LIVIVO - Search results -

Search results

Result 1 - 10 of total 63

Search options

Article: Sex Differences in Immune System Aging and Responsiveness to Vaccination.

Yanicke, Steven / Ucar, Duygu

2023 Volume 33, Issue 4, Page(s) 125–127

Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2740987-9
ISSN	2053-4892 ; 1055-3037
ISSN (online)	2053-4892
ISSN	1055-3037
DOI	10.1093/ppar/prad027
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS.

Nehar-Belaid, Djamel / Sokolowski, Mark / Ravichandran, Sathyabaarathi / Banchereau, Jacques / Chaussabel, Damien / Ucar, Duygu

Seminars in immunology

2023 Volume 70, Page(s) 101842

Abstract: Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In ...

Abstract	Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
MeSH term(s)	Humans ; Aged ; Vaccines ; Measles/prevention & control ; Vaccination ; COVID-19/prevention & control
Chemical Substances	Vaccines
Language	English
Publishing date	2023-09-15
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1018141-6
ISSN	1096-3618 ; 1044-5323
ISSN (online)	1096-3618
ISSN	1044-5323
DOI	10.1016/j.smim.2023.101842
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2843: 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)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: The effect of COVID-19 vaccinations on menstrual cycle and serum anti-Mullerian hormone levels in reproductive age women.

Hasdemir, Pinar Solmaz / Senol Akar, Sebnem / Goker, Asli / Kosova, Funda / Ucar, Duygu / Ozalp Ates, Funda Seher / Akcali, Sinem

Human fertility (Cambridge, England)

2023 Volume 26, Issue 1, Page(s) 153–161

Abstract: The aim of this prospective cohort study was to investigate the effect of coronavirus disease 2019 (COVID-19) vaccinations on menstrual cycle and ovarian reserve in reproductive aged-women. Health care providers ( ...

Abstract	The aim of this prospective cohort study was to investigate the effect of coronavirus disease 2019 (COVID-19) vaccinations on menstrual cycle and ovarian reserve in reproductive aged-women. Health care providers (
MeSH term(s)	Female ; Humans ; Adult ; Anti-Mullerian Hormone ; COVID-19 Vaccines ; Prospective Studies ; COVID-19/prevention & control ; SARS-CoV-2 ; Menstrual Cycle
Chemical Substances	Anti-Mullerian Hormone (80497-65-0) ; sinovac COVID-19 vaccine ; COVID-19 Vaccines
Language	English
Publishing date	2023-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2086960-5
ISSN	1742-8149 ; 1464-7273
ISSN (online)	1742-8149
ISSN	1464-7273
DOI	10.1080/14647273.2023.2181710
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5775: 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)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples.

Ahmed, Zeeshan / Ucar, Duygu

PeerJ

2017 Volume 5, Page(s) e4040

Abstract: Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of ... ...

Abstract	Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.
Language	English
Publishing date	2017-11-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.4040
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data.

Lawlor, Nathan / Marquez, Eladio J / Lee, Donghyung / Ucar, Duygu

Bioinformatics (Oxford, England)

2020 Volume 36, Issue 11, Page(s) 3582–3584

Abstract: Summary: Single-cell RNA-sequencing (scRNA-seq) technology enables studying gene expression programs from individual cells. However, these data are subject to diverse sources of variation, including 'unwanted' variation that needs to be removed in ... ...

Abstract	Summary: Single-cell RNA-sequencing (scRNA-seq) technology enables studying gene expression programs from individual cells. However, these data are subject to diverse sources of variation, including 'unwanted' variation that needs to be removed in downstream analyses (e.g. batch effects) and 'wanted' or biological sources of variation (e.g. variation associated with a cell type) that needs to be precisely described. Surrogate variable analysis (SVA)-based algorithms, are commonly used for batch correction and more recently for studying 'wanted' variation in scRNA-seq data. However, interpreting whether these variables are biologically meaningful or stemming from technical reasons remains a challenge. To facilitate the interpretation of surrogate variables detected by algorithms including IA-SVA, SVA or ZINB-WaVE, we developed an R Shiny application [Visual Surrogate Variable Analysis (V-SVA)] that provides a web-browser interface for the identification and annotation of hidden sources of variation in scRNA-seq data. This interactive framework includes tools for discovery of genes associated with detected sources of variation, gene annotation using publicly available databases and gene sets, and data visualization using dimension reduction methods. Availability and implementation: The V-SVA Shiny application is publicly hosted at https://vsva.jax.org/ and the source code is freely available at https://github.com/nlawlor/V-SVA. Contact: leed13@miamioh.edu or duygu.ucar@jax.org. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Gene Expression Profiling ; RNA-Seq ; Sequence Analysis, RNA ; Single-Cell Analysis ; Software
Language	English
Publishing date	2020-03-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa128
Database	MEDical Literature Analysis and Retrieval System OnLINE

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)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data.

Thibodeau, Asa / Khetan, Shubham / Eroglu, Alper / Tewhey, Ryan / Stitzel, Michael L / Ucar, Duygu

PLoS computational biology

2021 Volume 17, Issue 12, Page(s) e1009670

Abstract: Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors. ATAC-seq technology effectively identifies active cis-REs in a given cell type (including from ... ...

Abstract	Cis-Regulatory elements (cis-REs) include promoters, enhancers, and insulators that regulate gene expression programs via binding of transcription factors. ATAC-seq technology effectively identifies active cis-REs in a given cell type (including from single cells) by mapping accessible chromatin at base-pair resolution. However, these maps are not immediately useful for inferring specific functions of cis-REs. For this purpose, we developed a deep learning framework (CoRE-ATAC) with novel data encoders that integrate DNA sequence (reference or personal genotypes) with ATAC-seq cut sites and read pileups. CoRE-ATAC was trained on 4 cell types (n = 6 samples/replicates) and accurately predicted known cis-RE functions from 7 cell types (n = 40 samples) that were not used in model training (mean average precision = 0.80, mean F1 score = 0.70). CoRE-ATAC enhancer predictions from 19 human islet samples coincided with genetically modulated gain/loss of enhancer activity, which was confirmed by massively parallel reporter assays (MPRAs). Finally, CoRE-ATAC effectively inferred cis-RE function from aggregate single nucleus ATAC-seq (snATAC) data from human blood-derived immune cells that overlapped with known functional annotations in sorted immune cells, which established the efficacy of these models to study cis-RE functions of rare cells without the need for cell sorting. ATAC-seq maps from primary human cells reveal individual- and cell-specific variation in cis-RE activity. CoRE-ATAC increases the functional resolution of these maps, a critical step for studying regulatory disruptions behind diseases.
MeSH term(s)	Cells, Cultured ; Chromatin Immunoprecipitation Sequencing/methods ; Computational Biology ; DNA/analysis ; DNA/genetics ; Deep Learning ; Humans ; Islets of Langerhans/cytology ; Monocytes/cytology ; Regulatory Sequences, Nucleic Acid/genetics ; Single-Cell Analysis/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2021-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1009670
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Amplification of the bromodomain-containing protein 4 gene in ovarian high-grade serous carcinoma is associated with worse prognosis and survival.

Ucar, Duygu / Lin, Douglas I

Molecular and clinical oncology

2015 Volume 3, Issue 6, Page(s) 1291–1294

Abstract: High-grade serous carcinoma (HGSC) of the ovary is an aggressive and devastating neoplasm and the identification of novel therapeutic targets may result in a significant decrease in patient morbidity and mortality. Over the last few years, chromatin ... ...

Abstract	High-grade serous carcinoma (HGSC) of the ovary is an aggressive and devastating neoplasm and the identification of novel therapeutic targets may result in a significant decrease in patient morbidity and mortality. Over the last few years, chromatin regulators have become attractive targets for cancer therapy. More specifically, bromodomain-containing protein 4 (BRD4), a protein that is associated with acetylated chromatin and transcriptional activation, has been shown to selectively regulate the transcription of key oncogenic drivers, such as
Language	English
Publishing date	2015-08-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2796865-0
ISSN	2049-9469 ; 2049-9450
ISSN (online)	2049-9469
ISSN	2049-9450
DOI	10.3892/mco.2015.622
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Cell-specific gene promoters are marked by broader spans of H3K4me3 and are associated with robust gene expression patterns.

Ucar, Duygu / Bayarsaihan, Dashzeveg

Epigenomics

2015 Volume 7, Issue 2, Page(s) 129–131

MeSH term(s)	Epigenesis, Genetic ; Gene Expression ; Histones/chemistry ; Histones/metabolism ; Humans ; Lysine/metabolism ; Promoter Regions, Genetic
Chemical Substances	Histones ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2015
Publishing country	England
Document type	Editorial
ISSN	1750-192X
ISSN (online)	1750-192X
DOI	10.2217/epi.14.87
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Distinct baseline immune characteristics associated with responses to conjugated and unconjugated pneumococcal polysaccharide vaccines in older adults.

Ravichandran, Sathyabaarathi / Erra-Diaz, Fernando / Karakaslar, Onur E / Marches, Radu / Kenyon-Pesce, Lisa / Rossi, Robert / Chaussabel, Damien / Nehar-Belaid, Djamel / LaFon, David C / Pascual, Virginia / Palucka, Karolina / Paust, Silke / Nahm, Moon H / Kuchel, George A / Banchereau, Jacques / Ucar, Duygu

Nature immunology

2024 Volume 25, Issue 2, Page(s) 316–329

Abstract: Pneumococcal infections cause serious illness and death among older adults. The capsular polysaccharide vaccine PPSV23 and conjugated alternative PCV13 can prevent these infections; yet, underlying immunological responses and baseline predictors remain ... ...

Abstract	Pneumococcal infections cause serious illness and death among older adults. The capsular polysaccharide vaccine PPSV23 and conjugated alternative PCV13 can prevent these infections; yet, underlying immunological responses and baseline predictors remain unknown. We vaccinated 39 older adults (>60 years) with PPSV23 or PCV13 and observed comparable antibody responses (day 28) and plasmablast transcriptional responses (day 10); however, the baseline predictors were distinct. Analyses of baseline flow cytometry and bulk and single-cell RNA-sequencing data revealed a baseline phenotype specifically associated with weaker PCV13 responses, which was characterized by increased expression of cytotoxicity-associated genes, increased frequencies of CD16
MeSH term(s)	Male ; Humans ; Female ; Aged ; Vaccines, Conjugate ; Antibodies, Bacterial ; Double-Blind Method ; Streptococcus pneumoniae ; Vaccination ; Pneumococcal Vaccines ; Polysaccharides
Chemical Substances	Vaccines, Conjugate ; Antibodies, Bacterial ; Pneumococcal Vaccines ; Polysaccharides
Language	English
Publishing date	2024-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/s41590-023-01717-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5294: 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) ab Jg. 2022: Lesesaal (EG)
Zs.MG 42: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Concomitant inhibition of PPARγ and mTORC1 induces the differentiation of human monocytes into highly immunogenic dendritic cells.

Erra Diaz, Fernando / Mazzitelli, Ignacio / Bleichmar, Lucía / Melucci, Claudia / Thibodeau, Asa / Dalotto Moreno, Tomás / Marches, Radu / Rabinovich, Gabriel A / Ucar, Duygu / Geffner, Jorge

Cell reports

2023 Volume 42, Issue 3, Page(s) 112156

Abstract: Monocytes can differentiate into macrophages (Mo-Macs) or dendritic cells (Mo-DCs). The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) induces the differentiation of monocytes into Mo-Macs, while the combination of GM-CSF/interleukin ( ...

Abstract	Monocytes can differentiate into macrophages (Mo-Macs) or dendritic cells (Mo-DCs). The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) induces the differentiation of monocytes into Mo-Macs, while the combination of GM-CSF/interleukin (IL)-4 is widely used to generate Mo-DCs for clinical applications and to study human DC biology. Here, we report that pharmacological inhibition of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) in the presence of GM-CSF and the absence of IL-4 induces monocyte differentiation into Mo-DCs. Remarkably, we find that simultaneous inhibition of PPARγ and the nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) induces the differentiation of Mo-DCs with stronger phenotypic stability, superior immunogenicity, and a transcriptional profile characterized by a strong type I interferon (IFN) signature, a lower expression of a large set of tolerogenic genes, and the differential expression of several transcription factors compared with GM-CSF/IL-4 Mo-DCs. Our findings uncover a pathway that tailors Mo-DC differentiation with potential implications in the fields of DC vaccination and cancer immunotherapy.
MeSH term(s)	Humans ; Monocytes/metabolism ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; PPAR gamma/metabolism ; Interleukin-4/pharmacology ; Interleukin-4/metabolism ; Dendritic Cells/metabolism ; Cell Differentiation/physiology ; Cells, Cultured
Chemical Substances	Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1) ; PPAR gamma ; Interleukin-4 (207137-56-2)
Language	English
Publishing date	2023-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.112156
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito