• Title/Summary/Keyword: Tool-chain

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Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms

  • Dongwan Kim;Junhyeon Jeon;Minseo Kim;Jinuk Jeong;Young Mok Heo;Dong-Geol Lee;Dong Keon Yon;Kyudong Han
    • Genomics & Informatics
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    • v.21 no.4
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    • pp.52.1-52.10
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    • 2023
  • Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

Molecular identification of fruit bats, natural host of Nipah virus in Bangladesh, based on DNA barcode

  • Md. Maharub Hossain Fahim;Walid Hassan;Afia Afsin;Md. Mahfuzur Rahman;Md. Tanvir Rahman;Sang Jin Lim;Yeonsu Oh;Yung Chul Park;Hossain Md. Faruquee;Md. Mafizur Rahman
    • Journal of Ecology and Environment
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    • v.48 no.2
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    • pp.163-172
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    • 2024
  • Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.

Light-Chain Cardiac Amyloidosis: Cardiac Magnetic Resonance for Assessing Response to Chemotherapy

  • Yubo Guo;Xiao Li;Yajuan Gao;Kaini Shen;Lu Lin;Jian Wang;Jian Cao;Zhuoli Zhang;Ke Wan;Xi Yang Zhou;Yucheng Chen;Long Jiang Zhang;Jian Li;Yining Wang
    • Korean Journal of Radiology
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    • v.25 no.5
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    • pp.426-437
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    • 2024
  • Objective: Cardiac magnetic resonance (CMR) is a diagnostic tool that provides precise and reproducible information about cardiac structure, function, and tissue characterization, aiding in the monitoring of chemotherapy response in patients with light-chain cardiac amyloidosis (AL-CA). This study aimed to evaluate the feasibility of CMR in monitoring responses to chemotherapy in patients with AL-CA. Materials and Methods: In this prospective study, we enrolled 111 patients with AL-CA (50.5% male; median age, 54 [interquartile range, 49-63] years). Patients underwent longitudinal monitoring using biomarkers and CMR imaging. At follow-up after chemotherapy, patients were categorized into superior and inferior response groups based on their hematological and cardiac laboratory responses to chemotherapy. Changes in CMR findings across therapies and differences between response groups were analyzed. Results: Following chemotherapy (before vs. after), there were significant increases in myocardial T2 (43.6 ± 3.5 ms vs. 44.6 ± 4.1 ms; P = 0.008), recovery in right ventricular (RV) longitudinal strain (median of -9.6% vs. -11.7%; P = 0.031), and decrease in RV extracellular volume fraction (ECV) (median of 53.9% vs. 51.6%; P = 0.048). These changes were more pronounced in the superior-response group. Patients with superior cardiac laboratory response showed significantly greater reductions in RV ECV (-2.9% [interquartile range, -8.7%-1.1%] vs. 1.7% [-5.5%-7.1%]; P = 0.017) and left ventricular ECV (-2.0% [-6.0%-1.3%] vs. 2.0% [-3.0%-5.0%]; P = 0.01) compared with those with inferior response. Conclusion: Cardiac amyloid deposition can regress following chemotherapy in patients with AL-CA, particularly showing more prominent regression, possibly earlier, in the RV. CMR emerges as an effective tool for monitoring associated tissue characteristics and ventricular functional recovery in patients with AL-CA undergoing chemotherapy, thereby supporting its utility in treatment response assessment.

Identification of Mycobacterium Tuberculosis in Pleural Effusion by Polymerase Chain Reaction (PCR) (흉막삼출액에서 Polymerase Chain Reaction (PCR)을 이용한 결핵균의 검출에 관한 연구)

  • Kim, Ho-Joong;Kim, Young-Whan;Han, Sung-Koo;Shim, Young-Soo;Kim, Keun-Youl;Han, Yong-Chol
    • Tuberculosis and Respiratory Diseases
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    • v.40 no.5
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    • pp.509-518
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    • 1993
  • Background: By amplifying small amount of DNA, polymerase chain reaction (PCR) can be used for the detection of very small amount of microbial agent, and may be especially useful in certain cases which are difficult to be diagnosed microbiologically or serologically. Tuberculous pleurisy is a disease that can be diagnosed in only 70% of cases by conventional diagnostic tools, and PCR would be a very rapid, easy, and sensitive diagnostic method. Method: The specificity and sensitivity of PCR to detect Mycobacterium tuberculosis DNA were evaluated using various strains of Mycobacteria. To evaluate the diagnostic usefulness of PCR in tuberculous pleurisy, we used PCR to detect Mycobacterium tuberculosis DNA in pleural fluid. The amplification target was 123 base pair DNA, a part of IS6110 fragment, 10~16 copies of which are known to exist per genome. The diagnostic yield of PCR was compared with conventional methods, including pleural fluid adenosine deaminase (ADA) activity. Also, the significance of PCR in undiagnosed pleural effusion was evaluated prospectively with antituberculosis treatment. Results: 1) Using cultured Mycobacterium tuberculosis and other strains, PCR could detect upto 1 fg DNA and specific for only Mycobacterium tuberculosis and Mycobacterium bovis. 2) Using pleural effusions of proven tuberculosis cases, the sensitivity of PCR was 80.0% (16/20), and the specificity 95.0% (19/20). 3) Among 13 undiagnosed, but suspected tuberculous effusion, the positive rate was 60% in 10 improved cases after antituberculosis medications, and 0% in 3 cases of proven malignancy later. 4) Adenosine deaminase level of proven and clinically diagnosed tuberculous pleurisy patients was significantly higher than that of excluded patients, and correlated well with PCR results. Conclusion: We can conclude that PCR detection of Mycobacterium tuberculosis in pleural effusion has acceptable sensitivity and specificity, and could be an additional diagnostic tool for the diagnosis of tuberculous pleurisy.

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A Construction of the C_MDR(Component_MetaData Registry) for the Environment of Exchanging the Component (컴포넌트 유통환경을 위한 컴포넌트 메타데이타 레지스트리 구축 : C_MDR)

  • Song, Chee-Yang;Yim, Sung-Bin;Baik, Doo-Kwon;Kim, Chul-Hong
    • Journal of KIISE:Computing Practices and Letters
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    • v.7 no.6
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    • pp.614-629
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    • 2001
  • As the information-intensive society in 21c based on the environment of global internet is promoted, the software is getting more large and complex, and the demand for the software is increasing briskly. So, it becomes an important issue in academic and industrial field to activate reuse by developing and exchanging the standardized component. Currently, the information services as a product type of each company are provided in foreign market place for reusing a commercial component, but the components which are serviced in each market place are different, insufficient and unstandardized. That is, construction for Component Data Registry based on ISO 11179, is not accomplished. Hence, the national government has stepped up the plan for sending out public component at 2001. Therefore, the systems as a tool for sharing and exchange of data, have to support the meta-information of standardized component. In this paper, we will propose the C_MDR system: a tool to register and manage the standardized meta-information, based upon ISO 11179, for the commercialized common component. The purpose of this system is to systemically share and exchange the data in chain of acceleration of reusing the component. So, we will show the platform of specification for the component meta-information, then define the meta-information according to this platform, also represent the meta-information using XML for enhancing the interoperability of information with other system. Moreover, we will show that three-layered expression make modeling to be simple and understandable. The implementation of this system is to construct a prototype system of the component meta-information through the internet on www, this system uses ASP as a development language and RDBMS Oracle for PC. Thus, we may expect the standardization of the exchanged component metadata, and be able to apply to the exchanged reuse tool.

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A Study on Searching for Export Candidate Countries of the Korean Food and Beverage Industry Using Node2vec Graph Embedding and Light GBM Link Prediction (Node2vec 그래프 임베딩과 Light GBM 링크 예측을 활용한 식음료 산업의 수출 후보국가 탐색 연구)

  • Lee, Jae-Seong;Jun, Seung-Pyo;Seo, Jinny
    • Journal of Intelligence and Information Systems
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    • v.27 no.4
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    • pp.73-95
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    • 2021
  • This study uses Node2vec graph embedding method and Light GBM link prediction to explore undeveloped export candidate countries in Korea's food and beverage industry. Node2vec is the method that improves the limit of the structural equivalence representation of the network, which is known to be relatively weak compared to the existing link prediction method based on the number of common neighbors of the network. Therefore, the method is known to show excellent performance in both community detection and structural equivalence of the network. The vector value obtained by embedding the network in this way operates under the condition of a constant length from an arbitrarily designated starting point node. Therefore, it has the advantage that it is easy to apply the sequence of nodes as an input value to the model for downstream tasks such as Logistic Regression, Support Vector Machine, and Random Forest. Based on these features of the Node2vec graph embedding method, this study applied the above method to the international trade information of the Korean food and beverage industry. Through this, we intend to contribute to creating the effect of extensive margin diversification in Korea in the global value chain relationship of the industry. The optimal predictive model derived from the results of this study recorded a precision of 0.95 and a recall of 0.79, and an F1 score of 0.86, showing excellent performance. This performance was shown to be superior to that of the binary classifier based on Logistic Regression set as the baseline model. In the baseline model, a precision of 0.95 and a recall of 0.73 were recorded, and an F1 score of 0.83 was recorded. In addition, the light GBM-based optimal prediction model derived from this study showed superior performance than the link prediction model of previous studies, which is set as a benchmarking model in this study. The predictive model of the previous study recorded only a recall rate of 0.75, but the proposed model of this study showed better performance which recall rate is 0.79. The difference in the performance of the prediction results between benchmarking model and this study model is due to the model learning strategy. In this study, groups were classified by the trade value scale, and prediction models were trained differently for these groups. Specific methods are (1) a method of randomly masking and learning a model for all trades without setting specific conditions for trade value, (2) arbitrarily masking a part of the trades with an average trade value or higher and using the model method, and (3) a method of arbitrarily masking some of the trades with the top 25% or higher trade value and learning the model. As a result of the experiment, it was confirmed that the performance of the model trained by randomly masking some of the trades with the above-average trade value in this method was the best and appeared stably. It was found that most of the results of potential export candidates for Korea derived through the above model appeared appropriate through additional investigation. Combining the above, this study could suggest the practical utility of the link prediction method applying Node2vec and Light GBM. In addition, useful implications could be derived for weight update strategies that can perform better link prediction while training the model. On the other hand, this study also has policy utility because it is applied to trade transactions that have not been performed much in the research related to link prediction based on graph embedding. The results of this study support a rapid response to changes in the global value chain such as the recent US-China trade conflict or Japan's export regulations, and I think that it has sufficient usefulness as a tool for policy decision-making.

A Study of Genetic Polymonhisms of HLA-class I and II Genes Using Polymerase Chain Reaction (중합효소연쇄반응을 이용한 HLA-class I, II 유전자군의 유전적 다형성에 관한 연구)

  • Kyung-Ok Lee
    • Biomedical Science Letters
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    • v.4 no.1
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    • pp.11-25
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    • 1998
  • The HLA genes located in the short arm of chromosome 6 specify heterodimeric glycoproteins involved in the regulation of the immune response. Recently, in the elucidation of HLA polymorphism, serological and cellular typing methods have been replaced by DNA typing using polymerase chain reaction (PCR). The purpose of this study was to establish the HLA DNA typing methods and determine gene frequencies of HLA molecules in Koreans. PCR-SSP (sequence specific primers) and PCR-RFLP (restriction fragment length polymorphism) techniques were used for the analysis of HLA-A, -B, -C, DRBl genes and HLA-DQAl, DQBl, DPBl genes, respectively. The results of B-lymphoblastoid cells used for control experiment were consistent with the previous data identified in the 11th International Histocompatibility Workshop. Seventeen, 23, 16, 8, 16, 13 and 37 types of HLA-A, B, C, DQAl, DQBl, DPBl and DRBl alleles were found, respectively, in a total of unrelated 120 Korean individuals. The most frequent HLA alleles were $A^*$02 (27.0%), B$^*$40 (17.6%), Cw$^*$01 (19.2%), DQAl$^*$0301 (32.1%), DQBl$^*$0303 (12.9%), DPBl$^*$0501 (31.3%) and DRBl$^*$1501 (9.2%) among Koreans. This study shows that DNA typing method using PCR technique is a relatively simple, fast and practical tool for the determination of the HLA-class I and II genes. Moreover, the data of HLA gene frequencies could be useful for the Korean database before clinical applications, including organ and unrelated bone marrow transplantation, anthropological study, disease association and individual identification.

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Molecular Diagnosis of Streptococcus pneumoniae in Middle Ear Fluids from Children with Otitis Media with Effusion (삼출성 중이염 소아의 중이액에서 폐구균의 분자적 진단)

  • Byun, Sung Wan;Kim, Han Wool;Yoon, Seo Hee;Park, In Ho;Kim, Kyung-Hyo
    • Pediatric Infection and Vaccine
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    • v.22 no.2
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    • pp.106-112
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    • 2015
  • Purpose: The long-term administration of antibiotics interferes with bacterial culture in the middle ear fluids (MEFs) of young children with otitis media with effusion (OME). The purpose of this study is to determine whether molecular diagnostics can be used for rapid and direct detection of the bacterial pathogen in culture-negative MEFs. Methods: The specificity and sensitivity of both polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) to the lytA gene of Streptococcus pneumoniae were comparatively tested and then applied for pneumococcal detection in the clinical MEFs. Results: The detection limit of the PCR assay was approximately $10^4$ colony forming units (CFU), whereas that of LAMP was less than 10 CFU for the detection of S. pneumoniae. Both PCR and LAMP did not amplify nucleic acid at over $10^6$ CFU of H. influenzae or M. catarrhalis, both of which were irrelevant bacterial species. Of 22 culture-negative MEFs from children with OME, LAMP positivity was found in twelve MEFs (54.5%, 12/22), only three of which were PCR-positive (25%, 3/12). Our results showed that the ability of LAMP to detect pneumococcal DNA is over four times higher than that of PCR (P<0.01). Conclusions: As a high-resolution tool able to detect nucleic acid levels equivalent to <10 CFU of S. pneumoniae in MEFs without any cross-reaction with other pathogens, lytA -specific LAMP may be applied for diagnosing pneumococcus infection in OME as well as evaluating the impact of a pneumococcal conjugate vaccine against OME.

Survey of antibody on Orientia Tsutsugamushi among wild rodents in Gyeongnam area and detection by nested polymerase chain reaction (경남지역 야생들쥐에서 Orientia tsutsugamushi에 대한 항체 조사 및 PCR에 의한 검색)

  • Hah, Dae-Sik;Kim, Young-Hoon;Park, Jung-Ung;Park, Jae-Kap;Kim, Chung-Hui;Ryu, Jae-Doo;Jong, Myung-Ho;Heo, Jung-Ho;Shu, Jong-Lip;Cho, Myung-Heui;Lee, Kuk-Cheon;Kim, Gon-Sup;Kim, Eui-Kyung;Kim, Jong-Shu
    • Korean Journal of Veterinary Research
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    • v.44 no.2
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    • pp.241-249
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    • 2004
  • As a part of epidemiologic investigation of tsutsugamushi disease, the wild rodents which were captured in Gyeongnam area were diagnosed with indirect immunofluorescent antibody assay (IFA) and Polymerase Chain Reaction (PCR) to find if they have an antibody against Orientia tsutsugamushi. The conclusion was drawn as followings. (1) The captured 58 wild rodents showed that the subspecies distribution of Apodemus agrarius was 86.2%, Microtus fortis was 8.6% and Crocidura lasiura was 5.2%. (2) The antibody positive rate of O. tsutsugamushi Gilliam, Karp, Karto and Boryong by IFA method was 32.0% in Apodemus agrarius among 50 wild rodents and 40.0% in Microtus fortis among 5 wild rodents, respectively. It was negative in the case of all the 3 Crocidura lasiura. (3) The antibody titers on Apodemus agrarius, Microtus fortis and Crocidura lasiura against Gilliam, Karp, Karto and Boryong were measured between 1:20 and 1:640. The antibody titer against each antigen was in the order Boryong>Gilliam>Karp. (4) O. tsutsugamushi was detected from the blood, spleen and kidney from the artificially infected mice by IFA and PCR. IFA showed the positive response between 3 and 18 days after inoculation. On the other hand, positive response was found from all the samples by PCR. (5) From PCR of the genomic DNA extracted from the blood, spleen and kidney samples of the captured wild rodents, Boryong-specific amplification product with size of 210 bp, which is particular in Boryong, was detected from spleen and kidney samples, but not detected in the blood. (6) Boryong-specific amplification product was detected from spleen and kidney samples which were obtained at 3, 6, 12, 18 and 24 days after the infection with Boryong. But, it wasn't detected from the uninfected samples. (7) From PCR of spleen and kidney samples of the captured wild rodents, it was found that positive rate of O. tsutsugamushi in Apodemus agrarius and Microtus fortis were 25.0% (4/16) and 20.0% (1/5), respectively. From the above results, it can be concluded that Apodemus agrarius resided in Gyeongnam area carried O. tsutsugamushi and PCR method might be a simple, precise, rapid and useful diagnostic tool than IFA for the diagnosis of O. tsutsugamushi.

The Records and Archives Administrative Reform in China in 1930s (1930년대 중국 문서당안 행정개혁론의 이해)

  • Lee, Won-Kyu
    • The Korean Journal of Archival Studies
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    • no.10
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    • pp.276-322
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    • 2004
  • Historical interest in China in 1930s has been mostly focused on political characteristic of the National Government(國民政府) which was established by the KMT(中國國民黨) as a result of national unification. It is certain that China had a chance to construct a modern country by the establishment of the very unified revolutionary government. But, it was the time of expanding national crises that threatened the existence of the country such as the Manchurian Incident and the Chinese-Japanese War as well as the chaos of the domestic situation, too. So it has a good reason to examine the characteristic and pattern of the response of the political powers of those days. But, as shown in the recent studies, the manifestation method of political power by the revolutionary regime catches our attention through the understanding of internal operating system. Though this writing started from the fact that the Nationalist Government executed the administrative reform which aimed at "administrative efficiency" in the middle of 1930s, but it put stress on the seriousness of the problem and its solution rather than political background or results. "Committee on Administrative Efficiency(行政效率委員會)", the center of administrative reform movement which was established in 1934, examined the plan to execute the reform through legislation by the Executive Council(行政院) on the basis of the results of relevant studies. They claimed that the construction of a modern country should be performed by not political revolution anymore but by gradual improvement and daily reform, and that the operation of the government should become modern, scientific and efficient. There were many fields of administrative reform subjects, but especially, the field of records and archives adminstration(文書檔案行政) was studied intensively from the initial stage because that subject had already been discussed intensively. They recognized that records and archives were the basic tool of work performance and general activity but an inefficient field in spite of many input staff members, and most of all, archival reform bring about less conflicts than the fields of finance, organization and personnel. When it comes to the field of records adminstration, the key subjects that records should be written simply, the process of record treatment should be clear and the delay of that should be prevented were already presented in a records administrative meeting in 1922. That is, the unified law about record management was not established, so each government organization followed a conventional custom or performed independent improvement. It was through the other records administrative workshop of the Nationalist Government in 1933 when the new trend was appeared as the unified system improvement. They decided to unify the format of official records, to use marker and section, to unify the registration of receipt records and dispatch records and to strengthen the examination of records treatment. But, the method of records treatment was not unified yet, so the key point of records administrative reform was to establish a unified and standard record management system for preventing repetition by simplifying the treatment procedure and for intensive treatment by exclusive organizations. From the foundation of the Republic of China to 1930s, there was not big change in the field of archives administration, and archives management methods were prescribed differently even in the same section as well as same department. Therefore, the point at issue was to centralize scattered management systems that were performed in each section, to establish unified standard about filing and retention period allowance and to improve searching system through classification and proper number allowance. Especially, the problem was that each number system and classification system bring about different result due to dual operation of record registration and archives registration, and that strict management through mutual contrast, searching and application are impossible. Besides, various problems such as filing tools, arrangement method, preservation facilities & equipment, lending service and use method were raised also. In the process this study for the system improvement of records and archives management, they recognized that records and archives are the identical thing and reached to create a successive management method of records and archives called "Records and Archives Chain Management Method(文書檔案連鎖法)" as a potential alternative. Several principles that records and archives management should be performed unitedly in each organization by the general record recipient section and the general archives section under the principle of task centralization, a consistent classification system should be used by classification method decided in advance according to organizational constitution and work functions and an identical number system should be used in the process of record management stage and archive management stage by using a card-type register were established. Though, this "Records and Archives Chain Management Method" was developed to the stage of test application in several organizations, but it was not adopted as a regular system and discontinued. That was because the administrative reform of the Nationalist Government was discontinued by the outbreak of the Chinese-Japanese War. Even though the administrative reform in the middle of 1930s didn't produce practical results but merely an experimentation, it was verified that the reform against tradition and custom conducted by the Nationalist Government that aimed for the construction of a modern country was not only a field of politics, but on the other hand, the weak basis of the government operation became the obstacle to the realization of the political power of the revolutionary regime. Though the subject of records and archives administrative reform was postponed to the future, it should be understood that the consciousness of modern records and archives administration and overall studies began through this examination of administrative reform.