Search

Pine wilt disease (PWD) is a worldwide forest disease caused by pine wood nematode (PWN). In this article, we investigated the composition, organization, correlation, and function of the endophytic microbial community in Pinus massoniana field with and without PWN. Samples were taken from branches, upper, middle, and lower trunks, as well as soil, from both healthy and infected trees. The results showed that the fungal diversity of healthy pines is around 1.1 times that of infected pines, while the bacterial diversity is about 0.75 times that of infected pines at the OTUs level. An increase of the abundance of pathogenic fungus such as Saitozyma, Graphilbum, Diplodia, Candida, Pseudoxanthomonas, Dyella and Pantoea was witnessed in infected pines according to the result of LEfSe. Furthermore, Ophiostoma and saprophytic fungus such as Entomocorticium, ganoderma, tomentella, entomocorticium were exclusively prominent in infected pines, which were substantially and highly connected with other species (p < 0.05), indicating the trees’ vulnerability and making the wood blue. In healthy pines, the top three functional guilds are parasites, plant pathogens, and saprotrophs. Parasites (36.52%) are primarily found in the branches, plant pathogens (29.12%) are primarily found in the lower trunk, and saprotrophs (67.88%) are primarily found in the upper trunk of disease trees. Pines’ immunity is being eroded due to an increase in the quantity and types of diseases. PICRUSt2 research revealed that NADH or NADPH, as well as carbon-nitrogen bonds, were more abundant in healthy pines, but acid anhydrides and transferring phosphorus-containing groups were more abundant in infected pines. The shift in resin secretion lowers the tree’s potential and encourages pine wilt and mortality. In total, PWN may have disrupted the microbiological ecology and worked with the community to hasten the demise of pines.

Chemical compounds can be represented as attributed graphs. An attributed graph is a mathematical model of an object composed of two types of representations: nodes and edges. Nodes are individual components, and edges are relations between these components. In this case, pharmacophore-type node descriptions are represented by nodes and chemical bounds by edges. If we want to obtain the bioactivity dissimilarity between two chemical compounds, a distance between attributed graphs can be used. The Graph Edit Distance allows computing this distance, and it is defined as the cost of transforming one graph into another. Nevertheless, to define this dissimilarity, the transformation cost must be properly tuned. The aim of this paper is to analyse the structural-based screening methods to verify the quality of the Harper transformation costs proposal and to present an algorithm to learn these transformation costs such that the bioactivity dissimilarity is properly defined in a ligand-based virtual screening application. The goodness of the dissimilarity is represented by the classification accuracy. Six publicly available datasets—CAPST, DUD-E, GLL&GDD, NRLiSt-BDB, MUV and ULS-UDS—have been used to validate our methodology and show that with our learned costs, we obtain the highest ratios in identifying the bioactivity similarity in a structurally diverse group of molecules. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

In cooperative communication systems, hierarchical modulation is used to increase systems robustness and to send different information flows simultaneously. In cooperative communication systems which use hierarchical modulation, error propagation is the most important problem that prevents achieving full diversity gain. Thresholds that depend on the signal to noise ratio (SNR) value between the source and the relay can be used to mitigate error propagation. If the instantaneous SNR between the source and the relay is lower than the first threshold, the relay does not transmit. If the SNR is between the first and the second thresholds, the relay demodulates and forwards only the primary bits. If the SNR is higher than the second threshold, the relay demodulates and forwards both the primary and the secondary bits. Mitigating error propagation and achieving full diversity for both primary (high priority) and secondary (low priority) bits depend on setting the thresholds at the relay properly. In this work, the first and the second threshold values are determined so that full diversity gains are attained for both primary and secondary bits. Analytical and simulation results are provided to verify the analysis.

In cooperative communication systems, hierarchical modulation is used to increase systems robustness and to send different information flows simultaneously. In cooperative communication systems which use hierarchical modulation, error propagation is the most important problem that prevents achieving full diversity gain. Thresholds that depend on the signal to noise ratio (SNR) value between the source and the relay can be used to mitigate error propagation. If the instantaneous SNR between the source and the relay is lower than the first threshold, the relay does not transmit. If the SNR is between the first and the second thresholds, the relay demodulates and forwards only the primary bits. If the SNR is higher than the second threshold, the relay demodulates and forwards both the primary and the secondary bits. Mitigating error propagation and achieving full diversity for both primary (high priority) and secondary (low priority) bits depend on setting the thresholds at the relay properly. In this work, the first and the second threshold values are determined so that full diversity gains are attained for both primary and secondary bits. Analytical and simulation results are provided to verify the analysis.

Copyright © 2019 American Chemical Society. Extended reduced graphs provide summary representations of chemical structures using pharmacophore-type node descriptions to encode the relevant molecular properties. Commonly used similarity measures using reduced graphs convert these graphs into 2D vectors like fingerprints, before chemical comparisons are made. This study investigates the effectiveness of a graph-only driven molecular comparison by using extended reduced graphs along with graph edit distance methods for molecular similarity calculation as a tool for ligand-based virtual screening applications, which estimate the bioactivity of a chemical on the basis of the bioactivity of similar compounds. The results proved to be very stable and the graph editing distance method performed better than other methods previously used on reduced graphs. This is exemplified with six publicly available data sets: DUD-E, MUV, GLL&GDD, CAPST, NRLiSt BDB, and ULS-UDS. The screening and statistical tools available on the ligand-based virtual screening benchmarking platform and the RDKit were also used. In the experiments, our method performed better than other molecular similarity methods which use array representations in most cases. Overall, it is shown that extended reduced graphs along with graph edit distance is a combination of methods that has numerous applications and can identify bioactivity similarities in a structurally diverse group of molecules.

Computer simulation models can generate large numbers of scenarios, far more than can be effectively utilized in most decision support applications. How can one best select a small number of scenarios to consider? One approach calls for choosing scenarios that illuminate vulnerabilities of proposed policies. Another calls for choosing scenarios that span a diverse range of futures. This paper joins these two approaches for the first time, proposing an optimization-based method for choosing a small number of relevant scenarios that combine both vulnerability and diversity. The paper applies the method to a real case involving climate resilient infrastructure for three African river basins (Volta, Orange and Zambezi). Introducing selection criteria in a stepwise manner helps examine how different criteria influence the choice of scenarios. The results suggest that combining vulnerability- and diversity-based criteria can provide a systematic and transparent method for scenario selection., QC 20161111

Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5 g/100 seeds), into a blackeye seed type cultivar, CB27 (22 g/100 seed). Four recombinant inbred lines derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 28.7g/100 seed and 24.8 g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35 g/100 seeds). Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this quantitative trait locus has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.

Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5 g/100 seeds), into a blackeye seed type cultivar, CB27 (22 g/100 seed). Four recombinant inbred lines derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 28.7g/100 seed and 24.8 g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35 g/100 seeds). Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this quantitative trait locus has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.

Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE) with two primer pairs (344fGC/519r and 519f/915rGC) and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE profiles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no significant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs; however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A (mcrA) gene fragments amplified with real-time PCR showed all samples possessed a single peak at 82°C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase (including diet factor) other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.

It is shown that for four-transmitter systems, a family of four-by-four unit-rate complex quasi-orthogonal space-time block codes, where each entry equals a symbol variable up to a change of sign and/or complex conjugation, can be generated from any two independent codes via elementary operations. The two independent groups of codes in the family generally have different properties of diversity, but the codes in each group have the same diversity provided that the differential symbol constellation is symmetric. It is also shown that for four-transmitter systems, an eight-by-four unit-rate complex linear dispersion space-time block code can be constructed by using Hurwitz-Radon families of matrices of size eight such that diversity three is guaranteed even when all symbols are independently selected from any given constellation. This code is so far the only known unit-rate linear dispersion code that has diversity no less than three for four transmitters under any given constellation., Published in Signal Processing, v88 p2030-2062, 2008. Prepared in cooperation with Rambus, Inc., Los Altos, CA; University of Delaware, Newark; and Army Research Laboratory, Adelphi, MD.

This paper analyzes to what extent the multipath diversity is extracted by a cyclic prefixed single-carrier (CPSC) transmission. The state-of-the-art is currently pessimistic on that issue, and has to be moderated: if it is true that the asymptotical, i.e. at infinite signal to noise ratio (SNR), diversity order achieved by CPSC is equal to one, we prove that the block size has an influence on the performance at moderate SNR. In particular, for reasonably large values of the block size, we show that the multipath diversity can be extracted by CPSC for the range of bit error rate values typically used in practice. The influence of suboptimal linear receivers on the diversity extraction is also investigated.

Multiframe image superresolution has been an active research area for many years. In this approach image processing techniques are used to combine multiple low-resolution (LR) images capturing different views of an object. These multiple images are generally under-sampled, degraded by optical and pixel blurs, and corrupted by measurement noise. We exploit diversities in the imaging channels, namely, the number of cameras, magnification, position, and rotation, to undo degradations. Using an iterative back-projection (IBP) algorithm we quantify the improvements in image fidelity gained by using multiple frames compared to single frame, and discuss effects of system parameters on the reconstruction fidelity. As an example, for a system in which the pixel size is matched to optical blur size at a moderate detector noise, we can reduce the reconstruction root-mean-square-error by 570% by using 16 cameras and a large amount of diversity in deployment.We develop a new technique for superresolving binary imagery by incorporating finite-alphabet prior knowledge. We employ a message-passing based algorithm called two-dimensional distributed data detection (2D4) to estimate the object pixel likelihoods. We present a novel complexity-reduction technique that makes the algorithm suitable even for channels with support size as large as 5x5 object pixels. We compare the performance and complexity of 2D4 with that of IBP. In an imaging system with an optical blur spot matched to pixel size, and four 2x2 undersampled LR images, the reconstruction error for 2D4 is 300 times smaller than that for IBP at a signal-to-noise ratio of 38dB.We also present a transform-domain superresolution algorithm to efficiently incorporate sparsity as a form of prior knowledge. The prior knowledge that the object is sparse in some domain is incorporated in two ways: first we use the popular L1 norm as the regularization operator. Secondly we model wavelet coefficients of natural objects using generaliz

Spotted medics (Medicago arabica) have become naturalised in Australia, but the spiny nature of their pods has prevented commercial release of any cultivar. Fifty-eight accessions representing Medicago arabica in the Australian Medicago Genetic Resources Collection were grown as spaced plants at Turretfield, South Australia, and the variation for important agronomic traits was studied. There was large variation for traits including days to flowering, dry matter production, pod and seed yield, and pod spininess. Principal component and cluster analyses conducted for 13 traits revealed 5 clusters. One of the clusters identified comprised accessions originating from Greece and Cyprus, which were found to have high agronomic potential. The study has helped in identifying the relationship among traits, namely pod spininess, days to flowering, dry matter yield, and pod and seed yield, which would be useful to breeders for future breeding and selection programs. A sward trial at Moree, New South Wales, comprising a selected cohort of spotted medic accessions, enabled the identification of 2 early flowering and high dry matter yielding accessions; however, both exhibited spiny pods. These 2 accessions were crossed with a smooth-podded accession, and the F1 plants were confirmed using a microsatellite marker. Days to flowering showed a continuous pattern of variation in the F2, suggesting that the trait is quantitatively inherited, whereas segregation ratio revealed that a single recessive gene controlled the smooth pod trait. Early flowering, smooth-podded F2 plants were selected for cultivar development.