The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes.

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.

Lossless Coding of Light Fields Based on 4D Minimum Rate Predictors.

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.

Light Field Image Dataset of Skin Lesions.

Light field imaging technology has been attracting increasing interest because it enables capturing enriched visual information and expands the processing capabilities of traditional 2D imaging systems. Dense multiview, accurate depth maps and multiple focus planes are examples of different types of visual information enabled by light fields. This technology is also emerging in medical imaging research, like dermatology, allowing to find new features and improve classification algorithms, namely those based on machine learning approaches. This paper presents a contribution for the research community, in the form of a publicly available light field image dataset of skin lesions (named SKINL2 v1.0). This dataset contains 250 light fields, captured with a focused plenoptic camera and classified into eight clinical categories, according to the type of lesion. Each light field is comprised of 81 different views of the same lesion. The database also includes the dermatoscopic image of each lesion. A representative subset of 17 central view images of the light fields is further characterised in terms of spatial information (SI), colourfulness (CF) and compressibility. This dataset has high potential for advancing medical imaging research and development of new classification algorithms based on light fields, as well as in clinically-oriented dermatology studies.

Interdependency of efficient nodulation and arbuscular mycorrhization in Piptadenia gonoacantha, a Brazilian legume tree.

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.

Lossless Compression of Medical Images Using 3-D Predictors.

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.

Image Coding Using Generalized Predictors Based on Sparsity and Geometric Transformations.

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.

Intra Predictive Depth Map Coding Using Flexible Block Partitioning.

A complete encoding solution for efficient intra-based depth map compression is proposed in this paper. The algorithm, denominated predictive depth coding (PDC), was specifically developed to efficiently represent the characteristics of depth maps, mostly composed by smooth areas delimited by sharp edges. At its core, PDC involves a directional intra prediction framework and a straightforward residue coding method, combined with an optimized flexible block partitioning scheme. In order to improve the algorithm in the presence of depth edges that cannot be efficiently predicted by the directional modes, a constrained depth modeling mode, based on explicit edge representation, was developed. For residue coding, a simple and low complexity approach was investigated, using constant and linear residue modeling, depending on the prediction mode. The performance of the proposed intra depth map coding approach was evaluated based on the quality of the synthesized views using the encoded depth maps and original texture views. The experimental tests based on all intra configuration demonstrated the superior rate-distortion performance of PDC, with average bitrate savings of 6%, when compared with the current state-of-the-art intra depth map coding solution present in the 3D extension of a high-efficiency video coding (3D-HEVC) standard. By using view synthesis optimization in both PDC and 3D-HEVC encoders, the average bitrate savings increase to 14.3%. This suggests that the proposed method, without using transform-based residue coding, is an efficient alternative to the current 3D-HEVC algorithm for intra depth map coding.

Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis.

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.

Evaluating the nodulation status of leguminous species from the Amazonian forest of Brazil.

Numerous leguminous species are used or have potential uses for timber production, pharmacological products, or land reclamation. Through N(2)-fixation, many leguminous trees contribute to the N-balance of tropical wetlands and rainforests. Therefore, studies of the N(2)-fixation ability of leguminous species appear to be crucial for the better use and conservation of these resources. The global nodulation inventory in the Leguminosae family is constantly being enriched with new records, suggesting the existence of undiscovered nodulated species, especially in tropical natural ecosystems and other hot spots of biodiversity. In this respect, the nodulation of leguminous species from the Amazonian forest of Porto Trombetas (Brazil) was surveyed. Overall, 199 leguminous species from flooded and non-flooded areas, were examined for their nodulation status by combining field observations, seedling inoculations, and screening of N(2)-fixing bacterial strains from the collected nodules. The results revealed a tendency for a higher relative frequency of nodulation in the species from the flooded areas (74%) compared with those from the non-flooded areas (67%). Nodulation was observed in the Caesalpinioideae, Mimosoideae, and Papilionoideae, with 25, 88, and 84% of the examined species in each subfamily, respectively. Of the 137 nodulated leguminous species, 32 including three Caesalpinoideae, 19 Mimosoideae, and 10 Papilionoideae are new records. One new nodulated genus (Cymbosema) was found in the Papilionoideae. Twelve non-nodulating leguminous species were also observed for the first time. The results are discussed based on the systematics of the Leguminosae family and the influence of available nutrients to the legume-bacteria symbiosis.

Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil.

*An extensive survey of nodulation in the legume genus Mimosa was undertaken in two major biomes in Brazil, the Cerrado and the Caatinga, in both of which there are high degrees of endemicity of the genus. *Nodules were collected from 67 of the 70 Mimosa spp. found. Thirteen of the species were newly reported as nodulating. Nodules were examined by light and electron microscopy, and all except for M. gatesiae had a structure typical of effective Mimosa nodules. The endosymbiotic bacteria in nodules from all of the Mimosa spp. were identified as Burkholderia via immunolabelling with an antibody against Burkholderia phymatum STM815. *Twenty of the 23 Mimosa nodules tested were shown to contain nitrogenase by immunolabelling with an antibody to the nitrogenase Fe- (nifH) protein, and using the delta(15)N ((15)N natural abundance) technique, contributions by biological N(2) fixation of up to 60% of total plant N were calculated for Caatinga Mimosa spp. *It is concluded that nodulation in Mimosa is a generic character, and that the preferred symbionts of Brazilian species are Burkholderia. This is the first study to demonstrate N(2) fixation by beta-rhizobial symbioses in the field.

Scanned compound document encoding using multiscale recurrent patterns.

In this paper, we propose a new encoder for scanned compound documents, based upon a recently introduced coding paradigm called multidimensional multiscale parser (MMP). MMP uses approximate pattern matching, with adaptive multiscale dictionaries that contain concatenations of scaled versions of previously encoded image blocks. These features give MMP the ability to adjust to the input image's characteristics, resulting in high coding efficiencies for a wide range of image types. This versatility makes MMP a good candidate for compound digital document encoding. The proposed algorithm first classifies the image blocks as smooth (texture) and nonsmooth (text and graphics). Smooth and nonsmooth blocks are then compressed using different MMP-based encoders, adapted for encoding either type of blocks. The adaptive use of these two types of encoders resulted in performance gains over the original MMP algorithm, further increasing the performance advantage over the current state-of-the-art image encoders for scanned compound images, without compromising the performance for other image types.

Burkholderia species are ancient symbionts of legumes.

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.

On ECG signal compression with 1-D multiscale recurrent patterns allied to preprocessing techniques.

This paper presents the results of a multiscale pattern-matching-based ECG encoder, which employs simple preprocessing techniques for adapting the input signal. Experiments carried out with records from the Massachusetts Institute of Technology-Beth Israel Hospital database show that the proposed scheme is effective, outperforming some state-of-the-art schemes described in the literature.

Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia.

Two rhizobial strains, Br3407(T) and Br3405, were isolated from nitrogen-fixing nodules on the roots of Mimosa caesalpiniifolia, a legume tree native to Brazil. On the basis of 16S rRNA gene sequence similarities, both strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, pulsed-field gel electrophoresis of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia sabiae sp. nov. is proposed. The type strain is strain Br3407(T) (=LMG 24235(T) =BCRC 17587(T)).

On dictionary adaptation for recurrent pattern image coding.

In this paper, we exploit a recently introduced coding algorithm called multidimensional multiscale parser (MMP) as an alternative to the traditional transform quantization-based methods. MMP uses approximate pattern matching with adaptive multiscale dictionaries that contain concatenations of scaled versions of previously encoded image blocks. We propose the use of predictive coding schemes that modify the source's probability distribution, in order to favour the efficiency of MMP's dictionary adaptation. Statistical conditioning is also used, allowing for an increased coding efficiency of the dictionaries' symbols. New dictionary design methods, that allow for an effective compromise between the introduction of new dictionary elements and the reduction of codebook redundancy, are also proposed. Experimental results validate the proposed techniques by showing consistent improvements in PSNR performance over the original MMP algorithm. When compared with state-of-the-art methods, like JPEG2000 and H.264/AVC, the proposed algorithm achieves relevant gains (up to 6 dB) for nonsmooth images and very competitive results for smooth images. These results strongly suggest that the new paradigm posed by MMP can be regarded as an alternative to the one traditionally used in image coding, for a wide range of image types.

ECG signal compression based on Dc equalization and complexity sorting.

In this brief, we present new preprocessing techniques for electrocardiogram signals, namely, dc equalization and complexity sorting, which when applied can improve current 2-D compression algorithms. The experimental results with signals from the Massachusetts Institute of Technology - Beth Israel Hospital (MIT-BIH) database outperform the ones from many state-of-the-art schemes described in the literature.

Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella.

Three strains, Br3437(T), Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437(T)) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437(T) (=LMG 23741(T)=BCRC 17575(T)), was isolated from nodules of M. scabrella.

Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta.

* 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.

Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America.

Fourteen strains were isolated from nitrogen-fixing nodules on the roots of plants of the genus Mimosa growing in Taiwan, Brazil and Venezuela. On the basis of 16S rRNA gene sequence similarities, all of the strains were previously shown to be closely related to each other and to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA reassociation, whole-cell protein analysis, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains: all 14 strains were classified as representing a novel species, for which the name Burkholderia mimosarum sp. nov. is proposed. The type strain, PAS44(T) (=LMG 23256(T) =BCRC 17516(T)), was isolated from Mimosa pigra nodules in Taiwan.

Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America.

Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other beta-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known beta-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.