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Article ; Online: Membrane marker selection for segmenting single cell spatial proteomics data.

Dayao, Monica T / Brusko, Maigan / Wasserfall, Clive / Bar-Joseph, Ziv

2022 Volume 13, Issue 1, Page(s) 1999

Abstract: The ability to profile spatial proteomics at the single cell level enables the study of cell types, their spatial distribution, and interactions in several tissues and conditions. Current methods for cell segmentation in such studies rely on known ... ...

Abstract	The ability to profile spatial proteomics at the single cell level enables the study of cell types, their spatial distribution, and interactions in several tissues and conditions. Current methods for cell segmentation in such studies rely on known membrane or cell boundary markers. However, for many tissues, an optimal set of markers is not known, and even within a tissue, different cell types may express different markers. Here we present RAMCES, a method that uses a convolutional neural network to learn the optimal markers for a new sample and outputs a weighted combination of the selected markers for segmentation. Testing RAMCES on several existing datasets indicates that it correctly identifies cell boundary markers, improving on methods that rely on a single marker or those that extend nuclei segmentations. Application to new spatial proteomics data demonstrates its usefulness for accurately assigning cell types based on the proteins expressed in segmented cells.
MeSH term(s)	Cell Nucleus ; Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; Proteomics
Language	English
Publishing date	2022-04-14
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-29667-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.

Dong, Xiaoru / Leary, Jack R / Yang, Chuanhao / Brusko, Maigan A / Brusko, Todd M / Bacher, Rhonda

bioRxiv : the preprint server for biology

2023

Abstract: Single-cell RNA sequencing (scRNA-seq) experiments have become instrumental in developmental and differentiation studies, enabling the profiling of cells at a single or multiple time-points to uncover subtle variations in expression profiles reflecting ... ...

Abstract	Single-cell RNA sequencing (scRNA-seq) experiments have become instrumental in developmental and differentiation studies, enabling the profiling of cells at a single or multiple time-points to uncover subtle variations in expression profiles reflecting underlying biological processes. Benchmarking studies have compared many of the computational methods used to reconstruct cellular dynamics, however researchers still encounter challenges in their analysis due to uncertainties in selecting the most appropriate methods and parameters. Even among universal data processing steps used by trajectory inference methods such as feature selection and dimension reduction, trajectory methods' performances are highly dataset-specific. To address these challenges, we developed Escort, a framework for evaluating a dataset's suitability for trajectory inference and quantifying trajectory properties influenced by analysis decisions. Escort navigates single-cell trajectory analysis through data-driven assessments, reducing uncertainty and much of the decision burden associated with trajectory inference. Escort is implemented in an accessible R package and R/Shiny application, providing researchers with the necessary tools to make informed decisions during trajectory analysis and enabling new insights into dynamic biological processes at single-cell resolution.
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.18.572214
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Article: Impaired islet function with normal exocrine enzyme secretion is consistent across the head, body, and tail pancreas regions in type 1 diabetes.

Drotar, Denise M / Mojica-Avila, Ana Karen / Bloss, Drew T / Cohrs, Christian M / Manson, Cameron T / Posgai, Amanda L / Williams, MacKenzie D / Brusko, Maigan A / Phelps, Edward A / Wasserfall, Clive H / Speier, Stephan / Atkinson, Mark A

bioRxiv : the preprint server for biology

2024

Abstract: Histopathological heterogeneity in human pancreas has been well documented; however, functional evidence at the tissue level is scarce. Herein we ... ...

Abstract	Histopathological heterogeneity in human pancreas has been well documented; however, functional evidence at the tissue level is scarce. Herein we investigated
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.08.579175
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Article ; Online: Low-Dose Antithymocyte Globulin: A Pragmatic Approach to Treating Stage 2 Type 1 Diabetes.

Foster, Timothy P / Jacobsen, Laura M / Bruggeman, Brittany / Salmon, Chelsea / Hosford, Jennifer / Chen, Angela / Cintron, Miriam / Mathews, Clayton E / Wasserfall, Clive / Brusko, Maigan A / Brusko, Todd M / Atkinson, Mark A / Schatz, Desmond A / Haller, Michael J

Diabetes care

2023 Volume 47, Issue 2, Page(s) 285–289

Abstract: Objective: Low-dose antithymocyte globulin (ATG) (2.5 mg/kg) preserves C-peptide and reduces HbA1c in new-onset stage 3 type 1 diabetes, yet efficacy in delaying progression from stage 2 to stage 3 has not been evaluated.: Research design and methods!# ...

Abstract	Objective: Low-dose antithymocyte globulin (ATG) (2.5 mg/kg) preserves C-peptide and reduces HbA1c in new-onset stage 3 type 1 diabetes, yet efficacy in delaying progression from stage 2 to stage 3 has not been evaluated. Research design and methods: Children (n = 6) aged 5-14 years with stage 2 type 1 diabetes received off-label, low-dose ATG. HbA1c, C-peptide, continuous glucose monitoring, insulin requirements, and side effects were followed for 18-48 months. Results: Three subjects (50%) remained diabetes free after 1.5, 3, and 4 years of follow-up, while three developed stage 3 within 1-2 months after therapy. Eighteen months posttreatment, even disease progressors demonstrated near-normal HbA1c (5.1% [32 mmol/mol], 5.6% [38 mmol/mol], and 5.3% [34 mmol/mol]), time in range (93%, 88%, and 98%), low insulin requirements (0.17, 0.18, and 0.34 units/kg/day), and robust C-peptide 90 min after mixed meal (1.3 ng/dL, 2.3 ng/dL, and 1.4 ng/dL). Conclusions: These observations support additional prospective studies evaluating ATG in stage 2 type 1 diabetes.
MeSH term(s)	Child ; Humans ; Antilymphocyte Serum/therapeutic use ; Blood Glucose ; Blood Glucose Self-Monitoring ; C-Peptide ; Diabetes Mellitus, Type 1/drug therapy ; Diabetes Mellitus, Type 1/chemically induced ; Glycated Hemoglobin ; Hypoglycemic Agents ; Insulin ; Prospective Studies
Chemical Substances	Antilymphocyte Serum ; Blood Glucose ; C-Peptide ; Glycated Hemoglobin ; Hypoglycemic Agents ; Insulin
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	441231-x
ISSN	1935-5548 ; 0149-5992
ISSN (online)	1935-5548
ISSN	0149-5992
DOI	10.2337/dc23-1750
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Article ; Online: Infant T cells are developmentally adapted for robust lung immune responses through enhanced T cell receptor signaling.

Thapa, Puspa / Guyer, Rebecca S / Yang, Alexander Y / Parks, Christopher A / Brusko, Todd M / Brusko, Maigan / Connors, Thomas J / Farber, Donna L

Science immunology

2021 Volume 6, Issue 66, Page(s) eabj0789

Abstract: Infants require coordinated immune responses to prevent succumbing to multiple infectious challenges during early life, particularly in the respiratory tract. The mechanisms by which infant T cells are functionally adapted for these responses are not ... ...

Abstract	Infants require coordinated immune responses to prevent succumbing to multiple infectious challenges during early life, particularly in the respiratory tract. The mechanisms by which infant T cells are functionally adapted for these responses are not well understood. Here, we demonstrated using an in vivo mouse cotransfer model that infant T cells generated greater numbers of lung-homing effector cells in response to influenza infection compared with adult T cells in the same host, due to augmented T cell receptor (TCR)–mediated signaling. Mouse infant T cells showed increased sensitivity to low antigen doses, originating at the interface between T cells and antigen-bearing accessory cells—through actin-mediated mobilization of signaling molecules to the immune synapse. This enhanced signaling was also observed in human infant versus adult T cells. Our findings provide a mechanism for how infants control pathogen load and dissemination, which is important for designing developmentally targeted strategies for promoting immune responses at this vulnerable life stage.
MeSH term(s)	Animals ; CD4-Positive T-Lymphocytes/immunology ; Female ; Lung/immunology ; Male ; Mice ; Mice, Congenic ; Mice, Inbred C57BL ; Mice, Transgenic ; Receptors, Antigen, T-Cell/immunology ; Signal Transduction/immunology
Chemical Substances	Receptors, Antigen, T-Cell
Language	English
Publishing date	2021-12-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2470-9468
ISSN (online)	2470-9468
DOI	10.1126/sciimmunol.abj0789
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Article ; Online: Dendritic Cells Treated with Exogenous Indoleamine 2,3-Dioxygenase Maintain an Immature Phenotype and Suppress Antigen-specific T cell Proliferation.

Bracho-Sanchez, Evelyn / Hassanzadeh, Azadeh / Brusko, Maigan A / Wallet, Mark A / Keselowsky, Benjamin G

Journal of immunology and regenerative medicine

2019 Volume 5

Abstract: Indoleamine 2,3-dioxygenase (IDO), an intracellular enzyme responsible for catalyzing the rate limiting step of tryptophan catabolism, plays a critical role in immune cell suppression and tolerance. Indoleamine 2,3-dioxygenase-mediated depletion of the ... ...

Abstract	Indoleamine 2,3-dioxygenase (IDO), an intracellular enzyme responsible for catalyzing the rate limiting step of tryptophan catabolism, plays a critical role in immune cell suppression and tolerance. Indoleamine 2,3-dioxygenase-mediated depletion of the essential amino acid tryptophan increases susceptibility of T cells to apoptosis, while kynurenine and its downstream metabolites, such as 3-hydroxyanthranilic acid and quinolinic acid, have a direct cytotoxic effect on conventional effector T cells. Additionally, IDO-expressing antigen presenting cells (APCs) induce proliferation of regulatory T cells. When expressed by an APC, the immunosuppressive effects of IDO may act directly on the APC as well as indirectly upon local T cells. One approach to elicit immune tolerance or reduce inflammation therefore is to promote expression of IDO. However, this approach is constrained by several factors including the potential for deleterious biologic effects of conventional IDO-inducing agents such as interferon gamma (IFNγ), and the potential limitations of constitutive gene transfection. Alternatively, direct action of recombinant IDO enzyme supplied exogenously as a potential therapeutic in the extracellular space has not been investigated previously, and is the focus of this work. Results indicate exogenous recombinant human IDO supplementation influences murine dendritic cell (DC) maturation and ability to suppress antigen specific T cell proliferation. Following treatment, DCs were refractory to maturation by LPS as defined by co-stimulatory molecule expression (CD80 and CD86) and major histocompatibility complex II (MHC-II) expression. Dendritic cells exhibited skewing toward an anti-inflammatory cytokine release profile, with reduced secretion of IL-12p70 and maintained basal level of secreted IL-10. Notably, IDO-treated DCs suppressed proliferation of ovalbumin (OVA) antigen-specific CD4
Language	English
Publishing date	2019-02-10
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-4988
ISSN (online)	2468-4988
DOI	10.1016/j.regen.2019.100015
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Article: geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Missarova, Alsu / Jain, Jaison / Butler, Andrew / Ghazanfar, Shila / Stuart, Tim / Brusko, Maigan / Wasserfall, Clive / Nick, Harry / Brusko, Todd / Atkinson, Mark / Satija, Rahul / Marioni, John C.

Genome biology. 2021 Dec., v. 22, no. 1

2021

Abstract: scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre- ... ...

Abstract	scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.
Keywords	data collection ; genes ; transcriptomics
Language	English
Dates of publication	2021-12
Size	p. 333.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02548-z
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Immunomodulatory Dual-Sized Microparticle System Conditions Human Antigen Presenting Cells Into a Tolerogenic Phenotype

Brusko, Maigan A / Stewart, Joshua M / Posgai, Amanda L / Wasserfall, Clive H / Atkinson, Mark A / Brusko, Todd M / Keselowsky, Benjamin G

Frontiers in immunology

2020 Volume 11, Page(s) 574447

Abstract: Current monotherapeutic agents fail to restore tolerance to self-antigens in autoimmune individuals without systemic immunosuppression. We hypothesized that a combinatorial drug formulation delivered by a poly-lactic-co-glycolic acid (PLGA) dual-sized ... ...

Abstract	Current monotherapeutic agents fail to restore tolerance to self-antigens in autoimmune individuals without systemic immunosuppression. We hypothesized that a combinatorial drug formulation delivered by a poly-lactic-co-glycolic acid (PLGA) dual-sized microparticle (dMP) system would facilitate tunable drug delivery to elicit immune tolerance. Specifically, we utilized 30 µm MPs to provide local sustained release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and transforming growth factor β1 (TGF-β1) along with 1 µm MPs to facilitate phagocytic uptake of encapsulated antigen and 1α,25(OH)
MeSH term(s)	Antigen Presentation/drug effects ; Autoantigens/immunology ; Calcitriol/chemistry ; Calcitriol/pharmacology ; Dendritic Cells/drug effects ; Dendritic Cells/immunology ; Diabetes Mellitus, Type 1/immunology ; Drug Carriers/chemistry ; Drug Carriers/pharmacology ; Granulocyte-Macrophage Colony-Stimulating Factor/chemistry ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Humans ; Immune Tolerance/drug effects ; Immunomodulation ; Lymphocyte Activation ; Monocytes/drug effects ; Particle Size ; Phenotype ; Polylactic Acid-Polyglycolic Acid Copolymer/chemistry ; Polylactic Acid-Polyglycolic Acid Copolymer/pharmacology ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/drug effects ; T-Lymphocytes/immunology ; Transforming Growth Factor beta1/chemistry ; Transforming Growth Factor beta1/pharmacology
Chemical Substances	Autoantigens ; Drug Carriers ; Receptors, Antigen, T-Cell ; Transforming Growth Factor beta1 ; Polylactic Acid-Polyglycolic Acid Copolymer (1SIA8062RS) ; Granulocyte-Macrophage Colony-Stimulating Factor (83869-56-1) ; Calcitriol (FXC9231JVH)
Language	English
Publishing date	2020-10-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.574447
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Article ; Online: geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Missarova, Alsu / Jain, Jaison / Butler, Andrew / Ghazanfar, Shila / Stuart, Tim / Brusko, Maigan / Wasserfall, Clive / Nick, Harry / Brusko, Todd / Atkinson, Mark / Satija, Rahul / Marioni, John C

Genome biology

2021 Volume 22, Issue 1, Page(s) 333

Abstract	scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.
MeSH term(s)	Algorithms ; Cluster Analysis ; Gene Expression Profiling ; Humans ; RNA-Seq ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Transcriptome ; Exome Sequencing
Language	English
Publishing date	2021-12-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02548-z
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Article ; Online: Human immune phenotyping reveals accelerated aging in type 1 diabetes.

JCI insight

2023 Volume 8, Issue 17

Abstract: The proportions and phenotypes of immune cell subsets in peripheral blood undergo continual and dramatic remodeling throughout the human life span, which complicates efforts to identify disease-associated immune signatures in type 1 diabetes (T1D). We ... ...

Abstract	The proportions and phenotypes of immune cell subsets in peripheral blood undergo continual and dramatic remodeling throughout the human life span, which complicates efforts to identify disease-associated immune signatures in type 1 diabetes (T1D). We conducted cross-sectional flow cytometric immune profiling on peripheral blood from 826 individuals (stage 3 T1D, their first-degree relatives, those with ≥2 islet autoantibodies, and autoantibody-negative unaffected controls). We constructed an immune age predictive model in unaffected participants and observed accelerated immune aging in T1D. We used generalized additive models for location, shape, and scale to obtain age-corrected data for flow cytometry and complete blood count readouts, which can be visualized in our interactive portal (ImmScape); 46 parameters were significantly associated with age only, 25 with T1D only, and 23 with both age and T1D. Phenotypes associated with accelerated immunological aging in T1D included increased CXCR3+ and programmed cell death 1-positive (PD-1+) frequencies in naive and memory T cell subsets, despite reduced PD-1 expression levels on memory T cells. Phenotypes associated with T1D after age correction were predictive of T1D status. Our findings demonstrate advanced immune aging in T1D and highlight disease-associated phenotypes for biomarker monitoring and therapeutic interventions.
MeSH term(s)	Humans ; Infant ; Diabetes Mellitus, Type 1 ; Cross-Sectional Studies ; Programmed Cell Death 1 Receptor ; Autoantibodies ; Aging
Chemical Substances	Programmed Cell Death 1 Receptor ; Autoantibodies
Language	English
Publishing date	2023-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.170767
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