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  1. Article: Artificial Intelligence in Medicine and Dentistry.

    Vodanović, Marin / Subašić, Marko / Milošević, Denis / Savić Pavičin, Ivana

    Acta stomatologica Croatica

    2023  Volume 57, Issue 1, Page(s) 70–84

    Abstract: Introduction: Artificial intelligence has been applied in various fields throughout history, but its integration into daily life is more recent. The first applications of AI were primarily in academia and government research institutions, but as ... ...

    Abstract Introduction: Artificial intelligence has been applied in various fields throughout history, but its integration into daily life is more recent. The first applications of AI were primarily in academia and government research institutions, but as technology has advanced, AI has also been applied in industry, commerce, medicine and dentistry.
    Objective: Considering that the possibilities of applying artificial intelligence are developing rapidly and that this field is one of the areas with the greatest increase in the number of newly published articles, the aim of this paper was to provide an overview of the literature and to give an insight into the possibilities of applying artificial intelligence in medicine and dentistry. In addition, the aim was to discuss its advantages and disadvantages.
    Conclusion: The possibilities of applying artificial intelligence to medicine and dentistry are just being discovered. Artificial intelligence will greatly contribute to developments in medicine and dentistry, as it is a tool that enables development and progress, especially in terms of personalized healthcare that will lead to much better treatment outcomes.
    Language English
    Publishing date 2023-05-30
    Publishing country Croatia
    Document type Journal Article ; Review
    ZDB-ID 603047-6
    ISSN 0001-7019
    ISSN 0001-7019
    DOI 10.15644/asc57/1/8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Artificial Intelligence in Medicine and Dentistry

    Marin Vodanović / Marko Subašić / Denis Milošević / Ivana Savić Pavičin

    Acta Stomatologica Croatica, Vol 57, Iss 1, Pp 70-

    2023  Volume 84

    Abstract: Introduction: Artificial intelligence has been applied in various fields throughout history, but its integration into daily life is more recent. The first applications of AI were primarily in academia and government research institutions, but as ... ...

    Abstract Introduction: Artificial intelligence has been applied in various fields throughout history, but its integration into daily life is more recent. The first applications of AI were primarily in academia and government research institutions, but as technology has advanced, AI has also been applied in industry, commerce, medicine and dentistry. Objective: Considering that the possibilities of applying artificial intelligence are developing rapidly and that this field is one of the areas with the greatest increase in the number of newly published articles, the aim of this paper was to provide an overview of the literature and to give an insight into the possibilities of applying artificial intelligence in medicine and dentistry. In addition, the aim was to discuss its advantages and disadvantages. Conclusion:The possibilities of applying artificial intelligence to medicine and dentistry are just being discovered. Artificial intelligence will greatly contribute to developments in medicine and dentistry, as it is a tool that enables development and progress, especially in terms of personalized healthcare that will lead to much better treatment outcomes.
    Keywords Artificial Intelligence ; Precision Medicine ; Dentistry ; RK1-715
    Subject code 401
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher University of Zagreb. School of Dental Medicine
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression.

    Brümmer, Anneke / Kishore, Shivendra / Subasic, Deni / Hengartner, Michael / Zavolan, Mihaela

    RNA (New York, N.Y.)

    2013  Volume 19, Issue 10, Page(s) 1317–1326

    Abstract: To understand the function of the hundreds of RNA-binding proteins (RBPs) that are encoded in animal genomes it is important to identify their target RNAs. Although it is generally accepted that the binding specificity of an RBP is well described in ... ...

    Abstract To understand the function of the hundreds of RNA-binding proteins (RBPs) that are encoded in animal genomes it is important to identify their target RNAs. Although it is generally accepted that the binding specificity of an RBP is well described in terms of the nucleotide sequence of its binding sites, other factors such as the structural accessibility of binding sites or their clustering, to enable binding of RBP multimers, are also believed to play a role. Here we focus on GLD-1, a translational regulator of Caenorhabditis elegans, whose binding specificity and targets have been studied with a variety of methods such as CLIP (cross-linking and immunoprecipitation), RIP-Chip (microarray measurement of RNAs associated with an immunoprecipitated protein), profiling of polysome-associated mRNAs and biophysical determination of binding affinities of GLD-1 for short nucleotide sequences. We show that a simple biophysical model explains the binding of GLD-1 to mRNA targets to a large extent, and that taking into account the accessibility of putative target sites significantly improves the prediction of GLD-1 binding, particularly due to a more accurate prediction of binding in transcript coding regions. Relating GLD-1 binding to translational repression and stabilization of its target transcripts we find that binding sites along the entire transcripts contribute to functional responses, and that CDS-located sites contribute most to translational repression. Finally, biophysical measurements of GLD-1 affinity for a small number of oligonucleotides appear to allow an accurate reconstruction of the sequence specificity of the protein. This approach can be applied to uncover the specificity and function of other RBPs.
    MeSH term(s) Animals ; Binding Sites ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Gene Expression Regulation ; Immunoprecipitation ; Models, Theoretical ; Open Reading Frames/genetics ; Protein Binding ; Protein Biosynthesis ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances Caenorhabditis elegans Proteins ; GLD-1 protein, C elegans ; RNA, Messenger
    Language English
    Publishing date 2013-08-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.037531.112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Post-transcriptional control of executioner caspases by RNA-binding proteins.

    Subasic, Deni / Stoeger, Thomas / Eisenring, Seline / Matia-González, Ana M / Imig, Jochen / Zheng, Xue / Xiong, Lei / Gisler, Pascal / Eberhard, Ralf / Holtackers, René / Gerber, André P / Pelkmans, Lucas / Hengartner, Michael O

    Genes & development

    2016  Volume 30, Issue 19, Page(s) 2213–2225

    Abstract: Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent ... ...

    Abstract Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)-PUF-8, MEX-3, GLD-1, and CGH-1-that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3' untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3' UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
    MeSH term(s) 3' Untranslated Regions/genetics ; Animals ; Apoptosis/genetics ; Binding Sites ; Caenorhabditis elegans/enzymology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Caspases/genetics ; Caspases/metabolism ; Gene Expression Regulation, Developmental ; Germ Cells/cytology ; HeLa Cells ; Humans ; RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/metabolism
    Chemical Substances 3' Untranslated Regions ; Caenorhabditis elegans Proteins ; RNA-Binding Proteins ; Caspases (EC 3.4.22.-)
    Language English
    Publishing date 2016-10-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.285726.116
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  5. Article ; Online: MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

    Sendoel, Ataman / Subasic, Deni / Ducoli, Luca / Keller, Martin / Michel, Erich / Kohler, Ines / Singh, Kapil Dev / Zheng, Xue / Brümmer, Anneke / Imig, Jochen / Kishore, Shivendra / Wu, Yibo / Kanitz, Alexander / Kaech, Andres / Mittal, Nitish / Matia-González, Ana M / Gerber, André P / Zavolan, Mihaela / Aebersold, Ruedi /
    Hall, Jonathan / Allain, Frédéric H-T / Hengartner, Michael O

    Cell death and differentiation

    2019  Volume 26, Issue 10, Page(s) 2157–2178

    Abstract: Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects ... ...

    Abstract Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. How these RBPs control apoptosis is, however, largely unknown. Here, we identify mina-1(C41G7.3) in a RNA interference-based screen as a novel regulator of apoptosis, which is exclusively expressed in the adult germ line. The absence of MINA-1 causes a dramatic increase in germ cell apoptosis, a reduction in brood size, and an impaired P granules organization and structure. In vivo crosslinking immunoprecipitation experiments revealed that MINA-1 binds a set of mRNAs coding for RBPs associated with germ cell development. Additionally, a system-wide analysis of a mina-1 deletion mutant compared with wild type, including quantitative proteome and transcriptome data, hints to a post-transcriptional regulatory RBP network driven by MINA-1 during germ cell development in C. elegans. In particular, we found that the germline-specific Argonaute WAGO-4 protein levels are increased in mina-1 mutant background. Phenotypic analysis of double mutant mina-1;wago-4 revealed that contemporary loss of MINA-1 and WAGO-4 strongly rescues the phenotypes observed in mina-1 mutant background. To strengthen this functional interaction, we found that upregulation of WAGO-4 in mina-1 mutant animals causes hypersensitivity to exogenous RNAi. Our comprehensive experimental approach allowed us to describe a phenocritical interaction between two RBPs controlling germ cell apoptosis and exogenous RNAi. These findings broaden our understanding of how RBPs can orchestrate different cellular events such as differentiation and death in C. elegans.
    MeSH term(s) Animals ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Germ Cells ; RNA Interference
    Chemical Substances Argonaute Proteins ; Caenorhabditis elegans Proteins ; WAGO-4 protein, C elegans
    Language English
    Publishing date 2019-02-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1225672-9
    ISSN 1476-5403 ; 1350-9047
    ISSN (online) 1476-5403
    ISSN 1350-9047
    DOI 10.1038/s41418-019-0291-z
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  6. Article ; Online: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.

    Subasic, Deni / Brümmer, Anneke / Wu, Yibo / Pinto, Sérgio Morgado / Imig, Jochen / Keller, Martin / Jovanovic, Marko / Lightfoot, Helen Louise / Nasso, Sara / Goetze, Sandra / Brunner, Erich / Hall, Jonathan / Aebersold, Ruedi / Zavolan, Mihaela / Hengartner, Michael O

    Genome research

    2015  Volume 25, Issue 11, Page(s) 1680–1691

    Abstract: In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the ... ...

    Abstract In animals, microRNAs frequently form families with related sequences. The functional relevance of miRNA families and the relative contribution of family members to target repression have remained, however, largely unexplored. Here, we used the Caenorhabditis elegans miR-58 miRNA family, composed primarily of the four highly abundant members miR-58.1, miR-80, miR-81, and miR-82, as a model to investigate the redundancy of miRNA family members and their impact on target expression in an in vivo setting. We found that miR-58 family members repress largely overlapping sets of targets in a predominantly additive fashion. Progressive deletions of miR-58 family members lead to cumulative up-regulation of target protein and RNA levels. Phenotypic defects could only be observed in the family quadruple mutant, which also showed the strongest change in target protein levels. Interestingly, although the seed sequences of miR-80 and miR-58.1 differ in a single nucleotide, predicted canonical miR-80 targets were efficiently up-regulated in the mir-58.1 single mutant, indicating functional redundancy of distinct members of this miRNA family. At the aggregate level, target binding leads mainly to mRNA degradation, although we also observed some degree of translational inhibition, particularly in the single miR-58 family mutants. These results provide a framework for understanding how miRNA family members interact to regulate target mRNAs.
    MeSH term(s) Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Epigenetic Repression ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Proteomics ; RNA Stability/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Sequence Analysis, RNA ; Transcriptome ; Up-Regulation
    Chemical Substances Caenorhabditis elegans Proteins ; MIRN58 microRNA, C elegans ; MIRN80 microRNA, C elegans ; MicroRNAs ; RNA, Messenger
    Language English
    Publishing date 2015-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.183160.114
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  7. Article ; Online: DEPDC1/LET-99 participates in an evolutionarily conserved pathway for anti-tubulin drug-induced apoptosis.

    Sendoel, Ataman / Maida, Simona / Zheng, Xue / Teo, Youjin / Stergiou, Lilli / Rossi, Carlo-Alberto / Subasic, Deni / Pinto, Sergio M / Kinchen, Jason M / Shi, Moyin / Boettcher, Steffen / Meyer, Joel N / Manz, Markus G / Bano, Daniele / Hengartner, Michael O

    Nature cell biology

    2014  Volume 16, Issue 8, Page(s) 812–820

    Abstract: Microtubule-targeting chemotherapeutics induce apoptosis in cancer cells by promoting the phosphorylation and degradation of the anti-apoptotic BCL-2 family member MCL1. The signalling cascade linking microtubule disruption to MCL1 degradation remains ... ...

    Abstract Microtubule-targeting chemotherapeutics induce apoptosis in cancer cells by promoting the phosphorylation and degradation of the anti-apoptotic BCL-2 family member MCL1. The signalling cascade linking microtubule disruption to MCL1 degradation remains however to be defined. Here, we establish an in vivo screening strategy in Caenorhabditis elegans to uncover genes involved in chemotherapy-induced apoptosis. Using an RNAi-based screen, we identify three genes required for vincristine-induced apoptosis. We show that the DEP domain protein LET-99 acts upstream of the heterotrimeric G protein alpha subunit GPA-11 to control activation of the stress kinase JNK-1. The human homologue of LET-99, DEPDC1, similarly regulates vincristine-induced cell death by promoting JNK-dependent degradation of the BCL-2 family protein MCL1. Collectively, these data uncover an evolutionarily conserved mediator of anti-tubulin drug-induced apoptosis and suggest that DEPDC1 levels could be an additional determinant for therapy response upstream of MCL1.
    MeSH term(s) Animals ; Apoptosis/drug effects ; Apoptosis/genetics ; Apoptosis/physiology ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/drug effects ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Evolution, Molecular ; GTP-Binding Protein alpha Subunits/metabolism ; GTPase-Activating Proteins/genetics ; GTPase-Activating Proteins/metabolism ; Genes, Helminth/drug effects ; HeLa Cells ; Humans ; MAP Kinase Signaling System ; MCF-7 Cells ; Microtubules/genetics ; Microtubules/metabolism ; Mutation ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Phosphorylation/drug effects ; Proteolysis/drug effects ; RNA Interference ; Repressor Proteins/genetics ; Signal Transduction/genetics ; Tubulin Modulators/pharmacology ; Vincristine/pharmacology
    Chemical Substances Caenorhabditis elegans Proteins ; Ced-13 protein, C elegans ; DEPDC1 protein, human ; EGL-1 protein, C elegans ; GTP-Binding Protein alpha Subunits ; GTPase-Activating Proteins ; LET-99 protein, C elegans ; MCL1 protein, human ; Myeloid Cell Leukemia Sequence 1 Protein ; Neoplasm Proteins ; Repressor Proteins ; Tubulin Modulators ; Vincristine (5J49Q6B70F)
    Language English
    Publishing date 2014-07-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1474722-4
    ISSN 1476-4679 ; 1465-7392
    ISSN (online) 1476-4679
    ISSN 1465-7392
    DOI 10.1038/ncb3010
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  8. Article ; Online: The HUPO initiative on Model Organism Proteomes, iMOP.

    Jones, Alexandra M E / Aebersold, Ruedi / Ahrens, Christian H / Apweiler, Rolf / Baerenfaller, Katja / Baker, Mark / Bendixen, Emøke / Briggs, Steve / Brownridge, Philip / Brunner, Erich / Daube, Michael / Deutsch, Eric W / Grossniklaus, Ueli / Heazlewood, Joshua / Hengartner, Michael O / Hermjakob, Henning / Jovanovic, Marko / Lawless, Craig / Lochnit, Günter /
    Martens, Lennart / Ravnsborg, Christian / Schrimpf, Sabine P / Shim, Yhong-Hee / Subasic, Deni / Tholey, Andreas / Wijk, Klaas van / Mering, Christian von / Weiss, Manuel / Zheng, Xue

    Proteomics

    2012  Volume 12, Issue 3, Page(s) 340–345

    Abstract: The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model ... ...

    Abstract The community working on model organisms is growing steadily and the number of model organisms for which proteome data are being generated is continuously increasing. To standardize efforts and to make optimal use of proteomics data acquired from model organisms, a new Human Proteome Organisation (HUPO) initiative on model organism proteomes (iMOP) was approved at the HUPO Ninth Annual World Congress in Sydney, 2010. iMOP will seek to stimulate scientific exchange and disseminate HUPO best practices. The needs of model organism researchers for central databases will be better represented, catalyzing the integration of proteomics and organism-specific databases. Full details of iMOP activities, members, tools and resources can be found at our website http://www.imop.uzh.ch/ and new members are invited to join us.
    MeSH term(s) Animals ; Animals, Laboratory ; Arabidopsis/chemistry ; Databases, Protein ; Humans ; Models, Animal ; Proteome
    Chemical Substances Proteome
    Language English
    Publishing date 2012-01-31
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201290014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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