Mining characteristic relations bind to RNA secondary structures

The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. It has been recognized that there is an abundance of functional structures with frameshifting, regulation of translation, and splicing functions. However, the inherent signal for secondary structures is weak and generally not straightforward due to complex interleaving substrings. This makes it difficult to explore their potential functions from various structure data. Our approach, based on a collection of predicted RNA secondary structures, allows us to efficiently capture interesting characteristic relations in RNA and bring out the top-ranked rules for specified association groups. Our results not only point to a number of interesting associations and include a brief biological interpretation to them. It assists biologists in sorting out the most significant characteristic structure patterns and predicting structurefunction relationships in RNA

Discovery of structural and functional features in RNA pseudoknots

An RNA pseudoknot consists of nonnested double-stranded stems connected by single-stranded loops. There is increasing recognition that RNA pseudoknots are one of the most prevalent RNA structures and fulfill a diverse set of biological roles within cells, and there is an expanding rate of studies into RNA pseudoknotted structures as well as increasing allocation of function. These not only produce valuable structural data but also facilitate an understanding of structural and functional characteristics in RNA molecules. PseudoBase is a database providing structural, functional, and sequence data related to RNA pseudoknots. To capture the features of RNA pseudoknots, we present a novel framework using quantitative association rule mining to analyze the pseudoknot data. The derived rules are classified into specified association groups regarding structure, function, and category of RNA pseudoknots. The discovered association rules assist biologists in filtering out significant knowledge of structure-function and structure-category relationships. A brief biological interpretation to the relationships is presented, and their potential correlations with each other are highlighted.<br /

Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle

BACKGROUND: AMP-activated protein kinase (AMPK) has emerged as a significant signaling intermediary that regulates metabolisms in response to energy demand and supply. An investigation into the degree of activation and deactivation of AMPK subunits under exercise can provide valuable data for understanding AMPK. In particular, the effect of AMPK on muscle cellular energy status makes this protein a promising pharmacological target for disease treatment. As more AMPK regulation data are accumulated, data mining techniques can play an important role in identifying frequent patterns in the data. Association rule mining, which is commonly used in market basket analysis, can be applied to AMPK regulation. RESULTS: This paper proposes a framework that can identify the potential correlation, either between the state of isoforms of α, β and γ subunits of AMPK, or between stimulus factors and the state of isoforms. Our approach is to apply item constraints in the closed interpretation to the itemset generation so that a threshold is specified in terms of the amount of results, rather than a fixed threshold value for all itemsets of all sizes. The derived rules from experiments are roughly analyzed. It is found that most of the extracted association rules have biological meaning and some of them were previously unknown. They indicate direction for further research. CONCLUSION: Our findings indicate that AMPK has a great impact on most metabolic actions that are related to energy demand and supply. Those actions are adjusted via its subunit isoforms under specific physical training. Thus, there are strong co-relationships between AMPK subunit isoforms and exercises. Furthermore, the subunit isoforms are correlated with each other in some cases. The methods developed here could be used when predicting these essential relationships and enable an understanding of the functions and metabolic pathways regarding AMPK

Hydrological variations in central China over the past millennium and their links to the Tropic Pacific and North Atlantic Oceans

Variations of precipitation, aka the Meiyu rain, in East Asian summer monsoon (EASM) domain during the last millennium could help enlighten the hydrological response to future global warming. Here we present a precisely dated and highly resolved stalagmite δ18O record from the Yongxing Cave, central China. Our new record, combined with a previously published one from the same cave, indicates that the Meiyu rain has changed dramatically in association with the global temperature change. In particular, our record shows that the Meiyu rain has been weakened during the Medieval Climate Anomaly (MCA), but intensified during the Little Ice Age (LIA). During the Current Warm Period (CWP), our record indicates a similar weakening of the Meiyu rain. Furthermore, during the MCA and CWP, our records show that the atmospheric precipitation is similarly wet in northern China and similarly dry in central China, but relatively wet during the CWP in southern China. This spatial discrepancy indicates a complicated localized response of the regional precipitation to the anthropogenic forcing. The weakened (intensified) Meiyu rain during the MCA (LIA) matches well with the warm (cold) phases of Northern Hemisphere surface air temperature. This Meiyu rain pattern also corresponds well with the climatic conditions over the Tropical Indo-Pacific warm pool. On the other hand, our record shows a strong association with the North Atlantic climate as well. The reduced (increased) Meiyu rain correlates well with positive (negative) phases of North Atlantic Oscillation. In addition, our record links well with the strong (weak) Atlantic meridional overturning circulation during the MCA (LIA) period. All above-mentioned localized correspondences and remote teleconnections on decadal to centennial timescales indicate that the Meiyu rain is coupled closely with oceanic processes in the Tropical Pacific and North Atlantic Oceans during the MCA and LIA

Auricle shaping using 3D printing and autologous diced cartilage.

ObjectiveTo reconstruct the auricle using a porous, hollow, three-dimensional (3D)-printed mold and autologous diced cartilage mixed with platelet-rich plasma (PRP).MethodsMaterialise Magics v20.03 was used to design a 3D, porous, hollow auricle mold. Ten molds were printed by selective laser sintering with polyamide. Cartilage grafts were harvested from one ear of a New Zealand rabbit, and PRP was prepared using 10 mL of auricular blood from the same animal. Ear cartilage was diced into 0.5- to 2.0-mm pieces, weighed, mixed with PRP, and then placed inside the hollow mold. Composite grafts were then implanted into the backs of respective rabbits (n = 10) for 4 months. The shape and composition of the diced cartilage were assessed histologically, and biomechanical testing was used to determine stiffness.ResultsThe 3D-printed auricle molds were 0.6-mm thick and showed connectivity between the internal and external surfaces, with round pores of 0.1 to 0.3 cm. After 4 months, the diced cartilage pieces had fused into an auricular shape with high fidelity to the anthropotomy. The weight of the diced cartilage was 5.157 ± 0.230 g (P &gt; 0.05, compared with preoperative). Histological staining showed high chondrocyte viability and the production of collagen II, glycosaminoglycans, and other cartilaginous matrix components. In unrestricted compression tests, auricle stiffness was 0.158 ± 0.187 N/mm, similar to that in humans.ConclusionAuricle grafts were constructed successfully through packing a 3D-printed, porous, hollow auricle mold with diced cartilage mixed with PRP. The auricle cartilage contained viable chondrocytes, appropriate extracellular matrix components, and good mechanical properties.Levels of evidenceNA. Laryngoscope, 129:2467-2474, 2019

Fabrication of Three-Dimensional Concave or Convex Shell Structures with Shell Elements at Micrometer Resolution in SU-8

This chapter presents a photo-lithographically-based technology for mass production of three-dimensional (3D) micro-structures with shell elements. In this technology, shell elements are photo-lithographically fabricated at micron or sub-micron resolution by illuminating with ultraviolet light radiating an ultraviolet light beam onto UV-opaque SU-8 monomer. The technology does not require any steps involving micro-injection molding or micro-stereolithography. Several prototypes have been fabricated to demonstrate the feasibility of this technology

A framework for merging inconsistent beliefs in security protocol analysis

This paper proposes a framework for merging inconsistent beliefs in the analysis of security protocols. The merge application is a procedure of computing the inferred beliefs of message sources and resolving the conflicts among the sources. Some security properties of secure messages are used to ensure the correctness of authentication of messages. Several instances are presented, and demonstrate our method is useful in resolving inconsistent beliefs in secure messages. <br /