Multimodal estimation of distribution algorithms

Taking the advantage of estimation of distribution algorithms (EDAs) in preserving high diversity, this paper proposes a multimodal EDA. Integrated with clustering strategies for crowding and speciation, two versions of this algorithm are developed, which operate at the niche level. Then these two algorithms are equipped with three distinctive techniques: 1) a dynamic cluster sizing strategy; 2) an alternative utilization of Gaussian and Cauchy distributions to generate offspring; and 3) an adaptive local search. The dynamic cluster sizing affords a potential balance between exploration and exploitation and reduces the sensitivity to the cluster size in the niching methods. Taking advantages of Gaussian and Cauchy distributions, we generate the offspring at the niche level through alternatively using these two distributions. Such utilization can also potentially offer a balance between exploration and exploitation. Further, solution accuracy is enhanced through a new local search scheme probabilistically conducted around seeds of niches with probabilities determined self-adaptively according to fitness values of these seeds. Extensive experiments conducted on 20 benchmark multimodal problems confirm that both algorithms can achieve competitive performance compared with several state-of-the-art multimodal algorithms, which is supported by nonparametric tests. Especially, the proposed algorithms are very promising for complex problems with many local optima

PinX1 regulation of telomerase activity and apoptosis in nasopharyngeal carcinoma cells

<p>Abstract</p> <p>Background</p> <p>Human interacting protein X1 (PinX1) has been identified as a critical telomerase inhibitor and proposed to be a putative tumor suppressor gene. Loss of PinX1 has been found in a large variety of malignancies, however, its function in inhibiting telomerase activity of tumor cells is not well documented. Here we show that PinX1 is essential for down-regulation telomerase activity of nasopharyngeal carcinoma.</p> <p>Methods</p> <p>Expression vectors of human PinX1 (pEGFP-C3-PinX1) and its small interfering RNA (PinX1-FAM-siRNA) were constructed and transfected into NPC. Their effects on mRNA of telomerase catalytic subunit (hTERT), telomerase activity, cell proliferation, cell migration, wound healing, cell cycles and apoptosis were examined using semi-quantitative RT-PCR, stretch PCR, MTT assay, Transwell, scratch assay and flow cytometry, respectively.</p> <p>Results</p> <p>Transfection of pEGFP-C3-PinX1 and PinX1-FAM-siRNA increased and reduced PinX1 mRNA by 1.6-fold and 70%, respectively. Over-expression of PinX1 decreased hTERT mRNA by 21%, reduced telomerase activity, inhibited cell growth, migration and wound healing ability, arrested cells in G0/G1 phase, and increased apoptotic index. In contrast, down-regulation of PinX1 did not alter the above characteristics.</p> <p>Conclusions</p> <p>PinX1 may play important roles in NPC proliferation, migration and apoptosis and has application potential in tumor-targeted gene therapy.</p

TransGate: Knowledge Graph Embedding with Shared Gate Structure

Embedding knowledge graphs (KGs) into continuous vector space is an essential problem in knowledge extraction. Current models continue to improve embedding by focusing on discriminating relation-specific information from entities with increasingly complex feature engineering. We noted that they ignored the inherent relevance between relations and tried to learn unique discriminate parameter set for each relation. Thus, these models potentially suffer from high time complexity and large parameters, preventing them from efficiently applying on real-world KGs. In this paper, we follow the thought of parameter sharing to simultaneously learn more expressive features, reduce parameters and avoid complex feature engineering. Based on gate structure from LSTM, we propose a novel model TransGate and develop shared discriminate mechanism, resulting in almost same space complexity as indiscriminate models. Furthermore, to develop a more effective and scalable model, we reconstruct the gate with weight vectors making our method has comparative time complexity against indiscriminate model. We conduct extensive experiments on link prediction and triplets classification. Experiments show that TransGate not only outperforms state-of-art baselines, but also reduces parameters greatly. For example, TransGate outperforms ConvE and RGCN with 6x and 17x fewer parameters, respectively. These results indicate that parameter sharing is a superior way to further optimize embedding and TransGate finds a better trade-off between complexity and expressivity

Interaction of miR-181b and IFNA1 Polymorphisms on the Risk of Systemic Lupus Erythematosus

Introduction. A previous work has discovered that chromosome 1q32 locus linked to the risk of systemic lupus erythematosus (SLE) and miR-181b located on the susceptibility site with downregulation inversely correlating to its target molecular interferon alpha 1 (IFNA1). The purpose of this study was to investigate the association of miR-181b and IFNA1 polymorphisms with IS risk. Methods. The miR-181b rs322931, IFNA1 rs1332190, and rs10811543 were genotyped using a Multiplex SNaPshot assay. miR-181b expression levels in plasma of SLE patients and controls were analyzed using quantitative PCR. Results. The rs322931 CT, CT/TT, and T allele exerted an increased trend of SLE risk (CT vs. CC: adjusted OR=1.71, 95% CI 1.16-2.50, P=0.01; CT/TT vs. CC: adjusted OR=1.45, 95% CI 1.08-1.95, P=0.01; T vs. C: adjusted OR=1.38, 95% CI 1.07-1.79, P=0.01). Combined genotypes of the rs322931 CT/TT+rs1332190 TT and the rs322931 CC+rs10811543 AG/AA also revealed an increased risk of SLE. Gene-gene interaction analysis showed that a three-locus model consisting of rs322931, rs1332190, and rs10811543 attributed an increased risk of SLE. Further genotype-phenotype analysis revealed that rs322931 CT/TT carriers displayed lower levels of miR-181b. Conclusions. These findings indicate that the miR-181b rs322931 may be singly and jointly responsible for the etiology of SLE by altering miR-181b expression

A new species and new records species of Pluteus from Xinjiang Uygur Autonomous Region, China

Xinjiang Uyghur Autonomous Region in China embraces a unique geographical and ecological environment, and the macrofungi represent a rich resource. However, few studies on the genus Pluteus have been reported from Xinjiang. In 2021, the macrofungal resources in Xinjiang were surveyed, and 10 specimens belonging to the genus Pluteus were collected. Based on the morphological study and molecular analysis, three species were recognized, P. aletaiensis, P. brunneidiscus, and P. hongoi. Pluteus aletaiensis is proposed as a new species. It is characterized by its bright yellow lamellae and stipe, brittle texture, subfusiform to vesicular pleurocystidia, with short pedicels to broadly lageniform to obtuse at apices, a hymeniderm pileipellis, containing dark brown intracellular pigment, and it grows on the ground. Pluteus brunneidiscus, a new record to China, is characterized by uneven, smooth, grayish brown to brown pileus, with an entire margin, and pointed or flatter apices intermediate cystidia, without apical hooks. Pluteus hongoi, a new record to Xinjiang Uyghur Autonomous Region, China, is characterized by the apical hook’s structure (commonly bifid) of pleurocystidia. The nuclear internal transcribed spacer (nrITS) and translation elongation factor 1-alpha (TEF1-a) region were used for the molecular analysis. Phylogenetic trees were constructed using both the maximum likelihood analysis (ML) and Bayesian inference (BI). Detailed descriptions of the three species are presented herein. Finally, a key to the list of eight species of the genus Pluteus knew from Xinjiang is provided

Genesis, classification, and evaluation method of diagenetic facies

Based on the controlling of diagenesis and diagenetic facies on reservoir development, this article discusses the formation, classification, and evaluation of diagenetic facies and its application and significance in petroleum exploration. For constructive diagenetic facies such as clastic rock, carbonate rock, and igneous rock, eight kinds of genetic mechanisms are developed, including dissolution of organic acid, dolomitization, and so on. Nine constructive diagenetic facies and seven destructive diagenetic facies are classified. A naming scheme for diagenetic facies is proposed reflecting lithology, diagenesis, porosity, and permeability, that is, “porosity and permeability level + rock type + diagenesis type”. Diagenetic facies are evaluated synthetically and quantitatively on the basis of sedimentary facies, log facies, seismic facies, rock cores, and thin sections, and “four steps” and “superposition of three charts” are put forward as the methods of evaluation and mapping. Favored reservoirs, “sweet spots”, and lithostratigraphic traps can be predicted according to the distribution of different types of diagenetic facies. The development of the study on diagenetic facies is also discussed in the article. Key words: diagenetic facies, formation mechanism, classification and naming, evaluation method, petroleum exploration, diagenetic stud

Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis

<div><p>Objective</p><p>Rheumatoid arthritis (RA) is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations.</p><p>Methods</p><p>Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects). For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected ‘highly verified’ genes were measured by ELISA among our in-house RA cases and controls.</p><p>Results</p><p>A total of 221 RA-associated genes were newly identified by gene-based association study, including 71‘overlapped’, 76 ‘European-specific’ and 74 ‘Asian-specific’ genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 ‘overlapped’ (<i>ABCF1</i>, <i>FLOT1</i>, <i>HLA-F</i>, <i>IER3</i>, <i>TUBB</i>, <i>ZKSCAN4</i>, <i>BTN3A3</i>, <i>HSP90AB1</i>, <i>CUTA</i>, <i>BRD2</i>, <i>HLA-DMA)</i>, 5 ‘European-specific’ <i>(PHTF1</i>, <i>RPS18</i>, <i>BAK1</i>, <i>TNFRSF14</i>, <i>SUOX)</i> and 4 ‘Asian-specific’ (<i>RNASET2</i>, <i>HFE</i>, <i>BTN2A2</i>, <i>MAPK13</i>) genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes <i>FLOT1</i> (P value = 1.70E-02) and <i>HLA-DMA</i> (P value = 4.70E-02) in plasma were significantly different in our in-house samples.</p><p>Conclusion</p><p>Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and detected a long list of overlapped or ethnic specific RA genes. The study not only greatly increases our understanding of genetic susceptibility to RA, but also provides important insights into the ethno-genetic homogeneity and heterogeneity of RA in both ethnicities.</p></div