Selection of aptamers in SELEX process

Ahn, Ji-Young,Kim, Eunkyung,Ryu, Jae-Chun,Kim, Soyoun Springer-Verlag 2009 Toxicology and environmental health sciences Vol.1 No.1

A Sol-Gel-Based Microfluidics System Enhances the Efficiency of RNA Aptamer Selection

Ahn, Ji-Young,Jo, Minjoung,Dua, Pooja,Lee, Dong-ki,Kim, Soyoun Mary Ann Liebert 2011 Oligonucleotides Vol.21 No.2

A Sol-Gel-Integrated Protein Array System for Affinity Analysis of Aptamer-Target Protein Interaction

Ahn, Ji-Young,Kim, Eunkyung,Kang, Jeehye,Kim, Soyoun Mary Ann Liebert 2011 Nucleic acid therapeutics Vol.21 No.3

Sol-gel derived nanoporous compositions for entrapping small molecules and their outlook toward aptamer screening.

Ahn, Ji-Young,Lee, SangWook,Jo, Minjoung,Kang, Jeehye,Kim, Eunkyung,Jeong, Ok Chan,Laurell, Thomas,Kim, Soyoun American Chemical Society 2012 ANALYTICAL CHEMISTRY - Vol.84 No.6

<P>This paper reports for the first time the application of sol-gel microarrays for immobilizing nonsoluble small chemicals (Bisphenol-A; BPA). Also, known problems of sol-gel adhesion to conventional microtiter well plate substrates are circumvented by anchoring the sol-gel microspots to a porous silion surface so-called, PS-SG chips. We confirmed low molecular weight chemical immobilization inside a sol-gel network using fluorescein. BPA and the BPA specific aptamer were utilized as a model pair to verify the affinity specific interaction in the PS-SG selection system. The aptamer interacted specifically with BPA in the sol-gel spots, as shown in microarrays forming the letters 'L', 'U', 'N', and 'D'. Moreover, the bound aptamer was released by heat, recovered, and verified by gel electrophoresis. The developed PS-SG chip platform will be used for screening aptamers against numerous small molecules such as toxins, metabolites, or pesticide residues.</P>

웹디자인 서비스 아웃소싱 도입의 위험요인 연구

안진호 ( Ahn Jin-ho ),김소연 ( Kim Soyoun ) 한국디자인트렌드학회 2009 한국디자인포럼 Vol.24 No.-

기업의 웹서비스가 전문화되고 다양화됨에 따라 서비스로서의 웹디자인 아웃소싱 도입이 활발히 이루어지고 있다. 따라서 본 연구는 웹디자인 서비스를 아웃소싱 도입하려는 의사에 영향을 미치는 세부 위험요인을 알아보아 디자인 경영전략으로서의 웹디자인 아웃소싱 도입을 부각시키고자 한다. 연구의 방법으로는 웹디자인 서비스 아웃소싱의 위험요인을 도출하기 위하여 선행연구와 전문가 인터뷰를 진행하였으며 그 결과 계약측면, 관리측면, 품질측면, 환경측면의 4가지 위험요소와 세부 요인들을 도출할 수 있었다. 또한 좀더 세부적으로 4가지 위험요소가 웹디자인 서비스 아웃소싱 도입에 영향을 미치는 정도를 알아보기 위해 대기업 브랜드 사이트를 대상으로 설문조사와 함께 통계분석을 실시하였다. 연구의 결과, 관리와 품질측면의 위험요인은 웹디자인 서비스 아웃소싱 도입에 영향력을 미치는 것으로 나타났다. The introduction of Web design outsourcing as the service is actively underway with Web service of enterprise is specialized and diversified. This research, therefore, investigates how detail risk factors of Web design service outsourcing affects outsourcing intention, so would highlight the introduction of web design service outsourcing as design management strategy. By way of research, it progress previous research and interviews of leading experts, as a result can come up the 4 risk factors - Contracts, Management, Qualification and Environment - and the details. Questionnaire in the target of brand enterprise websites with statistical analysis is conducted to learn about in detial how 4 risk factors affects introduction of Web design outsourcing. As the result, 2 risk factors of management and qualification can affect introduction of web design outsourcing.

프로토타입 생성 기반 딥 러닝 모델 설명 방법

박재훈(Jae-hun Park),김광수(Kwang-su Kim) 한국컴퓨터정보학회 2022 한국컴퓨터정보학회 학술발표논문집 Vol.30 No.2

물리치료사의 근무실태와 직무만족 및 직장애착

안소윤,김원중,허영배,Ahn Soyoun,Kim Won-Joong,Huh Young-Bae 대한물리치료학회 2002 대한물리치료학회지 Vol.14 No.4

The main objective of this paper is to examine the working conditions of physical therapists and to investigate the level of job satisfaction and organizational commitment under different working conditions. A survey was conducted through structured questionnaire for the physical therapists working in Busan area, and data from 175 therapists were utilized in the final analysis. Survey items included general characteristics of the therapists(sex, age, education, marital status, religion, income, career years, etc.), their working conditions(kinds of organizations they work in, location of PT room, weekly working hours, average number of patients, number of co-workers, equipments/facilities, etc.), and organizational effectiveness measured in terms of job satisfaction and organizational commitment. Major results are as follows: 1) As for the general characteristics of the surveyed physical therapists, male(51.4$\%$) slightly exceeded female(48.6$\%$) and majority(more than 90$\%$) was 20-39 in age. Also, there were more single(57.7$\%$) than married(42.3$\%$), and 54.9$\%$ of the respondents had religion while 45.1$\%$ did not. In terms of the ranks in their organizations, only a few of them(6.9$\%$) were managers, and monthly salary mostly ranged from $\￦$1,000,000 to $\￦$2,500,000. More than half of them worked in various kinds of hospitals, with the remaining in health centers or social welfare institutions. 2) In regard to the working conditions of the respondents, 19.4$\%$ of PT rooms were located in basement areas while the remaining 80.6$\%$ in first to third floors. 34.3$\%$ of them treated 15 patients or less per day, whereas 25.1$\%$ treated 31 patients or more. Also, 52$\%$ recorded physical therapy charts periodically. As for the equipments and facilities, 25.1$\%$ felt 'sufficient' and 40$\%$'insufficient.' 3) The respondents provided various kinds of suggestions for the improvement of their working conditions, where the most important were 'salary raise' and 'reduction of working hours.' In addition, their requests to the PT Association included 'permission of opening of independent practice,' 'permission of legal specialty,' and 'vitalization of the Association.' 4) The comparative analysis of job satisfaction and organizational commitment among different characteristics of the respondents revealed that there was no significant difference between male and female, but in terms of age, the group of 40 or older was highest in both aspects. Besides, therapists who had 15 or more years of hospital career reported higher job satisfaction and organizational commitment than the others. It was also found that the level of organizational commitment increased as the rank of the respondents got higher. There were no significant differences in terms of marital status and religion. 5) Comparison with regard to working conditions showed that therapists employed in university hospitals, health centers and social welfare institutions felt higher job satisfaction and organizational commitment than those in community hospitals and clinics. Also, respondents who worked in basement areas had significantly lower job satisfaction than otherwise. The length of weekly working hours did not really affect the level of job satisfaction, but it was important to maintain 'regular working hours' for the hospitals to improve the employees' organizational commitment. As for the number of patients per day, 'medium level' (21-25 patients) had highest scores in both aspects. And, finally, sufficiency of equipments and facilities was found to be important for the improvement of organizational commitment.

Designed Nanocage Displaying Ligand-Specific Peptide Bunches for High Affinity and Biological Activity

Jeon, Jae Og,Kim, Soyoun,Choi, Eunsu,Shin, Kihyuk,Cha, Kiweon,So, In-Seop,Kim, Sun-Ji,Jun, Eunsung,Kim, Dohee,Ahn, Hyung Jun,Lee, Byung-Heon,Lee, Seung-Hyo,Kim, In-San American Chemical Society 2013 ACS NANO Vol.7 No.9

<P>Protein-cage nanoparticles are promising multifunctional platforms for targeted delivery of imaging and therapeutic agents owing to their biocompatibility, biodegradability, and low toxicity. The major advantage of protein-cage nanoparticles is the ability to decorate their surfaces with multiple functionalities through genetic and chemical modification to achieve desired properties for therapeutic and/or diagnostic purposes. Specific peptides identified by phage display can be genetically fused onto the surface of cage proteins to promote the association of nanoparticles with a particular cell type or tissue. Upon symmetrical assembly of the cage, peptides are clustered on the surface of the cage protein in bunches. The resulting PBNC (peptide bunches on nanocage) offers the potential of synergistically increasing the avidity of the peptide ligands, thereby enhancing their blocking ability for therapeutic purposes. Here, we demonstrated a proof-of-principle of PBNCs, fusing the interleukin-4 receptor (IL-4R)-targeting peptide, AP-1, identified previously by phage display, with ferritin-L-chain (FTL), which undergoes 24-subunit assembly to form highly stable AP-1-containing nanocage proteins (AP1-PBNCs). AP1-PBNCs bound specifically to the IL-4R-expressing cell line, A549, and their binding and internalization were specifically blocked by anti-IL-4R antibody. AP1-PBNCs exhibited dramatically enhanced binding avidity to IL-4R compared with AP-1 peptide, measured by surface plasmon resonance spectroscopy. Furthermore, treatment with AP1-PBNCs in a murine model of experimental asthma diminished airway hyper-responsiveness and eosinophilic airway inflammation along with decreased mucus hyperproduction. These findings hold great promise for the application of various PBNCs with ligand-specific peptides in therapeutics for different diseases, such as cancer.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancac3/2013/ancac3.2013.7.issue-9/nn403184u/production/images/medium/nn-2013-03184u_0007.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nn403184u'>ACS Electronic Supporting Info</A></P>

Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters

Park, Seung-min,Ahn, Ji-Young,Jo, Minjoung,Lee, Dong-ki,Lis, John T.,Craighead, Harold G.,Kim, Soyoun Royal Society of Chemistry 2009 Lab on a chip Vol.9 No.9

<P>RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX (Systematic Evolution of Ligands by EXponential enrichment) often requiring more than 10 successive cycles of selection and amplification, where each cycle normally takes 2 days per cycle of SELEX. Here, we have demonstrated the use of sol-gel arrays of proteins in a microfluidic system for efficient selection of RNA aptamers against multiple target molecules. The microfluidic chip incorporates five sol-gel binding droplets, within which specific target proteins are imbedded. The droplets are patterned on top of individually addressable electrical microheaters used for selective elution of aptamers bound to target proteins in the sol-gel droplets. We demonstrate that specific aptamers bind their respective protein targets and can be selectively eluted by micro-heating. Finally, our microfluidic SELEX system greatly improved selection efficiency, reducing the number of selection cycles needed to produce high affinity aptamers. The process is readily scalable to larger arrays of sol-gel-embedded proteins. To our knowledge, this is the first demonstration of a chip-based selection of aptamers using microfluidics, thereby allowing development of a high throughput and efficient SELEX procedures.</P> <P>Graphic Abstract</P><P>Sol-gel arrays of proteins in a microfluidic system for efficient selection of RNA aptamers against multiple target molecules <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b814993c'> </P>

PISTON: Predicting drug indications and side effects using topic modeling and natural language processing

Jang, Giup,Lee, Taekeon,Hwang, Soyoun,Park, Chihyun,Ahn, Jaegyoon,Seo, Sukyung,Hwang, Youhyeon,Yoon, Youngmi Elsevier 2018 Journal of biomedical informatics Vol.87 No.-

<P><B>Abstract</B></P> <P>The process of discovering novel drugs to treat diseases requires a long time and high cost. It is important to understand side effects of drugs as well as their therapeutic effects, because these can seriously damage the patients due to unexpected actions of the derived candidate drugs. In order to overcome these limitations, computational methods for predicting the therapeutic effects and side effects have been proposed. In particular, text mining is a widely used technique in the field of systems biology, because it can discover hidden relationships between drugs, genes and diseases from a large amount of literature data. Compared with <I>in vivo/in vitro</I> experiments, text mining derives meaningful results with less time and cost.</P> <P>In this study, we propose an algorithm for predicting novel drug-phenotype associations and drug-side effect associations using topic modeling and natural language processing (NLP). We extract sentences in which drugs and genes co-occur from the abstracts of the literature and identify words that describe the relationship between them using NLP. Considering the characteristics of the identified words, we determine if the drug has an up-regulation effect or a down-regulation effect on the gene. Based on genes that affect drugs and their regulatory relationships, we group the frequently occurring genes and regulatory relationships into topics, and build a drug-topic probability matrix by calculating the score that the drug will have a topic using topic modeling. Using the matrix, a classifier is constructed for predicting the novel indications and side effects of drugs considering the characteristics of known drug-phenotype associations or drug-side effect associations.</P> <P>The proposed method predicts both indications and side effects with a single algorithm, and it can exclude drugs with serious side effects or side effects that patients do not want to experience from among the candidate drugs provided for the treatment of the phenotype. Furthermore, lists of novel candidate drugs for phenotypes and side effects can be continuously updated with our algorithm every time a document is added. More than a thousand documents are produced per day, and it is possible for our algorithm to efficiently derive candidate drugs because it requires less cost than the existing drug repositioning methods. The resource of PISTON is available at databio.gachon.ac.kr/tools/PISTON.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We propose an algorithm for predicting novel drug-phenotype associations and drug-side effect associations using topic modeling and natural language processing (NLP). </LI> <LI> We identify genes that affect drugs and their regulatory relationships using NLP, and construct a drug-topic probability matrix and a classifier using topic modeling. </LI> <LI> The proposed method predicts both indications and side effects with a single algorithm, and it can exclude drugs with serious side effects or side effects that patients do not want to experience from among the candidate drugs provided for the treatment of the phenotype. </LI> <LI> Our method has higher classification accuracy for diseases and side effects than existing text mining techniques. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>