8f5d4d14230e0b57c24990a716279be0 pmc_11464785.pdf aa56710a9d9ea425079b4d7186f5e9ad36d84f9e pmc_11464785.pdf 099040027d01818b5b5846efa1da0d6f00cb749fbcf885a34386489cf070caf6 pmc_11464785.pdf Title: Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder Subject: Translational Psychiatry, doi:10.1038/s41398-024-03139-9 Keywords: Author: Eric Zillich Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Wed Oct 9 07:20:19 2024 CEST ModDate: Wed Oct 9 13:49:51 2024 CEST Custom Metadata: yes Metadata Stream: yes Tagged: no UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 14 Encrypted: no Page size: 595.276 x 790.866 pts Page rot: 0 File size: 8803998 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- MIDDKA+AdvMyriad_R Type 1C WinAnsi yes yes no 42 0 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Title: Methods Destination: A2 Children: Item: Title: Postmortem human brain tissue Destination: B1 Item: Title: DNA methylation data generation Destination: B2 Item: Title: Generation of gene expression data Destination: B3 Item: Title: Statistical analyses Destination: B4 Item: Title: DNA methylation analysis Destination: B5 Item: Title: Gene expression analysis Destination: B6 Item: Title: Cell type deconvolution analysis Destination: B7 Item: Title: Functional enrichment analysis Destination: B8 Item: Title: Weighted gene co-expression network analysis Destination: B9 Item: Title: Replication analysis of differential expression results Destination: B10 Item: Title: Signature-based drug repositioning analysis Destination: B11 Item: Title: Differential splicing analysis Destination: B12 Item: Title: Integrative gene locus analysis Destination: B13 Item: Title: Multi-omics factor analysis Destination: B14 Item: Title: GO enrichment analysis of CUD-associated gene sets Destination: B15 Item: Title: Results Destination: A3 Children: Item: Title: Sociodemographic characteristics and cell type composition estimation in the postmortem brain tissue cohort Destination: B16 Item: Title: Transcriptome-wide differential gene expression patterns in CUD are related to synaptic signaling, ion transport, and inflammatory processes Destination: B17 Item: Title: Network analysis highlights fatty acid metabolism and morphogenesis processes in CUD Destination: B18 Item: Title: Genes with alternative splicing events in CUD are involved in cell junction formation and the morphogenesis of axons and dendrites Destination: B19 Item: Title: Replication analysis in independent cohorts reveals FKBP4 and HSPA6 as conserved DEGs in CUD Destination: B20 Item: Title: Drug repositioning analysis highlights glucocorticoid receptor targeting drugs to reverse the CUD gene expression profile Destination: B21 Item: Title: Findings of the integrated analysis of DNA methylation and gene expression data converge at the gene and pathway levels Destination: B22 Children: Item: Title: Gene-level integration of epigenomic, transcriptomic and splicing alterations highlights ZBTB4 and INPP5E in CUD Destination: C1 Item: Title: Multi-omics factor analysis confirms cell junction, synaptic signaling, and neurogenesis as important biological processes in CUD Destination: C2 Item: Title: Integrative functional analysis reveals pathway modules related to neurotransmission, cell differentiation, cell junction organization, and fatty acid metabolism Destination: C3 Item: Title: Discussion Destination: A4 Item: Title: References Destination: A5 Item: Title: References Destination: A6 Item: Title: Acknowledgements Destination: A7 Item: Title: Author contributions Destination: A8 Item: Title: Funding Destination: A9 Item: Title: Competing interests Destination: A10 Item: Title: Ethics statement Destination: A11 Item: Title: ADDITIONAL INFORMATION Destination: M1 Info: Title: Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder Author: Eric Zillich Subject: Translational Psychiatry, doi:10.1038/s41398-024-03139-9 Keywords: Creator: Springer Producer: iText® 5.3.5 ©2000-2012 1T3XT BVBA (SPRINGER SBM; licensed version) CreationDate: Wed Oct 09 07:50:19 CEST 2024 ModDate: Wed Oct 09 13:49:51 CEST 2024 ID: 0x4c600fb04347b42eea26991beb6ede69, 0x2af12f4cd5b7d636b0709cd45d1c5c92 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1100 ImageHeight: 90 ColorSpace: black is zero BitsPerSample: 1 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/png ImageWidth: 43 ImageHeight: 105 BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/png ImageWidth: 3 ImageHeight: 4 ColorSpace: CMYK BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: 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Cabana-Domínguez Noèlia Fernàndez-Castillo Bru Cormand Janitza L. Montalvo-Ortiz Markus M. Nöthen Anita C. Hansson Marcella Rietschel Rainer Spanagel Stephanie H. Witt Lea Zillich Springer US Translational Psychiatry, doi:10.1038/s41398-024-03139-9 10.1038/s41398-024-03139-9 http://dx.doi.org/10.1038/s41398-024-03139-9 journal Translational Psychiatry © 2024, The Author(s) 2158-3188 10.1038/s41398-024-03139-9 springer.com springerlink.com 2010-04-23 True 10.1038/s41398-024-03139-9 springer.com springerlink.com Springer 2024-10-09T13:49:51+02:00 2024-10-09T10:50:19+05:30 2024-10-09T13:49:51+02:00 True VoR uuid:16de0bc0-498f-47c9-977b-fa6006c147f6 uuid:93950a16-0dd7-4cb1-bdd9-84b53d8ac8a4 default 1 converted uuid:92eb5493-5278-4741-b82a-11067bc1ab5f converted to PDF/A-2b pdfToolbox 2024-10-09T10:51:56+05:30 2 B Josef Frank http://orcid.org/0000-0003-4867-9465 Naguib Mechawar http://orcid.org/0000-0003-4960-756X Gustavo Turecki http://orcid.org/0000-0003-4075-2736 Judit Cabana-Domínguez http://orcid.org/0000-0002-4732-7284 Bru Cormand http://orcid.org/0000-0001-5318-4382 Janitza L. Montalvo-Ortiz http://orcid.org/0000-0002-7657-8365 Anita C. 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This can be a position at which the document has been changed since the most recent event history (stEvt:changed). For a resource within an xmpMM:Ingredients list, the ResourceRef uses this type to identify both the portion of the containing document that refers to the resource, and the portion of the referenced resource that is referenced. http://ns.adobe.com/xap/1.0/sType/Part# stPart Part http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/t/pg/ xmpTPg XMP Paged-Text internal XMP08 Spec: An ordered array of plate names that are needed to print the document (including any in contained documents). PlateNames Seq Text internal A structure containing the characteristics of a font used in a document Fonts Bag Font A structure containing the characteristics of a font used in a document. http://ns.adobe.com/xap/1.0/sType/Font# stFnt Font http://ns.adobe.com/pdfx/1.3/ pdfx pdfx internal ID of PDF/X standard GTS_PDFXVersion Text internal Conformance level of PDF/X standard GTS_PDFXConformance Text internal Company creating the PDF Company Text internal Date when document was last modified SourceModified Text external Mirrors crossmark:CrosMarkDomains CrossMarkDomains Seq Text internal Mirrors crossmark:DOI doi Text http://www.aiim.org/pdfa/ns/id/ pdfaid PDF/A ID Schema internal Part of PDF/A standard part Integer internal Amendment of PDF/A standard amd Text internal Conformance level of PDF/A standard conformance Text http://crossref.org/crossmark/1.0/ crossmark crossmark internal CrossMarkDomains CrossMarkDomains Seq Text internal CrossmarkDomainExclusive CrossmarkDomainExclusive Text internal Usual same as prism:doi DOI Text external The date when a publication was published. MajorVersionDate Text http://prismstandard.org/namespaces/basic/2.0/ prism Prism external The aggregation type specifies the unit of aggregation for a content collection. Comment PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. aggregationType Text external Copyright copyright Text external The Digital Object Identifier for the article. The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). doi Text external ISSN for an electronic version of the issue in which the resource occurs. Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. issn Text external Title of the magazine, or other publication, in which a resource was/will be published. Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” publicationName Text external This element provides the url for an article or unit of content. The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. url Text http://springernature.com/ns/xmpExtensions/2.0/ sn Springer Nature ORCID Schema external Author information: contains the name of each author and his/her ORCID (ORCiD: Open Researcher and Contributor ID). 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