Over the past few years, the gap between field-programmable gate array (FPGA) and application-specific integrated circuit (ASIC) performance levels has been narrowed due to the constant development ...of FPGA technology. The high performance, together with the lower development costs and a shorter time to market, turns FPGA-based platforms attractive for a huge range of applications, among them time-to-digital converters (TDCs). It is, therefore, important to analyze the evolution of FPGA-based TDCs to better understand where the research efforts should be focused in the near future. This article presents and discusses the improvements on the FPGA-based TDC research, aiming to be a starting point for new studies on this field, with some guidelines for future research. A state-of-the-art literature review on the FPGA-based TDC is presented, aiming to categorize and discuss the existing architectures. This discussion addresses architectures' characteristics, limitations, and areas of application.
Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a ...challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in
by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of
The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor
(
) as a putative
-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of
in a diverse population positively correlated with lignin content. Furthermore, overexpression of
in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that
is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in
.
Network Unfolding Map by Vertex-Edge Dynamics Modeling Alves Neto Verri, Filipe; Urio, Paulo Roberto; Liang Zhao
IEEE transaction on neural networks and learning systems,
02/2018, Letnik:
29, Številka:
2
Journal Article
Odprti dostop
The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique using distributed ...processing elements in a complex network, which are called particles, to solve semisupervised learning problems. Three actions govern the particles' dynamics: generation, walking, and absorption. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles. The result from the model evolution consists of sets of edges arranged by the label dominance. Each set tends to form a connected subnetwork to represent a data class. Although the intrinsic dynamics of the model is a stochastic one, we prove that there exists a deterministic version with largely reduced computational complexity; specifically, with linear growth. Furthermore, the edge domination process corresponds to an unfolding map in such way that edges "stretch" and "shrink" according to the vertex-edge dynamics. Consequently, the unfolding effect summarizes the relevant relationships between vertices and the uncovered data classes. The proposed model captures important details of connectivity patterns over the vertex-edge dynamics evolution, in contrast to the previous approaches, which focused on only vertex or only edge dynamics. Computer simulations reveal that the new model can identify nonlinear features in both real and artificial data, including boundaries between distinct classes and overlapping structures of data.
Common bean (
Phaseolus vulgaris
L.) is a nutrient-rich food, but its long cooking times hinder its wider utilization. The Yellow Bean Collection (YBC) was assembled with 295 genotypes from global ...sources to assess the genetic and phenotypic diversity for end-use quality traits in yellow beans. The panel was genotyped with over 2,000 SNPs identified via Genotyping-By-Sequencing (GBS). Through population structure analyses with the GBS markers, the YBC was determined to be 69% Andean, 26% Middle American, and 5% admixture. The YBC was grown in two major bean production regions in the U.S., Michigan (MI) and Nebraska (NE) over two years. The genotypes exhibited a wide diversity in days to flower, seed weight, water uptake, and cooking time. The cooking times of the YBC ranged from 17–123 min. The cooking time were longer and varied more widely in NE with many more genotypes exhibiting hardshell than in MI. Fast-cooking genotypes were identified with various yellow colors; 20 genotypes cooked within 20 min in MI, and eight genotypes cooked within 31 min in NE. Water uptake and cooking time were significantly affected by the environment, which included both the growing and cooking environment, and notably in relation to cooking, NE is higher elevation than MI. SNPs associated with cooking time were identified with genome-wide association analyses and a polygalacturonase gene on Pv04 was considered to be a candidate gene. The genotypic and phenotypic variability, fast-cooking genotypes, and the associated SNPs of the YBC will lay the foundation for utilizing yellow beans for breeding and genetic analyses.
We are happy to introduce this special issue of Abdominal Radiology on “diffuse liver disease”. We have invited imaging experts to discuss various topics pertaining to diffuse liver disease, covering ...a vast array of imaging techniques including ultrasound (US), CT, MRI and new molecular imaging agents. Below, we briefly discussed the current status, limitations, and future directions of imaging biomarkers of diffuse liver disease.
Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high ...levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species' genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.
We present a network community-detection technique based on properties that emerge from a nature-inspired flocking system. Our algorithm comprises two alternating mechanisms: first, we control the ...particles alignment in higher dimensional space and, second, we present an iterative process of edge removal. These mechanisms together can potentially reduce accidental alignment among particles from different communities and, consequently, the model can generate robust community-detection results. In the proposed model, a random-direction unit vector is assigned to each vertex initially. A nonlinear dynamic law is established, so that neighboring vertices try to become aligned with each other. After some time, the system stops and edges that connect the least-aligned pairs of vertices are removed. Then, the evolution starts over without the removed edges, and after enough number of removal rounds, each community becomes a connected component. The proposed approach is evaluated using widely accepted benchmarks and real-world networks. Experimental results reveal that the method is robust and excels on a wide variety of networks. For large sparse networks, the edge-removal process runs in quasilinear time, which enables application in large-scale networks. Moreover, the distributed nature of the process eases the parallel implementation of the model.
Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels ...of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters, and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e., Linnaeus’s two-toed sloth), but undetected in other closely related species (i.e., brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were probably lost independently among Xenarthra orders. Additionally, by expanding our analysis to 157 mammal genomes, we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia, and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy and endorses the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.
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