processing, or mountain mudflow simulations. The development of simplified a nalytical or numerical models can predict characteristics such as velocity, pressure, deviation length, and even temperature of such flows for geophysical and engineering purposes. In this context, there is considerable inter...
Bioinformatics pipeline to evaluate patterns of diversity in detoxification gen...
Barbosa, Daniela; Li, Fernanda; Bashir, Sana; Lopes, Ana; Yadró García, Carlos A.; Quaresma, Andreia; Rufino, José; Rosa-Fontana, AnneliseThe Western honey bee, Apis mellifera, displays significant genetic diversity in detoxification genes, which is pivotal for environmental adaptation and resilience. Herein, we developed a bioinformatics pipeline to investigate patterns of diversity in these genes, focusing on single nucleotide polymorphisms (SNPs) across A. mellifera populations, with variant annotation performed using both snpEff and the Varia...
Genomic insights into middle eastern honey bee subspecies: population structure...
Henriques, Dora; Yadró Garcia, Carlos A.; Honrado, Mónica; Amaral, Joana S.; Muz, Mustafa Necati; Muz, Dilek; Haddad, Nizar; Al Shagour, BananThe genetic patterns of Middle Eastern A. mellifera subspecies have been understudied, hindering a comprehensive understanding of honey bee evolutionary history. Here, we studied the genetic integrity of five Middle Eastern subspecies across a broad geographical range: Turkey (A. m. anatoliaca, N=97; A. m. caucasia, N=75; A. m. syriaca, N=18), Jordan and Lebanon (A. m. syriaca, N=238 and N=29), Iran (A. m. meda...
Diversity patterns of P450 and ABC transporter genes in 17 honey bee subspecies
Li, Fernanda; Rosa-Fontana, Annelise; Yadró Garcia, Carlos A.; Rufino, José; Verbinnen, Gilles; Graaf, Dirk C.; Smet, Lina de; Pinto, M. AliceHoney bees (Apis mellifera) inhabit a vast geographical range, spanning diverse natural and agricultural ecosystems. They are exposed to different levels and types of natural (such as plant allelochemicals) and synthetic (such as pesticides) xenobiotics within this range. Several genes have been implicated in the resistance of insects to pesticides, including the P450 monooxygenases superfamily and ATP-binding ...
Insights into population structure and conservation status of north African hon...
Yadró Garcia, Carlos A.; Henriques, Dora; Haider, Yamina; Eissa, Asmaa Anwar; Aglagane, Abdessamad; Rufino, José; Nanetti, AntonioThe population structure of North African A. mellifera subspecies has been overlooked. Here, WG generated from drones were analyzed to assess population structure and the conservation status of three A-lineage subspecies: A. m. lamarckii (Egypt, 68 samples), A. m. intermissa (Algeria, 69 samples), and A. m. sahariensis (Algeria, 68 samples; Morocco, 26 samples). Population structure was assessed by SNMF and PCA...
Exploring population structure and adaptation in honey bee subspecies from sout...
Yadró Garcia, Carlos A.; Henriques, Dora; Cilia, Giovanni; Rufino, José; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. AliceGlacial refugia harbor populations with complex diversity patterns. In honey bees, the Iberian and Italian Peninsulas served as two of the most important glacial refugia in Europe. Here, we analyzed whole genomes generated from drones to infer population structure, genetic diversity, and the molecular basis of the local adaptation for the two native subspecies of these Peninsulas: A. m. iberiensis (N=86; M-line...
Semi-automated sequence curation for reliable reference datasets in ITS2 vascul...
Quaresma, Andreia; Ankenbrand, Markus J.; Garcia, Carlos Ariel Yadró; Rufino, José; Honrado, Mónica; Amaral, Joana S.; Brodschneider, RobertOne of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and...
Parameterization and performance analysis of a scalable, near real-time packet ...
Oliveira, Rafael Cardoso de; Pedrosa, Tiago; Rufino, José; Lopes, Rui PedroThe rapid evolution of technology has fostered an exponential rise in the number of individuals and devices interconnected via the Internet. This interconnectedness has prompted companies to expand their computing and communication infrastructures significantly to accommodate the escalating demands. However, this proliferation of connectivity has also opened new avenues for cyber threats, emphasizing the critic...
Projeto MITE- Varroa e vírus transmitidos: monItorização de muTações e dEsenvol...
Henriques, Dora; Yadró Garcia, Carlos A.; Lopes, Ana Rita; Rufino, José; Costa, Maíra; Coelho, Marta; Martín-Hernández, Raquel; Higes, MarianoA abelha melífera (Apis melífera L.) tem sido ameaçada por diferentes fatores, tais como pesticidas, alterações climáticas, má nutrição, espécies invasoras tais como o predador Vespa velutina, a bactéria causadora da loque americana Paenibacillus larvae, e principalmente, o ácaro parasita Varroa destructor (vulgarmente conhecido como varroa), que é apontado como umas das mais importantes ameaças para a abelha m...