Common representations of light fields use four-dimensional data structures, where a given pixel is closely related not only to its spatial neighbours within the same view, but also to its angular ...neighbours, co-located in adjacent views. Such structure presents increased redundancy between pixels, when compared with regular single-view images. Then, these redundancies are exploited to obtain compressed representations of the light field, using prediction algorithms specifically tailored to estimate pixel values based on both spatial and angular references. This paper proposes new encoding schemes which take advantage of the four-dimensional light field data structures to improve the coding performance of Minimum Rate Predictors. The proposed methods expand previous research on lossless coding beyond the current state-of-the-art. The experimental results, obtained using both traditional datasets and others more challenging, show bit-rate savings no smaller than 10%, when compared with existing methods for lossless light field compression.
•Skin lesion classification using light-field data•Melanoma discrimination using Scattering Wavelet Transform features•CNN model using residual blocks on limited data•Comparison between colour (2D) ...and depth (3D) in skin cancer classification•High sensitivity results for melanoma discrimination
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Medical image classification through learning-based approaches has been increasingly used, namely in the discrimination of melanoma. However, for skin lesion classification in general, such methods commonly rely on dermoscopic or other 2D-macro RGB images. This work proposes to exploit beyond conventional 2D image characteristics, by considering a third dimension (depth) that characterises the skin surface rugosity, which can be obtained from light-field images, such as those available in the SKINL2 dataset. To achieve this goal, a processing pipeline was deployed using a morlet scattering transform and a CNN model, allowing to perform a comparison between using 2D information, only 3D information, or both. Results show that discrimination between Melanoma and Nevus reaches an accuracy of 84.00, 74.00 or 94.00% when using only 2D, only 3D, or both, respectively. An increase of 14.29pp in sensitivity and 8.33pp in specificity is achieved when expanding beyond conventional 2D information by also using depth. When discriminating between Melanoma and all other types of lesions (a further imbalanced setting), an increase of 28.57pp in sensitivity and decrease of 1.19pp in specificity is achieved for the same test conditions. Overall the results of this work demonstrate significant improvements over conventional approaches.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This paper describes a highly efficient method for lossless compression of volumetric sets of medical images, such as CTs or MRIs. The proposed method, referred to as 3-D-MRP, is based on the ...principle of minimum rate predictors (MRPs), which is one of the state-of-the-art lossless compression technologies presented in the data compression literature. The main features of the proposed method include the use of 3-D predictors, 3-D-block octree partitioning and classification, volume-based optimization, and support for 16-b-depth images. Experimental results demonstrate the efficiency of the 3-D-MRP algorithm for the compression of volumetric sets of medical images, achieving gains above 15% and 12% for 8- and 16-bit-depth contents, respectively, when compared with JPEG-LS, JPEG2000, CALIC, and HEVC, as well as other proposals based on the MRP algorithm.
Burkholderia is a diverse and dynamic genus, containing pathogenic species as well as species that form complex interactions with plants. Pathogenic strains, such as B. pseudomallei and B. mallei, ...can cause serious disease in mammals, while other Burkholderia strains are opportunistic pathogens, infecting humans or animals with a compromised immune system. Although some of the opportunistic Burkholderia pathogens are known to promote plant growth and even fix nitrogen, the risk of infection to infants, the elderly, and people who are immunocompromised has not only resulted in a restriction on their use, but has also limited the application of non-pathogenic, symbiotic species, several of which nodulate legume roots or have positive effects on plant growth. However, recent phylogenetic analyses have demonstrated that Burkholderia species separate into distinct lineages, suggesting the possibility for safe use of certain symbiotic species in agricultural contexts. A number of environmental strains that promote plant growth or degrade xenobiotics are also included in the symbiotic lineage. Many of these species have the potential to enhance agriculture in areas where fertilizers are not readily available and may serve in the future as inocula for crops growing in soils impacted by climate change. Here we address the pathogenic potential of several of the symbiotic Burkholderia strains using bioinformatics and functional tests. A series of infection experiments using Caenorhabditis elegans and HeLa cells, as well as genomic characterization of pathogenic loci, show that the risk of opportunistic infection by symbiotic strains such as B. tuberum is extremely low.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Nitrogen‐fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence ...suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2‐fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades.
We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen‐fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane‐bound symbiosomes (SYMs).
Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs.
We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species‐rich pantropical legume clade.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This letter proposes a method to obtain integer reversible discrete cosine transforms for generic transform-based coding schemes. The novelty of the proposed method, which is based on decomposition ...of the DCT-II matrix into two triangular and one diagonal matrices, is twofold: (i) the new matrices can be of arbitrary size, i.e., any square <inline-formula><tex-math notation="LaTeX">N\times N</tex-math></inline-formula> dimension, thus suitable for applications where non power-of-2 dimensions are required; (ii) they can be designed with adjustable precision in a trade-off with the number of representation bits. Furthermore, improvements are also proposed over the base scheme to avoid numerical issues when working with large matrices and to obtain more reliable approximations. The performance evaluation demonstrate the effectiveness of the proposed transforms to approximate the coding gain capabilities of the original DCT-II.
Tripartite interactions between legumes and their root symbionts (rhizobia and arbuscular mycorrhizal fungi, AMF) are poorly understood, although it is well established that only specific ...combinations of symbionts lead to optimal plant growth. A classic example in which to investigate such interactions is the Brazilian legume tree Piptadenia gonoacantha (Caesalpinioideae), for which efficient nodulation has been described as dependent on the presence of AMF symbiosis. In this study, we compared the nodulation behaviour of several rhizobial strains with or without AMF inoculation, and performed analyses on nodulation, nodule cytology, N‐fixing efficiency, and plant growth response. Nodulation of P. gonoacantha does not rely on the presence of AMF, but mycorrhization was rhizobial strain‐dependent, and nodule effectiveness and plant growth were dependent on the presence of specific combinations of rhizobial strains and AMF. The co‐occurrence of both symbionts within efficient nodules and the differentiation of bacteroids within nodule cells were also demonstrated. Novel close interactions and interdependency for the establishment and/or functioning of these symbioses were also revealed in Piptadenia, thanks to immunocytochemical analyses. These data are discussed in terms of the evolutionary position of the newly circumscribed mimosoid clade within the Caesalpinioid subfamily and its relative proximity to non‐nodulated (but AMF‐associated) basal subfamilies.
The context of this work is based on the observation that among the Caesalpinioideae, in a basal position of the legume phylogeny, are grouped together, nodulated and non‐nodulated clades of plants. All these plants are considered to be arbuscular mycorrhizal (AM), so we focused our attention on a group that includes the genus Piptadenia for which nodulation efficiency has been previously suggested to be directly linked to the presence of the AM symbiosis, taking into consideration the evolutionary relationship between both AM and rhizobial symbioses. On the nodulated tree Piptadenia gonoacantha, our hypothesis was that for optimum efficiency both nitrogen‐fixing and AM symbioses have to share a common niche to closely interact with each other, that is, the nodule. We showed that both symbioses not only coexist, but that they interdependently exist, with both microsymbionts interacting to specifically promote the establishment or functioning of the other, and then leading to improved growth of the host plant.
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8.
Burkholderia species are ancient symbionts of legumes Bontemps, Cyril; Elliott, Geoffrey N; Simon, Marcelo F ...
Molecular ecology,
2010, 2010-01, January 2010, 2010-Jan, 2010-01-00, 20100101, Volume:
19, Issue:
1
Journal Article
Peer reviewed
Burkholderia has only recently been recognized as a potential nitrogen-fixing symbiont of legumes, but we find that the origins of symbiosis in Burkholderia are much deeper than previously suspected. ...We sampled 143 symbionts from 47 native species of Mimosa across 1800 km in central Brazil and found that 98% were Burkholderia. Gene sequences defined seven distinct and divergent species complexes within the genus Burkholderia. The symbiosis-related genes formed deep Burkholderia-specific clades, each specific to a species complex, implying that these genes diverged over a long period within Burkholderia without substantial horizontal gene transfer between species complexes.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
• The ability of Burkholderia phymatum STM815 to effectively nodulate Mimosa spp., and to fix nitrogen ex planta, was compared with that of the known Mimosa symbiont Cupriavidus taiwanensis LMG19424. ...• Both strains were equally effective symbionts of M. pudica, but nodules formed by STM815 had greater nitrogenase activity. STM815 was shown to have a broader host range across the genus Mimosa than LMG19424, nodulating 30 out of 31 species, 21 of these effectively LMG19424 effectively nodulated only nine species. GFP-marked variants were used to visualise symbiont presence within nodules. • STM815 gave significant acetylene reduction assay (ARA) activity in semisolid JMV medium ex planta, but no ARA activity was detected with LMG19424.16S rDNA sequences of two isolates originally from Mimosa nodules in Papua New Guinea (NGR114 and NGR195A) identified them as Burkholderia phymatum also, with nodA, nodC and nifH genes of NGR195A identical to those of STM815. • B. phymatum is therefore an effective Mimosa symbiont with a broad host range, and is the first reported beta-rhizobial strain to fix nitrogen in free-living culture.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Directional intra prediction plays an important role in current state-of-the-art video coding standards. In directional prediction, neighbouring samples are projected along a specific direction to ...predict a block of samples. Ultimately, each prediction mode can be regarded as a set of very simple linear predictors, a different one for each pixel of a block. Therefore, a natural question that arises is whether one could use the theory of linear prediction in order to generate intra prediction modes that provide increased coding efficiency. However, such an interpretation of each directional mode as a set of linear predictors is too poor to provide useful insights for their design. In this paper, we introduce an interpretation of directional prediction as a particular case of linear prediction, which uses the first-order linear filters and a set of geometric transformations. This interpretation motivated the proposal of a generalized intra prediction framework, whereby the first-order linear filters are replaced by adaptive linear filters with sparsity constraints. In this context, we investigate the use of efficient sparse linear models, adaptively estimated for each block through the use of different algorithms, such as matching pursuit, least angle regression, least absolute shrinkage and selection operator, or elastic net. The proposed intra prediction framework was implemented and evaluated within the state-of-the-art high efficiency video coding standard. Experiments demonstrated the advantage of this predictive solution, mainly in the presence of images with complex features and textured areas, achieving higher average bitrate savings than other related sparse representation methods proposed in the literature.
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