Efficient Algorithms for Node Disjoint Subgraph Homeomorphism Determination

Recently, great efforts have been dedicated to researches on the management of large scale graph based data such as WWW, social networks, biological networks. In the study of graph based data management, node disjoint subgraph homeomorphism relation between graphs is more suitable than (sub)graph isomorphism in many cases, especially in those cases that node skipping and node mismatching are allowed. However, no efficient node disjoint subgraph homeomorphism determination (ndSHD) algorithms have been available. In this paper, we propose two computationally efficient ndSHD algorithms based on state spaces searching with backtracking, which employ many heuristics to prune the search spaces. Experimental results on synthetic data sets show that the proposed algorithms are efficient, require relative little time in most of the testing cases, can scale to large or dense graphs, and can accommodate to more complex fuzzy matching cases.Comment: 15 pages, 11 figures, submitted to DASFAA 200

Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways

AbstractThe RNase III enzyme Dicer processes RNA into siRNAs and miRNAs, which direct a RNA-induced silencing complex (RISC) to cleave mRNA or block its translation (RNAi). We have characterized mutations in the Drosophila dicer-1 and dicer-2 genes. Mutation in dicer-1 blocks processing of miRNA precursors, whereas dicer-2 mutants are defective for processing siRNA precursors. It has been recently found that Drosophila Dicer-1 and Dicer-2 are also components of siRNA-dependent RISC (siRISC). We find that Dicer-1 and Dicer-2 are required for siRNA-directed mRNA cleavage, though the RNase III activity of Dicer-2 is not required. Dicer-1 and Dicer-2 facilitate distinct steps in the assembly of siRISC. However, Dicer-1 but not Dicer-2 is essential for miRISC-directed translation repression. Thus, siRISCs and miRISCs are different with respect to Dicers in Drosophila

Functional Conservation of Cis-Regulatory Elements of Heat-Shock Genes over Long Evolutionary Distances

Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple “on-off” response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly

Rainfall-oriented resilient design for slope system: Resilience-enhancing strategies

The concept of resilience has been extensively investigated for various systems to assess and reduce risk in dynamic environments. However, universal rainfall-resilient design criteria for artificially designed and naturally shaped slope systems have rarely been considered. This study proposes a novel methodology for implementing rainfall-resilient design for the slope system under rainfall. This approach incorporates the resilience design philosophy and the stability analysis of the slope system under rainfall. The stability analysis is solved by combining saturated–unsaturated seepage analysis and the Morgenstern–Price method. A design-oriented resilient criterion, including absorption and recovery measures, is proposed for the sound design of the slope system. An illustrative case of rainfall-resilient design for the slope system in the coastal area of Southeast China is presented. The spatial variability of geomaterial properties is considered to identify critical time points for recovery strategies. The resilience characteristics containing the absorption capacity, restorative capacity, and recovery time of eight restorative strategies for the resilience enhancement of the slope system were analyzed. The traditional design criteria were considered for comparison to verify the effectiveness of the proposed rainfall-resilient design method. The rainfall-resilient design can provide critical support to landslide mitigation in the coastal area of Southeast China

Functional Conservation of <i>Cis</i>-Regulatory Elements of Heat-Shock Genes over Long Evolutionary Distances

Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple “on-off” response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly.</p

The complete chloroplast genome of Verbascum chinense (L.) Santapau

Verbascum chinense is a perennial plant in the Scrophulariaceae family that is traditionally used as sedative, astringent, febrifuge, and for skin eruptions. Here, we determined the complete chloroplast(cp) genome sequence for V. chinense using genome skimming sequencing. The cp genome was 153,618 bp and consisted of a large single copy (LSC) region (84,834 bp), a small single copy (SSC) region (17,884 bp), and two inverted repeats (IRs) (25,450 bp). It encodes 114 unique genes, including 80 protein-coding genes, four rRNAs, and 30 tRNAs. Phylogenetic analysis indicates that V. chinense exhibits a closer relationship with V. phoeniceum rather than Scrophularia

Self-adaptive manifold discriminant analysis for feature extraction from hyperspectral imagery

Traditional manifold learning methods generally include a single projection stage that maps high-dimensional data into lower-dimensional space. However, these methods cannot guarantee that the projection matrix is optimal for classification, which limits their practical application. To address this issue, we propose a two-stage projection matrix optimization model termed self-adaptive manifold discriminant analysis (SAMDA). In pre-training projection stage, SAMDA obtains an initial projection matrix by constructing an interclass graph and an intraclass graph under the graph embedding (GE) framework. In weight optimization stage, a maximal manifold margin criterion is developed to further optimize the weights of projection matrix by feature similarity. A self-adaptive optimization process is introduced to increase the margins among different manifolds in low-dimensional space and extract discriminant features that are beneficial to classification. Experimental results on PaviaU, Indian Pines and Heihe data sets demonstrate that the proposed SAMDA method can achieve better classification results than some state-of-the-art methods

The Combination of Cell Cultured Technology and In Silico Model to Inform the Drug Development

Human-derived in vitro models can provide high-throughput efficacy and toxicity data without a species gap in drug development. Challenges are still encountered regarding the full utilisation of massive data in clinical settings. The lack of translated methods hinders the reliable prediction of clinical outcomes. Therefore, in this study, in silico models were proposed to tackle these obstacles from in vitro to in vivo translation, and the current major cell culture methods were introduced, such as human-induced pluripotent stem cells (hiPSCs), 3D cells, organoids, and microphysiological systems (MPS). Furthermore, the role and applications of several in silico models were summarised, including the physiologically based pharmacokinetic model (PBPK), pharmacokinetic/pharmacodynamic model (PK/PD), quantitative systems pharmacology model (QSP), and virtual clinical trials. These credible translation cases will provide templates for subsequent in vitro to in vivo translation. We believe that synergising high-quality in vitro data with existing models can better guide drug development and clinical use

Mitochondrial Ca2+ oscillation induces mitophagy initiation through the PINK1-Parkin pathway

Abstract Dysregulation of the PINK1/Parkin-mediated mitophagy is essential to Parkinson’s disease. Although important progress has been made in previous researches, the biochemical reagents that induce global and significant mitochondrial damage may still hinder deeper insights into the mechanisms of mitophagy. The origin of PINK1/Parkin pathway activation in mitophagy remains elusive. In this study, we develop an optical method, ultra-precise laser stimulation (UPLaS) that delivers a precise and noninvasive stimulation onto a submicron region in a single mitochondrial tubular structure. UPLaS excites localized mitochondrial Ca2+ (mitoCa2+) oscillations with tiny perturbation to mitochondrial membrane potential (MMP) or mitochondrial reactive oxygen species. The UPLaS-induced mitoCa2+ oscillations can directly induce PINK1 accumulation and Parkin recruitment on mitochondria. The Parkin recruitment by UPLaS requires PINK1. Our results provide a precise and noninvasive technology for research on mitophagy, which stimulates target mitochondria with little damage, and reveal mitoCa2+ oscillation directly initiates the PINK1-Parkin pathway for mitophagy without MMP depolarization