PrivGraph: Differentially Private Graph Data Publication by Exploiting Community Information

Graph data is used in a wide range of applications, while analyzing graph data without protection is prone to privacy breach risks. To mitigate the privacy risks, we resort to the standard technique of differential privacy to publish a synthetic graph. However, existing differentially private graph synthesis approaches either introduce excessive noise by directly perturbing the adjacency matrix, or suffer significant information loss during the graph encoding process. In this paper, we propose an effective graph synthesis algorithm PrivGraph by exploiting the community information. Concretely, PrivGraph differentially privately partitions the private graph into communities, extracts intra-community and inter-community information, and reconstructs the graph from the extracted graph information. We validate the effectiveness of PrivGraph on six real-world graph datasets and seven commonly used graph metrics.Comment: To Appear in the 32nd USENIX Security Symposiu

Allelic Interactions among Pto-MIR475b and Its Four Target Genes Potentially Affect Growth and Wood Properties in Populus

MicroRNAs (miRNAs) play crucial roles in plant growth and development, but few studies have illuminated the allelic interactions among miRNAs and their targets in perennial plants. Here, we combined analysis of expression patterns and single-nucleotide polymorphism (SNP)-based association studies to explore the interactions between Pto-MIR475b and its four target genes (Pto-PPR1, Pto-PPR2, Pto-PPR3, and Pto-PPR4) in 435 unrelated individuals of Populus tomentosa. Expression patterns showed a significant negative correlation (r = -0.447 to -0.411, P < 0.01) between Pto-MIR475b and its four targets in eight tissues of P. tomentosa, suggesting that Pto-miR475b may negatively regulate the four targets. Single SNP-based association studies identified 93 significant associations (P < 0.01, Q < 0.1) representing associations of 80 unique SNPs in Pto-MIR475b and its four targets with nine traits, revealing their potential roles in tree growth and wood formation. Moreover, one common SNP in the precursor region significantly altered the secondary structure of the pre-Pto-miR475b and changed the expression level of Pto-MIR475b. Analysis of epistatic interactions identified 115 significant SNP–SNP associations (P < 0.01) representing 45 unique SNPs from Pto-MIR475b and its four targets for 10 traits, revealing that genetic interactions between Pto-MIR475b and its targets influence quantitative traits of perennial plants. Our study provided a feasible strategy to study population genetics in forest trees and enhanced our understanding of miRNAs by dissecting the allelic interactions between this miRNA and its targets in P. tomentosa

Formation Flight in Dense Environments

Formation flight has a vast potential for aerial robot swarms in various applications. However, existing methods lack the capability to achieve fully autonomous large-scale formation flight in dense environments. To bridge the gap, we present a complete formation flight system that effectively integrates real-world constraints into aerial formation navigation. This paper proposes a differentiable graph-based metric to quantify the overall similarity error between formations. This metric is invariant to rotation, translation, and scaling, providing more freedom for formation coordination. We design a distributed trajectory optimization framework that considers formation similarity, obstacle avoidance, and dynamic feasibility. The optimization is decoupled to make large-scale formation flights computationally feasible. To improve the elasticity of formation navigation in highly constrained scenes, we present a swarm reorganization method which adaptively adjusts the formation parameters and task assignments by generating local navigation goals. A novel swarm agreement strategy called global-remap-local-replan and a formation-level path planner is proposed in this work to coordinate the swarm global planning and local trajectory optimizations efficiently. To validate the proposed method, we design comprehensive benchmarks and simulations with other cutting-edge works in terms of adaptability, predictability, elasticity, resilience, and efficiency. Finally, integrated with palm-sized swarm platforms with onboard computers and sensors, the proposed method demonstrates its efficiency and robustness by achieving the largest scale formation flight in dense outdoor environments.Comment: Submitted for IEEE Transactions on Robotic

Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects

Wood formation is an excellent model system for quantitative trait analysis due to the strong associations between the transcriptional and metabolic traits that contribute to this complex process. Investigating the genetic architecture and regulatory mechanisms underlying wood formation will enhance our understanding of the quantitative genetics and genomics of complex phenotypic variation. Genome-wide association studies (GWASs) represent an ideal statistical strategy for dissecting the genetic basis of complex quantitative traits. However, elucidating the molecular mechanisms underlying many favorable loci that contribute to wood formation and optimizing GWAS design remain challenging in this omics era. In this review, we summarize the recent progress in GWAS-based functional genomics of wood property traits in major timber species such as Eucalyptus, Populus, and various coniferous species. We discuss several appropriate experimental designs for extensive GWAS in a given undomesticated tree population, such as omics-wide association studies and high-throughput phenotyping technologies. We also explain why more attention should be paid to rare allelic and major structural variation. Finally, we explore the potential use of GWAS for the molecular breeding of trees. Such studies will help provide an integrated understanding of complex quantitative traits and should enable the molecular design of new cultivars

Natural variation in the prolyl 4-hydroxylase gene PtoP4H9 contributes to perennial stem growth in Populus

Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars

Transcriptome and association mapping revealed functional genes respond to drought stress in Populus

Drought frequency and severity are exacerbated by global climate change, which could compromise forest ecosystems. However, there have been minimal efforts to systematically investigate the genetic basis of the response to drought stress in perennial trees. Here, we implemented a systems genetics approach that combines co-expression analysis, association genetics, and expression quantitative trait nucleotide (eQTN) mapping to construct an allelic genetic regulatory network comprising four key regulators (PtoeIF-2B, PtoABF3, PtoPSB33, and PtoLHCA4) under drought stress conditions. Furthermore, Hap_01PtoeIF-2B, a superior haplotype associated with the net photosynthesis, was revealed through allelic frequency and haplotype analysis. In total, 75 candidate genes related to drought stress were identified through transcriptome analyses of five Populus cultivars (P. tremula × P. alba, P. nigra, P. simonii, P. trichocarpa, and P. tomentosa). Through association mapping, we detected 92 unique SNPs from 38 genes and 104 epistatic gene pairs that were associated with six drought-related traits by association mapping. eQTN mapping unravels drought stress-related gene loci that were significantly associated with the expression levels of candidate genes for drought stress. In summary, we have developed an integrated strategy for dissecting a complex genetic network, which facilitates an integrated population genomics approach that can assess the effects of environmental threats

Exploring the Secrets of Long Noncoding RNAs

High-throughput sequencing has revealed that the majority of RNAs have no capacity to encode protein. Among these non-coding transcripts, recent work has focused on the roles of long noncoding RNAs (lncRNAs) of >200 nucleotides. Although many of their attributes, such as patterns of expression, remain largely unknown, lncRNAs have key functions in transcriptional, post-transcriptional, and epigenetic gene regulation; Also, new work indicates their functions in scaffolding ribonuclear protein complexes. In plants, genome-wide identification of lncRNAs has been conducted in several species, including Zea mays, and recent research showed that lncRNAs regulate flowering time in the photoperiod pathway, and function in nodulation. In this review, we discuss the basic mechanisms by which lncRNAs regulate key cellular processes, using the large body of knowledge on animal and yeast lncRNAs to illustrate the significance of emerging work on lncRNAs in plants

Effect of Y Addition on the Semi-Solid Microstructure Evolution and the Coarsening Kinetics of SIMA AZ80 Magnesium Alloy

Semi-solid feedstock of AZ80 magnesium alloy modified by trace rare-earth Y element (0, 0.2, 0.4, 0.8 wt. %) was fabricated by strain-induced melting activation (SIMA) in the form of extrusion and partial remelting. The effect of Y addition on the microstructure evolution of the extruded and isothermally heat treated alloy was observed by using an optical microscope (OM), scanning electron microscope (SEM), X-ray diffraction (XRD) and quantitative analysis. The results show that the Y addition can refine the microstructure and make the β-Mg17Al12 phases agglomerate. During the subsequent isothermal treatment at 570 °C, the average solid grain size, shape factor and liquid fractions increased with the prolonged soaking time. The smaller spheroidal solid grains and larger shape factor were obtained in the semi-solid microstructure due to Y addition. The coalescence and Ostwald ripening mechanism operated the coarsening process of solid grains simultaneously. The coarsening rate constants of AZ80M1 (0.2 wt. % Y addition) of 164.22 μm3 s−1 was approximately four times less than the un-modified AZ80 alloy of 689.44 μm3 s−1. In contrast, the desirable semi-solid structure featured, with fine and well globular solid grains, an appropriate liquid fraction, and shape factor was achieved in AZ80M1 alloy treated at 570 °C for 20–30 min

Crack Coalescence Behavior of Rock-Like Specimens Containing Two Circular Embedded Flaws

AbstractExperimental research on the growth of internal flaws has rarely been reported due to the fact that it is difficult to cut internal flaws in specimens and cannot capture the initiation and propagation processes of internal flaws through direct observations. This paper proposed a method for creating internal flaws in specimens by utilizing the volatilization of camphor. A series of compression tests were performed on rock-like specimens including two embedded circular flaws, and CT techniques were used to investigate the internal damage behavior of flawed specimens. Experimental results illustrate that the strength and deformation properties of flawed specimens increase nonlinearly with the confining pressure as well as flaw inclination angle. Crack coalescence patterns and failure modes of flawed specimens depend on not only the confining pressure but also the flaw inclination angle. The crack coalescence pattern varies from wing crack coalescence to mixed tension-shear crack coalescence and then to the shear crack coalescence as the crack inclination angle increases. Confining pressure contributes to shear crack growth and has an inhibiting effect on the propagation of tension cracks. For specimens with the same flaw inclination angle, the failure mode changed from tension failure to mixed shear-tension failure or from mixed shear-tension failure to pure shear failure with the increase of confining pressure