189 research outputs found
The Canadian Cropland Dataset: A New Land Cover Dataset for Multitemporal Deep Learning Classification in Agriculture
Monitoring land cover using remote sensing is vital for studying
environmental changes and ensuring global food security through crop yield
forecasting. Specifically, multitemporal remote sensing imagery provides
relevant information about the dynamics of a scene, which has proven to lead to
better land cover classification results. Nevertheless, few studies have
benefited from high spatial and temporal resolution data due to the difficulty
of accessing reliable, fine-grained and high-quality annotated samples to
support their hypotheses. Therefore, we introduce a temporal patch-based
dataset of Canadian croplands, enriched with labels retrieved from the Canadian
Annual Crop Inventory. The dataset contains 78,536 manually verified and
curated high-resolution (10 m/pixel, 640 x 640 m) geo-referenced images from 10
crop classes collected over four crop production years (2017-2020) and five
months (June-October). Each instance contains 12 spectral bands, an RGB image,
and additional vegetation index bands. Individually, each category contains at
least 4,800 images. Moreover, as a benchmark, we provide models and source code
that allow a user to predict the crop class using a single image (ResNet,
DenseNet, EfficientNet) or a sequence of images (LRCN, 3D-CNN) from the same
location. In perspective, we expect this evolving dataset to propel the
creation of robust agro-environmental models that can accelerate the
comprehension of complex agricultural regions by providing accurate and
continuous monitoring of land cover.Comment: 24 pages, 5 figures, dataset descripto
BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts
International audienceVarious types of genome and gene similarity networks along with their characteristics have been increasingly used for retracing different kinds of evolutionary and ecological relationships. Here, we present a new polynomial time algorithm and the corresponding software (BRIDES) to provide characterization of different types of paths existing in evolving (or augmented) similarity networks under the constraint that such paths contain at least one node that was not present in the original network. These different paths are denoted as Breakthroughs , Roadblocks, Impasses, Detours, Equal paths, and Shortcuts. The analysis of their distribution can allow discriminating among different evolutionary hypotheses concerning genomes or genes at hand. Our approach is based on an original application of the popular shortest path Dijkstra's and Yen's algorithms
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The draft genome of Ditylenchus dipsaci.
Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU. Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU
Report of a European Movement conference arranged by the Central & Eastern European commission. Brussels, January 1964
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress
Background: Wheat is a major staple crop with broad adaptability to a wide range of environmental conditions.This adaptability involves several stress and developmentally responsive genes, in which microRNAs (miRNAs) have emerged as important regulatory factors. However, the currently used approaches to identify miRNAs in this\ud
polyploid complex system focus on conserved and highly expressed miRNAs avoiding regularly those that are often lineage-specific, condition-specific, or appeared recently in evolution. In addition, many environmental and biological factors affecting miRNA expression were not yet considered, resulting still in an incomplete repertoire of wheat miRNAs.\ud
Results: We developed a conservation-independent technique based on an integrative approach that combines machine learning, bioinformatic tools, biological insights of known miRNA expression profiles and universal criteria of plant miRNAs to identify miRNAs with more confidence. The developed pipeline can potentially identify novel wheat miRNAs that share features common to several species or that are species specific or clade specific. It allowed the discovery of 199 miRNA candidates associated with different abiotic stresses and development stages. We also highlight from the raw data 267 miRNAs conserved with 43 miRBase families. The predicted miRNAs are highly associated with abiotic stress responses, tolerance and development. GO enrichment analysis showed that they may play biological and physiological roles associated with cold, salt and aluminum (Al) through auxin signaling pathways, regulation of gene expression, ubiquitination, transport, carbohydrates, gibberellins, lipid, glutathione and secondary metabolism, photosynthesis, as well as floral transition and flowering.\ud
Conclusion: This approach provides a broad repertoire of hexaploid wheat miRNAs associated with abiotic stress responses, tolerance and development. These valuable resources of expressed wheat miRNAs will help in elucidating the regulatory mechanisms involved in freezing and Al responses and tolerance mechanisms as well as for development and flowering. In the long term, it may help in breeding stress tolerant plants
Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data
International audienceExplaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct timescales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks
Casein kinase I delta controls centrosome positioning during T cell activation
CK1delta binds and phosphorylates the microtubule plus-endâbinding protein
EB1 and promotes centrosome translocation to the immunological synapse in T
cells
Structural evolution and membrane interactions of Alzheimer's amyloidâbeta peptide oligomers: New knowledge from singleâmolecule fluorescence studies
AmyloidâÎČ peptide (AÎČ) oligomers may represent the proximal neurotoxin in Alzheimer's disease. Singleâmolecule microscopy (SMM) techniques have recently emerged as a method for overcoming the innate difficulties of working with amyloidâÎČ, including the peptide's low endogenous concentrations, the dynamic nature of its oligomeric states, and its heterogeneous and complex membrane interactions. SMM techniques have revealed that small oligomers of the peptide bind to model membranes and cells at low nanomolarâtoâpicomolar concentrations and diffuse at rates dependent on the membrane characteristics. These methods have also shown that oligomers grow or dissociate based on the presence of specific inhibitors or promoters and on the ratio of AÎČ40 to AÎČ42. Here, we discuss several types of singleâmolecule imaging that have been applied to the study of AÎČ oligomers and their membrane interactions. We also summarize some of the recent insights SMM has provided into oligomer behavior in solution, on planar lipid membranes, and on living cell membranes. A brief overview of the current limitations of the technique, including the lack of sensitive assays for AÎČâinduced toxicity, is included in hopes of inspiring future development in this area of research.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107477/1/pro2479.pd
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