Motif Size Research Articles

HI(Hospital identity)요소 활용 치유적 환자복 디자인 개발 : 경희대학교병원 환자복을 중심으로

This study aims to develop a patient clothing design that not only reflects the hospital identity, but also considers therapeutic aspects that could enhance patient"s psychological stability and convenience. The research method included case analysis and the development of a design for patient clothing that reflected the hospital identity. The results are as follows. Firstly, by analyzing existing cases of patient clothing design that reflect hospitals’ identity, it was evident that many patient clothes were directly patterned using elements of hospital identity. For example, there were many vertical lines or parallel arrangement patterns that emphasized hospital identities. In some cases, pattern designs were developed by extracting some elements of the hospital identity that related to the vision or mission of the affiliated medical institution, or by combining motifs that reflected healing aspects. However, due to the specificity of patient clothing design, there were few differentiated shape designs. Secondly, based on the results of the case analysis, the patient clothing design was developed as follows. Among elements of the hospital identity, the healing aspect was illustrated through a nature image motif. Various sizes of motifs were arranged all-over to convey vitality. The motifs were arranged freely but followed eight directions at intervals of 45 degrees to create a sense of stability. The spaces between the motifs were arranged at leisurely intervals to create a sense of comfort. The shape was made to reduce potential patient anxiety about exposure and to ensure their comfort. The color was selected by considering the healing aspect. Through this study, it has been determined that even if a hospital identity, – which has been used as a service design for a medical institution - was introduced into patient clothing, the patient clothing can provide comfort to a patient when combined with the healing aspect.

Discovery of network motifs based on induced subgraphs using a dynamic expansion tree

Biological networks are powerful representations of topological features in biological systems. Finding network motifs in biological networks is a computationally hard problem due to their huge size and abrupt increase of search space with the increase of motif size. Motivated by the computational challenges of network motif discovery and considering the importance of this topic, an efficient and scalable network motif discovery algorithm based on induced subgraphs in a dynamic expansion tree is proposed. This algorithm uses a pruning strategy to overcome the space limitation of the static expansion tree. The proposed algorithm can identify large network motifs up to size 15 by significantly reducing the computationally expensive subgraph isomorphism checks. Further, the present work avoids the unnecessary growth of patterns that do not have any statistical significance. The runtime performance of the proposed algorithm outperforms most of the existing algorithms for large network motifs.

Preferential Screen Resolution Setting in Adobe Photoshop for Actual Motif Print Sizes in Textile Design

The use of Adobe Photoshop, a graphic design software, as a tool in textile designing has come to stay. There are numerous advantages derived from this software in textile designing, even though it is a graphic design program. Despite the numerous design advantages, the software presents technical constraints to textile design students and beginners in its visual representation of motif and texture pattern sizes. This problem of screen resolution settings affected the actual view of motif print sizes and texture patterns when printed in hard copy in relation to the soft copy for screen development. Furthermore, it affects design details during colour separation, screen copying and developing, and printing. The study employed the practiced-led research method in its approach to explore the possibilities of finding preferential screen resolution settings suitable for textile designing in Adobe Photoshop. The study revealed adjustments or modifications of the view-preferential settings of the program to ascertain the required screen resolution settings for textile motif and texture pattern sizes. This revelation bridged the visual differences between the soft copy and hard copy sizes of motif and texture pattern during and after designing. The research recommends that textile design students and beginners, as a prerequisite, adjust the view-preferential settings of Adobe Photoshop to obtain accurate motif and texture pattern sizes during and after designing.

Fine tuning of specific surface area and CO2 capture performance in hyper-cross-linked heterocyclic networks with tetrazinyl linker

Abstract We herein report the synthesis of three different building blocks with pyrrolyl (Py), indolyl (In), and carbazolyl (Cz) motifs connecting by tetrazinyl linker. The corresponding hyper-cross-linked networks (HCTPy, HCTIn, and HCTCz) have been synthesized by the Friedel-Crafts knitting strategy using both Lewis acid (FeCl3 and AlCl3) and organic Bronsted acid (CF3SO3H) as the catalysts. It is demonstrated that the specific surface area (SSA) of the resultant HCTPy, HCTIn, and HCTCz networks can be finely tuned by the size of reactive motifs, in which the SSA increases with the size of reactive motifs and follows the order of HCTPy

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole-genome sequencing to perform association analysis between copy number of ∼70,000 VNTRs (motif size ≥ 10bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using an independent cohort, we validated 73%-80% of signals observed in the two discovery cohorts, while allelic analysis of VNTR length and CpG methylation in 30 Oxford Nanopore genomes gave additional support for mVNTR loci, thus providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we define sets of VNTRs that show highly divergent copy numbers among human populations and show that these are enriched for regulatory effects and preferentially associate with genes that have been linked with human phenotypes through GWASs. Our study provides strong evidence supporting functional variation at thousands of VNTRs and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.

An extended scale-free network evolution model based on global coupling motif embedding

The BA scale-free network evolution model assumes that one node enters at every unit time, which does not adequately reflect team entries that usually occur during the evolution of many practical networks, i.e. the phenomenon of motif embedment. Unfortunately, there are no specific studies on how the motif embedment mechanism affects the degree distribution of networks. In order to solve this problem, an extended scale-free network evolution model with global coupling motif embedment and with the motif size obeying an arbitrary discrete probability distribution (called the MEEBA model for short) is formulated with the help of the ‘motif’ concept. Using the Markov chain method, the accurate analytical expression of the network degree distribution of the MEEBA model is obtained and the correctness of the equation is verified through comparisons with numerical simulation results. The study results show that the right tail of the degree distribution of the MEEBA model still has a power-law behavior, while its left tail reflects the horse-head-like shapes of the degree distribution of many real networks. Furthermore, the power-law exponent and the horse-head shapes are both related to the distribution of the motif size. When the motif size follows a one-point distribution, the network degree distribution of the MEEBA model degenerates into a two-parameter Waring-like distribution and its horse-head shapes disappear. In particular, if the expectation of the one-point distribution is 1, the MEEBA model further degenerates to the BA model. Finally, the practicality and effectiveness of the MEEBA model are verified through a case study.

Genetically Encoded and Biologically Produced All‐DNA Nanomedicine Based on One‐Pot Assembly of DNA Dendrimers for Targeted Gene Regulation

AbstractAll‐DNA nanomedicines have emerged as potential anti‐tumor drugs. DNA nanotechnology provides all‐DNA nanomedicines with unlimited possibilities in controlling the diversification of size, shape, and loads of the therapeutic motifs. As DNA is a biological polymer, it is possible to genetically encode and produce the all‐DNA nanomedicines in living bacteria. Herein, DNA‐dendrimer‐based nanomedicines are designed to adapt to the biological production, which is constructed by the flexible 3‐arm building blocks to enable a highly efficient one‐pot DNA assembly. For the first time, a DNA nanomedicine, D4‐3‐As‐DzSur, is successfully genetically encoded, biotechnologically produced, and directly self‐assembled. The performance of the biologically produced D4‐3‐As‐DzSur in targeted gene regulation has been confirmed by in vitro and in vivo studies. The biological production capability will fulfill the low‐cost and large‐scale production of all‐DNA nanomedicines and promote clinical applications.

Genetically Encoded and Biologically Produced All-DNA Nanomedicine Based on One-Pot Assembly of DNA Dendrimers for Targeted Gene Regulation.

All-DNA nanomedicines have emerged as potential anti-tumor drugs. DNA nanotechnology provides all-DNA nanomedicines with unlimited possibilities in controlling the diversification of size, shape, and loads of the therapeutic motifs. As DNA is a biological polymer, it is possible to genetically encode and produce the all-DNA nanomedicines in living bacteria. Herein, DNA-dendrimer-based nanomedicines are designed to adapt to the biological production, which is constructed by the flexible 3-arm building blocks to enable a highly efficient one-pot DNA assembly. For the first time, a DNA nanomedicine, D4-3-As-DzSur, is successfully genetically encoded, biotechnologically produced, and directly self-assembled. The performance of the biologically produced D4-3-As-DzSur in targeted gene regulation has been confirmed by in vitro and in vivo studies. The biological production capability will fulfill the low-cost and large-scale production of all-DNA nanomedicines and promote clinical applications.

In vitro selections with RNAs of variable length converge on a robust catalytic core.

In vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.

Parallelization of network motif discovery using star contraction

Network motifs are widely used to uncover structural design principles of complex networks. Current sequential network motif discovery algorithms become inefficient as motif size grows, thus parallelization methods have been proposed in the literature. In this study, we use star contraction algorithm to partition complex networks efficiently for parallel discovery of network motifs. We propose two new heuristics to make star contraction more suitable for partitioning of complex networks. The effectiveness of our partitioning strategies is verified using the ESU algorithm for subgraph counting. We also propose a ghost vertices detection algorithm to ensure that all the motifs located in multiple parts are exactly found. We implement our method using MPI libraries and tested on real-life complex networks of different domains. We compared speedups of star contraction algorithm with speedups of other graph partitioning algorithms. Our algorithm obtained better speedups than those of other partitioning algorithms for most cases. Our algorithm provides significant speedups when compared to sequential ESU algorithm allowing discovery of larger network motifs.

Review of tools and algorithms for network motif discovery in biological networks.

Network motifs are recurrent and over‐represented patterns having biological relevance. This is one of the important local properties of biological networks. Network motif discovery finds important applications in many areas such as functional analysis of biological components, the validity of network composition, classification of networks, disease discovery, identification of unique subunits etc. The discovery of network motifs is a computationally challenging task due to the large size of real networks, and the exponential increase of search space with respect to network size and motif size. This problem also includes the subgraph isomorphism check, which is Nondeterministic Polynomial (NP)‐complete. Several tools and algorithms have been designed in the last few years to address this problem with encouraging results. These tools and algorithms can be classified into various categories based on exact census, mapping, pattern growth, and so on. In this study, critical aspects of network motif discovery, design principles of background algorithms, and their functionality have been reviewed with their strengths and limitations. The performances of state‐of‐art algorithms are discussed in terms of runtime efficiency, scalability, and space requirement. The future scope, research direction, and challenges of the existing algorithms are presented at the end of the study.

Genome-wide detection of tandem DNA repeats that are expanded in autism.

Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.

Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G-Quadruplexes.

Infrared spectroscopy detects the formation of G-quadruplexes in guanine-rich nucleic acid sequences through shifts in the guanine C=O stretch mode. Here, we use ultrafast 2D infrared (IR) spectroscopy and isotope substitution to show that these shifts arise from vibrational delocalization among stacked G-quartets. This provides a direct measure of the sizes of locally ordered motifs in heterogeneous samples with substantial disordered regions. We find that parallel-stranded, potassium-bound DNA G-quadruplexes are limited to five consecutive G-quartets and 3-4 consecutive layers are preferred for longer polyguanine tracts. The resulting potassium-dependent G-quadruplex assembly landscape reflects the polyguanine tract lengths found in genomes, the ionic conditions prevalent in healthy mammalian cells, and the onset of structural disorder in disease states. Our study describes spectral markers that can be used to probe other G-quadruplex structures and provides insight into the fundamental limits of their formation in biological and artificial systems.

Promiscuity and specificity of eukaryotic glycosyltransferases.

Glycosyltransferases are a large family of enzymes responsible for covalently linking sugar monosaccharides to a variety of organic substrates. These enzymes drive the synthesis of complex oligosaccharides known as glycans, which play key roles in inter-cellular interactions across all the kingdoms of life; they also catalyze sugar attachment during the synthesis of small-molecule metabolites such as plant flavonoids. A given glycosyltransferase enzyme is typically responsible for attaching a specific donor monosaccharide, via a specific glycosidic linkage, to a specific moiety on the acceptor substrate. However these enzymes are often promiscuous, able catalyze linkages between a variety of donors and acceptors. In this review we discuss distinct classes of glycosyltransferase promiscuity, each illustrated by enzymatic examples from small-molecule or glycan synthesis. We highlight the physical causes of promiscuity, and its biochemical consequences. Structural studies of glycosyltransferases involved in glycan synthesis show that they make specific contacts with ‘recognition motifs’ that are much smaller than the full oligosaccharide substrate. There is a wide range in the sizes of glycosyltransferase recognition motifs: highly promiscuous enzymes recognize monosaccharide or disaccharide motifs across multiple oligosaccharides, while highly specific enzymes recognize large, complex motifs found on few oligosaccharides. In eukaryotes, the localization of glycosyltransferases within compartments of the Golgi apparatus may play a role in mitigating the glycan variability caused by enzyme promiscuity.

Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics.

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

Implementation of Art and Technology in Batik Purwakarta

Indonesia is dominated by cities that have a history of batik, but Purwakarta does not have a history of batik. But thanks to the persistence of policy holders, Purwakarta currently has batik obtained by elevating the local wisdom of the city of Purwakarta. After surveys and interviews, several batik motifs were designed. The batik motif shape, size and position will be studied which will formulate mathematical equations based on basic geometric shapes such as circles, arches, lines, rectangles, which are implemented into the form of computer graphics (turtles) graph and explained in the form of an algorithm (pseudocode) computer programming to make autogenerative motifs on Purwakarta batik that did not exist before. Batik design is inspired by food and tourist locations which form the basis of the formation of typical Purwakarta batik motifs. Jatiluhur Dam, Datura Metel L. Flower, Sate Maranggi, Mangosteen Fruit is a local wisdom owned by the city of Purwakarta. The results of the morning glory batik design and Jatiluhur dew through mathematical and turtle charts are then formulated so that the batik motif design can be saved by documenting the mathematical equation or the pseudocode of the batik motif. With the results of digital motifs, the process of repeating patterns, duplicating and storing data becomes easier.

Micro/nano-structured TiO2 surface with dual-functional antibacterial effects for biomedical applications

Implant-associated infections are generally difficult to cure owing to the bacterial antibiotic resistance which is attributed to the widespread usage of antibiotics. Given the global threat and increasing influence of antibiotic resistance, there is an urgent demand to explore novel antibacterial strategies other than using antibiotics. Recently, using a certain surface topography to provide a more persistent antibacterial solution attracts more and more attention. However, the clinical application of biomimetic nano-pillar array is not satisfactory, mainly because its antibacterial ability against Gram-positive strain is not good enough. Thus, the pillar array should be equipped with other antibacterial agents to fulfill the bacteriostatic and bactericidal requirements of clinical application. Here, we designed a novel model substrate which was a combination of periodic micro/nano-pillar array and TiO2 for basically understanding the topographical bacteriostatic effects of periodic micro/nano-pillar array and the photocatalytic bactericidal activity of TiO2. Such innovation may potentially exert the synergistic effects by integrating the persistent topographical antibacterial activity and the non-invasive X-ray induced photocatalytic antibacterial property of TiO2 to combat against antibiotic-resistant implant-associated infections. First, to separately verify the topographical antibacterial activity of TiO2 periodic micro/nano-pillar array, we systematically investigated its effects on bacterial adhesion, growth, proliferation, and viability in the dark without involving the photocatalysis of TiO2. The pillar array with sub-micron motif size can significantly inhibit the adhesion, growth, and proliferation of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Such antibacterial ability is mainly attributed to a spatial confinement size-effect and limited contact area availability generated by the special topography of pillar array. Moreover, the pillar array is not lethal to S. aureus and E. coli in 24 h. Then, the X-ray induced photocatalytic antibacterial property of TiO2 periodic micro/nano-pillar array in vitro and in vivo will be systematically studied in a future work. This study could shed light on the direction of surface topography design for future medical implants to combat against antibiotic-resistant implant-associated infections without using antibiotics.

Relationship Between G-Quadruplex Sequence Composition in Viruses and Their Hosts.

A subset of guanine-rich nucleic acid sequences has the potential to fold into G-quadruplex (G4) secondary structures, which are functionally important for several biological processes, including genome stability and regulation of gene expression. Putative quadruplex sequences (PQSs) G3+N1–7G3+N1–7G3+N1–7G3+ are widely found in eukaryotic and prokaryotic genomes, but the base composition of the N1-7 loops is biased across species. Since the viruses partially hijack their hosts’ cellular machinery for proliferation, we examined the PQS motif size, loop length, and nucleotide compositions of 7370 viral genome assemblies and compared viral and host PQS motifs. We studied seven viral taxa infecting five distant eukaryotic hosts and created a resource providing a comprehensive view of the viral quadruplex motifs. Overall, short-looped PQSs are predominant and with a similar composition across viral taxonomic groups, albeit subtle trends emerge upon classification by hosts. Specifically, there is a higher frequency of pyrimidine loops in viruses infecting animals irrespective of the viruses’ genome type. This observation is confirmed by an in-depth analysis of the Herpesviridae family of viruses, which showed a distinctive accumulation of thermally stable C-looped quadruplexes in viruses infecting high-order vertebrates. The occurrence of viral C-looped G4s, which carry binding sites for host transcription factors, as well as the high prevalence of viral TTA-looped G4s, which are identical to vertebrate telomeric motifs, provide concrete examples of how PQSs may help viruses impinge upon, and benefit from, host functions. More generally, these observations suggest a co-evolution of virus and host PQSs, thus underscoring the potential functional significance of G4s.

Relaxing Dense Scatter Plots with Pixel-Based Mappings.

Scatter plots are the most commonly employed technique for the visualization of bivariate data. Despite their versatility and expressiveness in showing data aspects, such as clusters, correlations, and outliers, scatter plots face a main problem. For large and dense data, the representation suffers from clutter due to overplotting. This is often partially solved with the use of density plots. Yet, data overlap may occur in certain regions of a scatter or density plot, while other regions may be partially, or even completely empty. Adequate pixel-based techniques can be employed for effectively filling the plotting space, giving an additional notion of the numerosity of data motifs or clusters. We propose the Pixel-Relaxed Scatter Plots, a new and simple variant, to improve the display of dense scatter plots, using pixel-based, space-filling mappings. Our Pixel-Relaxed Scatter Plots make better use of the plotting canvas, while avoiding data overplotting, and optimizing space coverage and insight in the presence and size of data motifs. We have employed different methods to map scatter plot points to pixels and to visually present this mapping. We demonstrate our approach on several synthetic and realistic datasets, and we discuss the suitability of our technique for different tasks. Our conducted user evaluation shows that our Pixel-Relaxed Scatter Plots can be a useful enhancement to traditional scatter plots.

Characterization of Duck (Anas platyrhynchos) Short Tandem Repeat Variation by Population-Scale Genome Resequencing.

Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-scale analysis of STR variation using genome resequencing in mallard and Pekin duck. Our analysis provided the first genome-wide duck STR reference including 198,022 STR loci with motif size of 2–6 base pairs. We observed a relatively uneven distribution of STRs in different genomic regions, which indicates that the occurrence of STRs in duck genome is not random, but undergoes a directional selection pressure. Using genome resequencing data of 23 mallard and 26 Pekin ducks, we successfully identified 89,891 polymorphic STR loci. Intensive analysis of this dataset suggested that shorter repeat motif, longer reference tract length, higher purity, and residing outside of a coding region are all associated with an increase in STR variability. STR genotypes were utilized for population genetic analysis, and the results showed that population structure and divergence patterns among population groups can be efficiently captured. In addition, comparison between Pekin duck and mallard identified 3,122 STRs with extremely divergent allele frequency, which overlapped with a set of genes related to nervous system, energy metabolism and behavior. The evolutionary analysis revealed that the genes containing divergent STRs may play important roles in phenotypic changes during duck domestication. The variation analysis of STRs in population scale provides valuable resource for future study of genetic diversity and genome evolution in duck.