• 제목/요약/키워드: Library transformation

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Online Submission and Review System for Open Science: A Case of AccessON Peer Review Management System Plus (ACOMS+)

  • Jaemin Chung;Eunkyung Nam;Sung-Nam Cho;Jeong-Mee Lee;Hyunjung Kim;Hye-Sun Kim;Wan Jong Kim
    • Journal of Information Science Theory and Practice
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    • 제12권1호
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    • pp.87-101
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    • 2024
  • As the academic publishing environment evolves rapidly and the open science paradigm emerges, the demand for efficient and transparent peer review is growing. This study outlines efforts to actively introduce advanced concepts in scholarly communication into the submission and review system. AccessON Peer Review Management System Plus (ACOMS+), developed and operated by the Korea Institute of Science and Technology Information, is an online submission and peer review system that aims for open science. This study provides an overview of ACOMS+ and presents its four main features: open peer review, open access publishing and self-archiving, online quantitative/qualitative evaluation, and peer reviewer invitation. The directions for further developing ACOMS+ to fully support open science are also discussed. ACOMS+ is the first system in Korea to introduce the open peer review process and is distinguished as a system that supports open access publishing and digital transformation of academic journals. Furthermore, ACOMS+ is expected to contribute to the advancement of the academic publishing environment through the increasing shift toward open access publishing, transparent peer review, and open science.

인삼의 유용유전자원 확보를 위한 기능 유전체연구 (Functional Genomics for Mass Analysis of Useful Genes in Panax ginseng C.A. Meyer)

  • 양덕춘
    • 고려인삼학회:학술대회논문집
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    • 고려인삼학회 2004년도 춘계 총회 및 학술대회
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    • pp.17-28
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    • 2004
  • 현재 재배되고 있는 고려인삼은 혼계상태로서 개체간의 형질변이가 대단히 심하며, 종자채취를 4년 후에 하기 때문에 신품종육성을 위해서는 매우 오랜 기간이 필요하다. 그러나 식물형질전환기술의 발달로 목적하는 유전자를 식물체에 재도입하여 새로운 품종을 육성할 수 있는 기술이 보급되어 유용유전자만 있다면 단시간에 고기능성 신품종을 육성할 수 있을 것이다. 본 과제에서는 인삼의 유용유전자를 대량으로 발굴하기 위하여 인삼의 조직별, 종간 및 처리간에 의한 cDNA library 총 10종 이상을 제작하고 이들 cDNA library로부터 인삼의 유용유전자원을 확보하기 위하여 EST 20,000개를 5' 한쪽 방향에서 분석하고 이들 분석된 EST clone의 데이터는 data base화 하여 많은 연구자들이 연구정보를 공유한 수 있게 하였다. 그리고 EST clone 중에서 완전한 단백질의 유전정보를 포함하고 있는 clone을100개 선발하여 전장의 염기서열(full length sequence)을 분석하고 data base를 구축하고parental clone을 선발하여 cDNA chip을 제작하였다. 특히 257 clone 주에서 기능성 및 내재해성 유용유전자를 선발하여 전염기서열분석(full length sequencing)을 한 후 인상에 재도입하여 고기능성 및 내재해성 인삼의 분자육종을 비교적 단시간내에 할 수 있는 형질전환 및 재분화 시스템을 개발하고 토양순화 시스템을 확립하고자 하였다.

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길항세균 Pseudomonas fluorescens의 Complemented Mutant에 대한 특성조사에 및 길항물질 유전자 Cloning (Characterization of Complemented Mutants in Pseudomonas fluorescens and Cloning of the DNA Region Related in Antibiotic Biosynthesis)

  • Kim, Young;Cho, Yong-Sup
    • 한국식물병리학회지
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    • 제10권3호
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    • pp.151-156
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    • 1994
  • Pseudomonas fluorescens produces the antibiotic, 2,4-diacetylphloroglucinol (Phl), which promotes plant growth by inhibiting bacteria and fungi. Cosmids (genomic library) were mobilized into Phl-nonproducing mutants through the triparental matings with pRK2013 as the helper plasmid at the frequency of 8.37$\times$10-4. Complemented mutants that showed antibiotic activity were selected among about 2,000 transconjugants. The complemented mutants were confirmed by acquired drug resistances (kanamycin and tetracycline). The antibiotic substances of wild type and complemented mutants showed the most excellent anti-bacterial activity. Inhibitory effects of complemented P. fluorescens against phytopathogenic fungi were equal to the parental strain. Complemented mutant and wild type of P. fluorescens were causal microbes of fungal morphological abnormalities. Complemented mutants in potato dextrose agar supplemented with bromothymol blue also showed restoration of glucose utilization as wild type. Plasmids of complemented mutants were isolated from transconjugant sand transformed into competent cells of E. coli DH5$\alpha$. The plamid DNA was reisolated from transformed E. coli DH5$\alpha$.

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칼라 역 해프토닝을 위한 새로운 평활화 마스크의 설계 (Design of New Smoothing Mask of Color Inverse Halftoning)

  • 김종민;김민환
    • 한국멀티미디어학회논문지
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    • 제1권2호
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    • pp.183-193
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    • 1998
  • 칼라 역 해프토닝(Color inverse half toning)은 해프토닝된 칼라 영상을 시각적으로 보다 자연스러운 연속 계조 칼라영상으로 변환해 주는 방법이다. 본 논문에서는, 칼라 채널 영상에서 나타나는 해프톤 셀 패턴을 효과적으로 제거할 수 있는 새로운 평활화 마스크를 제안하고, 이를 칼라 역 해프토닝에 활용하였다 제안한 평활화 마스크는 기존의 평활화 마스크가 잘 제거하지 못했던 해프톤 셀 패턴올 시각적으로 보다 자연스럽게 평활화할 수 있으며, 마스크의 특성이 다양한 해프톤 영상에 적합하게 자동 조정될 수 있도록 설계하였다 실험을통해, 기폰의 방법과본논문에서 제안한방법에 의한결과 영상을다양한측면에서 비교분석함으로써 제안한 평활화 마스크의 유용성올 확인하였다. 제안한 방법은 전자 출판, 칼라 팩스, 디지힐 도서관 구축 퉁과 같은 멀티미디어 분야에서 활용될 수 있다.

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Identification of the Genes Involved in the Fruiting Body Production and Cordycepin Formation of Cordyceps militaris Fungus

  • Zheng, Zhuang-Li;Qiu, Xue-Hong;Han, Ri-Chou
    • Mycobiology
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    • 제43권1호
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    • pp.37-42
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    • 2015
  • A mutant library of Cordyceps militaris was constructed by improved Agrobacterium tumefaciens-mediated transformation and screened for degradation features. Six mutants with altered characters in in vitro and in vivo fruiting body production, and cordycepin formation were found to contain a single copy T-DNA. T-DNA flanking sequences of these mutants were identified by thermal asymmetric interlaced-PCR approach. ATP-dependent helicase, cytochrome oxidase subunit I and ubiquitin-like activating enzyme were involved in in vitro fruiting body production, serine/threonine phosphatase involved in in vivo fruiting body production, while glucose-methanol-choline oxidoreductase and telomerase reverse transcriptase involved in cordycepin formation. These genes were analyzed by bioinformatics methods, and their molecular function and biology process were speculated by Gene Ontology (GO) analysis. The results provided useful information for the control of culture degeneration in commercial production of C. militaris.

Aspartate계 아미노산 대사 효모 유전자 HOM6의 cloning 및 구조분석 (Molecular cloning and restriction endonuclease mapping of homoserine dehydrogenase gene (HOM6) in yeast saccharomyces cerevisiae)

  • 김응기;이호주
    • 미생물학회지
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    • 제24권4호
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    • pp.357-363
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    • 1986
  • Synthesis of threonine and methionine in yeast, Saccharomyces cerevisiae shares a common pathway from aspartate via homoserine. HOM6 gene encodes homoserine dehydrogenase (HSDH) which catalyzes the inter-conversion of beta-aspartate semialdehyde and homoserine. The level of HSDH is under methionine specific control. A recombinant plasmid (pEK1: 13.3kb), containing HOM6 gene, has been isolated and cloned into E. coli by complenemtary transformation of a homoserine auxotrophic yeast strain M-20-20D (hom6, trp1, ura3) to a prototrophic M20-20D/pEK1, using a library of yeast genomic DNA fragments in a yeast centromeric plasmid, YCp50(8.0kb). Isolation of HOM6has been primarily confirmed by retransformation of the original yeast strain M20-20D, using the recombinant plasmid DNA which was extracted from M20-20D/pEK1 and subsequently amplified in E. coli. Eleven cleavage sites in the insery (5.3kb) have been localized through fragment analysis for 8 restriction endonucleases; Bgl II(2 site), Bgl II(1), Cla I(3), Eco RI(1), Hind III(2), Kpn I (1), Pvu II(1) and Xho I(1).

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The Future Past of Humanities Research: Musing Methodology in the Digital Convergence Era

  • Kim, Jiyun
    • International journal of advanced smart convergence
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    • 제9권3호
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    • pp.161-168
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    • 2020
  • Over the last half-century, computer science has revolutionarily changed the landscape of humanities research. This digital shift in research methodology has reached from the brainstorming process to preserving, constructing, collecting, visualizing, and even analyzing materials. Such transformation has brought about the birth of the new field of study: Digital Humanities (DH). DH undeniably has saved much of the physical chores and provided a new angle to interpret the text, thereby making its meteoric rise as a promising future of the humanities. Based on such innovation, electronic circuitry can seem to replace the imagination that detects relationships and significances of research data with ever-improving interfaces. However, despite hitherto technological development, the thousands-year-old essence of traditional liberal arts-human creativity-remains the heart of humanities research and always will. This paper starts by proving this proposition in the way of comparing the old and new liberal arts research methods, focusing on literary studies. Meanwhile, it thoroughly investigates how digitalized bibliographies, search engines, databases, and digital projects provide the most useful data preservation and virtual experience of browsing in the library, along with their limitations due to the intrinsic quality of humanities research data. Also, it probes the differences between traditional and digital data analysis in current methods of literary studies, ultimately presenting the ideal direction for humanities development in the era of digital convergence.

An analytical approach of behavior change for concrete dam by panel data model

  • Gu, Hao;Yang, Meng;Gu, Chongshi;Cao, Wenhan;Huang, Xiaofei;Su, Huaizhi
    • Steel and Composite Structures
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    • 제36권5호
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    • pp.521-531
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    • 2020
  • The behavior variation of concrete dam is investigated, based on a new method for analyzing the data model of concrete dam in service process for the limitation of wavelet transform for solving concrete dam service process model. The study takes into account the time and position of behavior change during the process of concrete dam service. There is no dependence on the effect quantity for overcoming the shortcomings of the traditional identification method. The panel data model is firstly proposed for analyzing the behavior change of composite concrete dam. The change-point theory is used to identify whether the behavior of concrete dams changes during service. The phase space reconstruction technique is used to reconstruct the phase plane of the trend effect component. The time dimension method is used to solve the construction of multi-transformation model of composite panel data. An existing 76.3-m-high dam is used to investigate some key issues on the behavior change. Emphasis is placed on conversion time and location for three time periods consistent with the practical analysis report for evaluating the validity of the analysis method of the behavior variation of concrete dams presented in this paper.

Compression of 3D Mesh Geometry and Vertex Attributes for Mobile Graphics

  • Lee, Jong-Seok;Choe, Sung-Yul;Lee, Seung-Yong
    • Journal of Computing Science and Engineering
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    • 제4권3호
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    • pp.207-224
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    • 2010
  • This paper presents a compression scheme for mesh geometry, which is suitable for mobile graphics. The main focus is to enable real-time decoding of compressed vertex positions while providing reasonable compression ratios. Our scheme is based on local quantization of vertex positions with mesh partitioning. To prevent visual seams along the partitioning boundaries, we constrain the locally quantized cells of all mesh partitions to have the same size and aligned local axes. We propose a mesh partitioning algorithm to minimize the size of locally quantized cells, which relates to the distortion of a restored mesh. Vertex coordinates are stored in main memory and transmitted to graphics hardware for rendering in the quantized form, saving memory space and system bus bandwidth. Decoding operation is combined with model geometry transformation, and the only overhead to restore vertex positions is one matrix multiplication for each mesh partition. In our experiments, a 32-bit floating point vertex coordinate is quantized into an 8-bit integer, which is the smallest data size supported in a mobile graphics library. With this setting, the distortions of the restored meshes are comparable to 11-bit global quantization of vertex coordinates. We also apply the proposed approach to compression of vertex attributes, such as vertex normals and texture coordinates, and show that gains similar to vertex geometry can be obtained through local quantization with mesh partitioning.

Field Studios of In-situ Aerobic Cometabolism of Chlorinated Aliphatic Hydrocarbons

  • Semprini, Lewts
    • 한국지하수토양환경학회:학술대회논문집
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    • 한국지하수토양환경학회 2004년도 총회 및 춘계학술발표회
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    • pp.3-4
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    • 2004
  • Results will be presented from two field studies that evaluated the in-situ treatment of chlorinated aliphatic hydrocarbons (CAHs) using aerobic cometabolism. In the first study, a cometabolic air sparging (CAS) demonstration was conducted at McClellan Air Force Base (AFB), California, to treat chlorinated aliphatic hydrocarbons (CAHs) in groundwater using propane as the cometabolic substrate. A propane-biostimulated zone was sparged with a propane/air mixture and a control zone was sparged with air alone. Propane-utilizers were effectively stimulated in the saturated zone with repeated intermediate sparging of propane and air. Propane delivery, however, was not uniform, with propane mainly observed in down-gradient observation wells. Trichloroethene (TCE), cis-1, 2-dichloroethene (c-DCE), and dissolved oxygen (DO) concentration levels decreased in proportion with propane usage, with c-DCE decreasing more rapidly than TCE. The more rapid removal of c-DCE indicated biotransformation and not just physical removal by stripping. Propane utilization rates and rates of CAH removal slowed after three to four months of repeated propane additions, which coincided with tile depletion of nitrogen (as nitrate). Ammonia was then added to the propane/air mixture as a nitrogen source. After a six-month period between propane additions, rapid propane-utilization was observed. Nitrate was present due to groundwater flow into the treatment zone and/or by the oxidation of tile previously injected ammonia. In the propane-stimulated zone, c-DCE concentrations decreased below tile detection limit (1 $\mu$g/L), and TCE concentrations ranged from less than 5 $\mu$g/L to 30 $\mu$g/L, representing removals of 90 to 97%. In the air sparged control zone, TCE was removed at only two monitoring locations nearest the sparge-well, to concentrations of 15 $\mu$g/L and 60 $\mu$g/L. The responses indicate that stripping as well as biological treatment were responsible for the removal of contaminants in the biostimulated zone, with biostimulation enhancing removals to lower contaminant levels. As part of that study bacterial population shifts that occurred in the groundwater during CAS and air sparging control were evaluated by length heterogeneity polymerase chain reaction (LH-PCR) fragment analysis. The results showed that an organism(5) that had a fragment size of 385 base pairs (385 bp) was positively correlated with propane removal rates. The 385 bp fragment consisted of up to 83% of the total fragments in the analysis when propane removal rates peaked. A 16S rRNA clone library made from the bacteria sampled in propane sparged groundwater included clones of a TM7 division bacterium that had a 385bp LH-PCR fragment; no other bacterial species with this fragment size were detected. Both propane removal rates and the 385bp LH-PCR fragment decreased as nitrate levels in the groundwater decreased. In the second study the potential for bioaugmentation of a butane culture was evaluated in a series of field tests conducted at the Moffett Field Air Station in California. A butane-utilizing mixed culture that was effective in transforming 1, 1-dichloroethene (1, 1-DCE), 1, 1, 1-trichloroethane (1, 1, 1-TCA), and 1, 1-dichloroethane (1, 1-DCA) was added to the saturated zone at the test site. This mixture of contaminants was evaluated since they are often present as together as the result of 1, 1, 1-TCA contamination and the abiotic and biotic transformation of 1, 1, 1-TCA to 1, 1-DCE and 1, 1-DCA. Model simulations were performed prior to the initiation of the field study. The simulations were performed with a transport code that included processes for in-situ cometabolism, including microbial growth and decay, substrate and oxygen utilization, and the cometabolism of dual contaminants (1, 1-DCE and 1, 1, 1-TCA). Based on the results of detailed kinetic studies with the culture, cometabolic transformation kinetics were incorporated that butane mixed-inhibition on 1, 1-DCE and 1, 1, 1-TCA transformation, and competitive inhibition of 1, 1-DCE and 1, 1, 1-TCA on butane utilization. A transformation capacity term was also included in the model formation that results in cell loss due to contaminant transformation. Parameters for the model simulations were determined independently in kinetic studies with the butane-utilizing culture and through batch microcosm tests with groundwater and aquifer solids from the field test zone with the butane-utilizing culture added. In microcosm tests, the model simulated well the repetitive utilization of butane and cometabolism of 1.1, 1-TCA and 1, 1-DCE, as well as the transformation of 1, 1-DCE as it was repeatedly transformed at increased aqueous concentrations. Model simulations were then performed under the transport conditions of the field test to explore the effects of the bioaugmentation dose and the response of the system to tile biostimulation with alternating pulses of dissolved butane and oxygen in the presence of 1, 1-DCE (50 $\mu$g/L) and 1, 1, 1-TCA (250 $\mu$g/L). A uniform aquifer bioaugmentation dose of 0.5 mg/L of cells resulted in complete utilization of the butane 2-meters downgradient of the injection well within 200-hrs of bioaugmentation and butane addition. 1, 1-DCE was much more rapidly transformed than 1, 1, 1-TCA, and efficient 1, 1, 1-TCA removal occurred only after 1, 1-DCE and butane were decreased in concentration. The simulations demonstrated the strong inhibition of both 1, 1-DCE and butane on 1, 1, 1-TCA transformation, and the more rapid 1, 1-DCE transformation kinetics. Results of tile field demonstration indicated that bioaugmentation was successfully implemented; however it was difficult to maintain effective treatment for long periods of time (50 days or more). The demonstration showed that the bioaugmented experimental leg effectively transformed 1, 1-DCE and 1, 1-DCA, and was somewhat effective in transforming 1, 1, 1-TCA. The indigenous experimental leg treated in the same way as the bioaugmented leg was much less effective in treating the contaminant mixture. The best operating performance was achieved in the bioaugmented leg with about over 90%, 80%, 60 % removal for 1, 1-DCE, 1, 1-DCA, and 1, 1, 1-TCA, respectively. Molecular methods were used to track and enumerate the bioaugmented culture in the test zone. Real Time PCR analysis was used to on enumerate the bioaugmented culture. The results show higher numbers of the bioaugmented microorganisms were present in the treatment zone groundwater when the contaminants were being effective transformed. A decrease in these numbers was associated with a reduction in treatment performance. The results of the field tests indicated that although bioaugmentation can be successfully implemented, competition for the growth substrate (butane) by the indigenous microorganisms likely lead to the decrease in long-term performance.

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