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  1. Article ; Online: Impacts of COVID-19 crisis and some related factors on the mental health of 37150 Vietnamese students: a cross-sectional online study.

    Duong, Chau Bao / Van Tran, Nhi / Nguyen, An Hoang / Le, Thong Nhat / Ha, Bien Huy / Do, Chau Ngoc Phuc / Huynh, Khon / Le, Thong Minh / Nguyen, Thao Phuong / Nguyen, Hoai Thi Thu

    BMC public health

    2023  Volume 23, Issue 1, Page(s) 445

    Abstract: Background: University students are vulnerable to changes due to COVID-19 pandemic. Although warning has been made about the impact of this crisis on students' mental health, there are barely any sufficient study. This work investigated how the pandemic ...

    Abstract Background: University students are vulnerable to changes due to COVID-19 pandemic. Although warning has been made about the impact of this crisis on students' mental health, there are barely any sufficient study. This work investigated how the pandemic affected the mental health of students at the Vietnam National University of Ho Chi Minh City (VNU-HCMC) and efficiency of available mental health supportive methods.
    Methods: An online survey was conducted among students at Vietnam National University of Ho Chi Minh City (VNU-HCMC) from October 18, 2021, to October 25, 2021. Microsoft Excel 16.51 (Microsoft, USA) and R language, Epi packages 2.44 and 4.1.1 (rdrr.io) were used for data analysis.
    Results: Thirty-seven thousand one hundred fifty students participated in the survey, including 48.4% female and 51.6% male. Online learning pressure was mainly recorded (65.1%). Many students suffered from sleeping disorders (56.2%). Some reported being victims of abuse (5.9%). Female students expressed a significantly higher level of distress than males, particularly the feeling of ambiguity about the purpose of life (p-value < 0.0001, OR: 0.94, 95% CI: [0.95-0.98]). Third-year students suffered higher stress levels than others, especially in online learning (68.8%, p-value < 0.05). Mental health statuses among students of different lockdown status regions were not significantly different. Therefore, lockdown status did not affect the stress levels of students which suggested that poor mental health outcomes seemed to root in the suspension of everyday university life rather than the prohibition of going out.
    Conclusions: During COVID-19, students experienced lots of stress and mental problems. These findings underscore the importance of academic and innovative activities, bringing attention to the needs of interactive study and extra-curricular activities.
    MeSH term(s) Female ; Humans ; Male ; Communicable Disease Control ; COVID-19/epidemiology ; Cross-Sectional Studies ; Mental Health ; Pandemics ; Southeast Asian People ; Vietnam/epidemiology ; Students/psychology
    Language English
    Publishing date 2023-03-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-15317-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Discovery of tandem and interspersed segmental duplications using high-throughput sequencing.

    Soylev, Arda / Le, Thong Minh / Amini, Hajar / Alkan, Can / Hormozdiari, Fereydoun

    Bioinformatics (Oxford, England)

    2019  Volume 35, Issue 20, Page(s) 3923–3930

    Abstract: Motivation: Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, ... ...

    Abstract Motivation: Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions, likewise, duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants.
    Results: We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing datasets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real datasets. In the simulation experiments, using a 30× coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state-of-the-art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (<5% for the top 50 predictions).
    Availability and implementation: TARDIS source code is available at https://github.com/BilkentCompGen/tardis, and a corresponding Docker image is available at https://hub.docker.com/r/alkanlab/tardis/.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Algorithms ; Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Segmental Duplications, Genomic ; Software
    Language English
    Publishing date 2019-03-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btz237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article ; Online: Analysis of peptide-SLA binding by establishing immortalized porcine alveolar macrophage cells with different SLA class II haplotypes.

    Van Chanh Le, Quy / Le, Thong Minh / Cho, Hye-Sun / Kim, Won-Il / Hong, Kwonho / Song, Hyuk / Kim, Jin-Hoi / Park, Chankyu

    Veterinary research

    2018  Volume 49, Issue 1, Page(s) 96

    Abstract: Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells' short lifespan. We immortalized primary PAMs by transfecting them with both ... ...

    Abstract Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells' short lifespan. We immortalized primary PAMs by transfecting them with both hTERT and SV40LT and established two immortalized cell lines (iPAMs) actively proliferating even after 35 passages. These cells possessed the characteristics of primary PAMs, including strong expression of swine leukocyte antigen (SLA) class II genes and the inability to grow anchorage-independently. We characterized their SLA genes and subsequently performed peptide-SLA binding assays using a peptide from porcine circovirus type 2 open reading frame 2 to experimentally measure the binding affinity of the peptide to SLA class II. The number of peptides bound to cells measured by fluorescence was very low for PK15 cells (7.0% ± 1.5), which are not antigen-presenting cells, unlike iPAM61 (33.7% ± 3.4; SLA-DQA*0201/0303, DQB1*0201/0901, DRB1*0201/1301) and iPAM303 (73.3% ± 5.4; SLA DQA*0106/0201, DQB1*0202/0701, DRB1*0402/0602). The difference in peptide binding between the two iPAMs was likely due to the allelic differences between the SLA class II molecules that were expressed. The development of an immortal PAM cell panel harboring diverse SLA haplotypes and the use of an established method in this study can become a valuable tool for evaluating the interaction between antigenic peptides and SLA molecules and is important for many applications in veterinary medicine including vaccine development.
    MeSH term(s) Animals ; Cell Line ; Genes, MHC Class II/physiology ; Histocompatibility Antigens Class I/metabolism ; Macrophages, Alveolar/metabolism ; Peptides/metabolism ; Protein Binding ; Swine/metabolism
    Chemical Substances Histocompatibility Antigens Class I ; Peptides ; swine leukocyte antigen
    Language English
    Publishing date 2018-09-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1146298-x
    ISSN 1297-9716 ; 0928-4249
    ISSN (online) 1297-9716
    ISSN 0928-4249
    DOI 10.1186/s13567-018-0590-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1313: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: Analysis of peptide-SLA binding by establishing immortalized porcine alveolar macrophage cells with different SLA class II haplotypes

    Van Chanh Le, Quy / Le, Thong Minh / Cho, Hye-Sun / Kim, Won-Il / Hong, Kwonho / Song, Hyuk / Kim, Jin-Hoi / Park, Chankyu

    Veterinary research. 2018 Dec., v. 49, no. 1

    2018  

    Abstract: Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells’ short lifespan. We immortalized primary PAMs by transfecting them with both ... ...

    Abstract Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells’ short lifespan. We immortalized primary PAMs by transfecting them with both hTERT and SV40LT and established two immortalized cell lines (iPAMs) actively proliferating even after 35 passages. These cells possessed the characteristics of primary PAMs, including strong expression of swine leukocyte antigen (SLA) class II genes and the inability to grow anchorage-independently. We characterized their SLA genes and subsequently performed peptide-SLA binding assays using a peptide from porcine circovirus type 2 open reading frame 2 to experimentally measure the binding affinity of the peptide to SLA class II. The number of peptides bound to cells measured by fluorescence was very low for PK15 cells (7.0% ± 1.5), which are not antigen-presenting cells, unlike iPAM61 (33.7% ± 3.4; SLA-DQA*0201/0303, DQB1*0201/0901, DRB1*0201/1301) and iPAM303 (73.3% ± 5.4; SLA DQA*0106/0201, DQB1*0202/0701, DRB1*0402/0602). The difference in peptide binding between the two iPAMs was likely due to the allelic differences between the SLA class II molecules that were expressed. The development of an immortal PAM cell panel harboring diverse SLA haplotypes and the use of an established method in this study can become a valuable tool for evaluating the interaction between antigenic peptides and SLA molecules and is important for many applications in veterinary medicine including vaccine development.
    Keywords Porcine circovirus-2 ; antigen-presenting cells ; antigens ; binding capacity ; cell lines ; fluorescence ; genes ; haplotypes ; immune response ; leukocytes ; longevity ; macrophages ; open reading frames ; peptides ; swine ; vaccine development ; veterinary medicine
    Language English
    Dates of publication 2018-12
    Size p. 96.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 1146298-x
    ISSN 1297-9716 ; 0928-4249
    ISSN (online) 1297-9716
    ISSN 0928-4249
    DOI 10.1186/s13567-018-0590-2
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2609: Show issues

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  5. Article ; Online: β2-microglobulin gene duplication in cetartiodactyla remains intact only in pigs and possibly confers selective advantage to the species.

    Le, Thong Minh / Le, Quy Van Chanh / Truong, Dung Minh / Lee, Hye-Jeong / Choi, Min-Kyeung / Cho, Hyesun / Chung, Hak-Jae / Kim, Jin-Hoi / Do, Jeong-Tae / Song, Hyuk / Park, Chankyu

    PloS one

    2017  Volume 12, Issue 8, Page(s) e0182322

    Abstract: Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), ... ...

    Abstract Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1. Through experimental validation, we confirmed the functional duplication of the B2M gene with a completely identical coding sequence between two copies in pigs. Considering the importance of B2M in the immune system, we performed the phylogenetic analysis of B2M duplication in ten mammalian species, confirming the presence of B2M duplication in cetartioldactyls, like cattle, sheep, goats, pigs and whales, but non-cetartiodactyl species, like mice, cats, dogs, horses, and humans. The density of long interspersed nuclear element (LINE) at the edges of duplicated blocks (39 to 66%) was found to be 2 to 3-fold higher than the average (20.12%) of the pig genome, suggesting its role in the duplication event. The B2M mRNA expression level in pigs was 12.71 and 7.57 times (2-ΔΔCt values) higher than humans and mice, respectively. However, we were unable to experimentally demonstrate the difference in the level of B2M protein because species specific anti-B2M antibodies are not available. We reported, for the first time, the functional duplication of the B2M gene in animals. The identification of partially remaining duplicated B2M sequences in the genomes of only cetartiodactyls indicates that the event was lineage specific. B2M duplication could be beneficial to the immune system of pigs by increasing the availability of MHC class I light chain protein, B2M, to complex with the proteins encoded by the relatively large number of MHC class I heavy chain genes in pigs. Further studies are necessary to address the biological meaning of increased expression of B2M.
    MeSH term(s) Animals ; Base Sequence ; Cell Line ; DNA, Complementary ; Gene Duplication ; Gene Expression ; Genome ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Immunohistochemistry ; Mammals/genetics ; Mice ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Selection, Genetic ; Swine ; beta 2-Microglobulin/genetics ; beta 2-Microglobulin/metabolism
    Chemical Substances DNA, Complementary ; RNA, Messenger ; beta 2-Microglobulin
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0182322
    Database MEDical Literature Analysis and Retrieval System OnLINE

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