• Molecules and Cells
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• 제44권8호
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• pp.591-601
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• 2021

Cilia are highly specialized organelles that extend from the cell membrane and function as cellular signaling hubs. Thus, cilia formation and the trafficking of signaling molecules into cilia are essential cellular processes. TULP3 and Tubby (TUB) are members of the tubby-like protein (TULP) family that regulate the ciliary trafficking of G-protein coupled receptors, but the functions of the remaining TULPs (i.e., TULP1 and TULP2) remain unclear. Herein, we explore whether these four structurally similar TULPs share a molecular function in ciliary protein trafficking. We found that TULP3 and TUB, but not TULP1 or TULP2, can rescue the defective cilia formation observed in TULP3-knockout (KO) hTERT RPE-1 cells. TULP3 and TUB also fully rescue the defective ciliary localization of ARL13B, INPP5E, and GPR161 in TULP3 KO RPE-1 cells, while TULP1 and TULP2 only mediate partial rescues. Furthermore, loss of TULP3 results in abnormal IFT140 localization, which can be fully rescued by TUB and partially rescued by TULP1 and TULP2. TUB's capacity for binding IFT-A is essential for its role in cilia formation and ciliary protein trafficking in RPE-1 cells, whereas its capacity for PIP₂ binding is required for proper cilia length and IFT140 localization. Finally, chimeric TULP1 containing the IFT-A binding domain of TULP3 fully rescues ciliary protein trafficking, but not cilia formation. Together, these two TULP domains play distinct roles in ciliary protein trafficking but are insufficient for cilia formation in RPE-1 cells. In addition, TULP1 and TULP2 play other unknown molecular roles that should be addressed in the future.

• International Journal of Computer Science & Network Security
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• 제22권2호
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• pp.1-8
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• 2022

This work provides a reliable and classified stocks dataset merged with Saudi stock news. This dataset allows researchers to analyze and better understand the realities, impacts, and relationships between stock news and stock fluctuations. The data were collected from the Saudi stock market via the Corporate News (CN) and Historical Data Stocks (HDS) datasets. As their names suggest, CN contains news, and HDS provides information concerning how stock values change over time. Both datasets cover the period from 2011 to 2019, have 30,098 rows, and have 16 variables-four of which they share and 12 of which differ. Therefore, the combined dataset presented here includes 30,098 published news pieces and information about stock fluctuations across nine years. Stock news polarity has been interpreted in various ways by native Arabic speakers associated with the stock domain. Therefore, this polarity was categorized manually based on Arabic semantics. As the Saudi stock market massively contributes to the international economy, this dataset is essential for stock investors and analyzers. The dataset has been prepared for educational and scientific purposes, motivated by the scarcity of data describing the impact of Saudi stock news on stock activities. It will, therefore, be useful across many sectors, including stock market analytics, data mining, statistics, machine learning, and deep learning. The data evaluation is applied by testing the data distribution of the categories and the sentiment prediction-the data distribution over classes and sentiment prediction accuracy. The results show that the data distribution of the polarity over sectors is considered a balanced distribution. The NB model is developed to evaluate the data quality based on sentiment classification, proving the data reliability by achieving 68% accuracy. So, the data evaluation results ensure dataset reliability, readiness, and high quality for any usage.

• Journal of Veterinary Science
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• 제22권1호
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• pp.12.1-12.11
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• 2021

Background: Bats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV). Objectives: The objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor. Methods: The phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA. Results: Phylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2. Conclusions: These results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.

• Molecules and Cells
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• 제44권11호
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• pp.805-829
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• 2021

CCCTC-binding factor (CTCF) critically contributes to 3D chromatin organization by determining topologically associated domain (TAD) borders. Although CTCF primarily binds at TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking the putative CTCF-binding sites remains largely elusive. Here, we show that the ATP-dependent chromatin remodeler, chromodomain helicase DNA-binding 4 (CHD4), regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 short interspersed nuclear elements (SINEs) in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible and aberrant CTCF recruitment occurs within TADs, resulting in disorganization of local TADs. RNA-binding intrinsically disordered domains (IDRs) of CHD4 are required to prevent this aberrant CTCF binding, and CHD4 is critical for the repression of B2 SINE transcripts. These results collectively reveal that a CHD4-mediated mechanism ensures appropriate CTCF binding and associated TAD organization in mESCs.

• 한국지진공학회논문집
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• 제27권2호
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• pp.77-82
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• 2023

The structural analysis module is an essential part of any integrated structural system. Diverse integrated systems today require, from the analysis module, efficient real-time responses to real-time input such as earthquake signals, extreme weather-related forces, and man-made accidents. An integrated system may also be for the entire life span of a civil structure conceived during the initial conception, developed throughout various design stages, effectively used in construction, and utilized during usage and maintenance. All these integrated systems' essential part is the structural analysis module, which must be automated and computationally efficient so that responses may be almost immediate. The finite element method is often used for structural analysis, and for automation, many effective finite element meshes must be automatically generated for a given analysis. A computationally efficient finite element mesh generation scheme based on the r-h method of mesh refinement using strain deviations from the values at the Gauss points as error estimates from the previous mesh is described. Shape factors are used to sort out overly distorted elements. A standard cantilever beam analyzed by four-node plane stress elements is used as an example to show the effectiveness of the automated algorithm for a time-domain dynamic analysis. Although recent developments in computer hardware and software have made many new applications in integrated structural systems possible, structural analysis still needs to be executed efficiently in real-time. The algorithm applies to diverse integrated systems, including nonlinear analyses and general dynamic problems in earthquake engineering.

• Parasites, Hosts and Diseases
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• 제61권1호
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• pp.24-32
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• 2023

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the polymorphic var multigene family, is a highly polymorphic antigen that plays a crucial role in the pathology of malaria. The contribution of the genetic diversity of var toward the immune escape of P. falciparum has not yet been fully elucidated. This study aimed to characterize the diversity of var repertoires by screening P. falciparum Duffy-binding-like α domain (PfDBLα) among field isolates from central Myanmar. Genetic analysis revealed that the D-H segments of var in Myanmar populations have an extensive polymorphic repertoire, with high numbers of unique sequence types in each individual. However, var genes from the global population, including Myanmar, shared close genetic lineages regardless of their geographic origins, indicating that they have not undergone rapid evolutionary changes.

• Genomics & Informatics
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• 제21권2호
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• pp.18.1-18.11
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• 2023

Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell-derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55⁺) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.

• Journal of Life Science
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• 제11권2호
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• pp.111-115
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• 2001

This study was designed to clone the SNF2/SW12 helicase-related genes from the fission yeast Schizosaccha-romyces pombe and thereafter to elucidate the common functions of the proteins in this family. The $hrp^{2+}$gene was cloned by polymerase chain reaction amplification using degenerative primers from conserved SNF2 motifs within the ERCC6 gene, which encodes a protein involved in DNA excision repair. Like other SNF2/SW12 family proteins, the deduced amino acid sequence of Hrp2 contains DNA-dependent ATPase/7 helicase domains as well as the chromodomain and the DNA binding domain. This configuration is similar to that of mCHD1 (mouse chromo-ATPase/helicase-DNA-dinding protein 1), suggesting that Hrp2 is a S. pombe homolog of mCHD1, which is thought to function in altering the chromatin structure to control the gene expression. To characterize the function of Hrp2, 4 Uracil-Hrp2 fusion protein, it was purified near homogeneity by affinity chromatography on $Ni^{2+}$-NTA agarose, DEAE-Sepharose ion exchange arid Sephacryl S-200 gel filtration chromatographies. The purified fusion protein exhibited DNA-dependent ATPase activity, which was stimulated by both double-stranded and single-stranded DNA. To determine the steady-state level of $hrp^{2+}$ transcripts during growth, cells were cultured in medium and collected at every 2hr to prepare total RNAs. The northern blot analysis showed that the level of $hrp^{2+}$ transcripts reached its maximum before the cells entered the exponential growth phase and then decreased gradually, This result implies that Hrp2 may be required at early stages of cell growth.h.

• 대한의용생체공학회:의공학회지
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• 제44권6호
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• pp.428-442
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• 2023

In this study, we have a goal to develop usability evaluation guidelines for heuristic-based artificial intelligence-based Software as a Medical Device (SaMD) in the medical field. We conducted a gap analysis between medical hardware (H/W) and non-medical software (S/W) based on ten heuristic principles. Through severity assessments, we identified 69 evaluation domains and 112 evaluation criteria aligned with the ten heuristic principles. Subsequently, we categorized each evaluation domain into five types, including user safety, data integrity, regulatory compliance, patient therapeutic effectiveness, and user convenience. We proposed usability evaluation guidelines that apply the newly derived heuristic-based Software as a Medical Device (SaMD) evaluation factors to the risk management process. In the discussion, we also have proposed the potential applications of the research findings and directions for future research. We have emphasized the importance of the judicious application of AI technology in the medical field and the evaluation of usability evaluation and offered valuable guidelines for various stakeholders, including medical device manufacturers, healthcare professionals, and regulatory authorities.

• 한국수학교육학회지시리즈C:초등수학교육
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• 제27권2호
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• pp.155-171
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• 2024

본 연구는 '삼각형 세 각의 크기의 합'의 학습에서 수학수업의 도입 초점을 측정과 기하의 두 측면으로 달리하였을 때 학생들의 추론 과정 및 정당화 방식을 비교 분석하였다. 이를 확인하기 위하여 경기도 수원시에 위치한 H초등학교 4학년 1개 학급을 선정하여 연구를 실시하였다. 이 연구를 통해 얻은 결론은 다음과 같다. 첫째, '삼각형 세각의 크기의 합'을 수학 수업에서 도입할 때, 측정 관점에서 도입하는 것과 도형 관점에서 도입하는 것은 유의미한 차이가 있다. 둘째, '삼각형 세 각의 크기의 합은 180°이다.'를 정당화하기 위해 '세 각을 모으면 평각이 된다.'와 같은 도형 방식보다 '세 각의 크기를 더하면 180°이다.'와 같은 측정 방식으로 참임을 설명하는 것이 더 도움이 된다. 초등학생은 조작적 활동을 통해 수학적 지식을 이해하기 때문에, 활동의 수준은 수학 학습의 질로 연결된다. 이러한 추론 과정에 대한 연구는 2022 개정 교육과정의 '도형과 측정'이라는 하나 영역 속에서 '삼각형의 세 각의 크기의 합'을 어떤 계열로 접근할 것인지 기초 자료가 될 것이다.