LIVIVO - Search results -

Search results

Result 1 - 10 of total 64

Search options

Article ; Online: Neighborhood violent crime exposure is associated with PrEP non-use among black sexually minoritized men and transgender women: A GPS Study.

Flores, John M / Moline, Tyrone / Regan, Seann D / Chen, Yen-Tyng / Shrader, Cho-Hee / Schneider, John A / Duncan, Dustin T / Kim, Byoungjun

AIDS (London, England)

2024

Abstract: Objective: The objective of this study is to use GPS technology to determine if violent and property crime exposure to participants activity spaces affect outcomes of the HIV prevention and care continuum (PCC) among Young Black sexually minoritized men ...

Abstract	Objective: The objective of this study is to use GPS technology to determine if violent and property crime exposure to participants activity spaces affect outcomes of the HIV prevention and care continuum (PCC) among Young Black sexually minoritized men (YBSMM) and Transgender women (TW), a subgroup at high vulnerability for new HIV diagnoses. Exposure to violent and property crime adversely affects a variety of acute and chronic medical conditions; however the relationship between exposure to violent and property crime and HIV risk (e.g., PrEP non use) is unknown. Spatial analytic analysis using dynamic Global Position Systems (GPS) technology can accurately detect geospatial associations between the crime exposure and objective HIV related outcomes. Methods: With the Neighborhoods and Networks (N2) Cohort Study, GPS technology to identify the activity space of 286 (123 PLWH and 163 PWoH) YBSMM & TW living in Chicago, IL, to identified spatial associations between violent and property crime exposures with HIV PCC outcomes. Results: We found that YBSMM & TGW with higher exposure areas with higher levels of violent crime were less likely to use HIV preexposure prophylaxis (PrEP) therapy (aOR 0.76, 95% CI 0.63-0.91, p = 0.03). Conclusion: This study demonstrates the importance of clinical providers to consider violent crime as a potential sociostructural barrier that may impact medication adherence and health care outcomes among vulnerable populations. Additionally, GPS technology offers an alternative data analytic process that may be used to future studies to assist in identifying barriers to ending the HIV epidemic.
Language	English
Publishing date	2024-04-10
Publishing country	England
Document type	Journal Article
ZDB-ID	639076-6
ISSN	1473-5571 ; 0269-9370 ; 1350-2840
ISSN (online)	1473-5571
ISSN	0269-9370 ; 1350-2840
DOI	10.1097/QAD.0000000000003906
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2228: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Integrative computational epigenomics to build data-driven gene regulation hypotheses.

Chen, Tyrone / Tyagi, Sonika

GigaScience

2020 Volume 9, Issue 6

Abstract: Background: Diseases are complex phenotypes often arising as an emergent property of a non-linear network of genetic and epigenetic interactions. To translate this resulting state into a causal relationship with a subset of regulatory features, many ... ...

Abstract	Background: Diseases are complex phenotypes often arising as an emergent property of a non-linear network of genetic and epigenetic interactions. To translate this resulting state into a causal relationship with a subset of regulatory features, many experiments deploy an array of laboratory assays from multiple modalities. Often, each of these resulting datasets is large, heterogeneous, and noisy. Thus, it is non-trivial to unify these complex datasets into an interpretable phenotype. Although recent methods address this problem with varying degrees of success, they are constrained by their scopes or limitations. Therefore, an important gap in the field is the lack of a universal data harmonizer with the capability to arbitrarily integrate multi-modal datasets. Results: In this review, we perform a critical analysis of methods with the explicit aim of harmonizing data, as opposed to case-specific integration. This revealed that matrix factorization, latent variable analysis, and deep learning are potent strategies. Finally, we describe the properties of an ideal universal data harmonization framework. Conclusions: A sufficiently advanced universal harmonizer has major medical implications, such as (i) identifying dysregulated biological pathways responsible for a disease is a powerful diagnostic tool; (2) investigating these pathways further allows the biological community to better understand a disease's mechanisms; and (3) precision medicine also benefits from developments in this area, particularly in the context of the growing field of selective epigenome editing, which can suppress or induce a desired phenotype.
MeSH term(s)	Computational Biology/methods ; Epigenesis, Genetic ; Epigenomics/methods ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Software
Keywords	covid19
Language	English
Publishing date	2020-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giaa064
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A Survey of Current Resources to Study lncRNA-Protein Interactions.

Philip, Melcy / Chen, Tyrone / Tyagi, Sonika

Non-coding RNA

2021 Volume 7, Issue 2

Abstract: Phenotypes are driven by regulated gene expression, which in turn are mediated by complex interactions between diverse biological molecules. Protein-DNA interactions such as histone and transcription factor binding are well studied, along with RNA-RNA ... ...

Abstract	Phenotypes are driven by regulated gene expression, which in turn are mediated by complex interactions between diverse biological molecules. Protein-DNA interactions such as histone and transcription factor binding are well studied, along with RNA-RNA interactions in short RNA silencing of genes. In contrast, lncRNA-protein interaction (LPI) mechanisms are comparatively unknown, likely directed by the difficulties in studying LPI. However, LPI are emerging as key interactions in epigenetic mechanisms, playing a role in development and disease. Their importance is further highlighted by their conservation across kingdoms. Hence, interest in LPI research is increasing. We therefore review the current state of the art in lncRNA-protein interactions. We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation. We discovered that algorithm development is heavily reliant on a few generic databases containing curated LPI information. Additionally, these databases house information at gene-level as opposed to transcript-level annotations. We show that early methods predict LPI using molecular docking, have limited scope and are slow, creating a data processing bottleneck. Recently, machine learning has become the strategy of choice in LPI prediction, likely due to the rapid growth in machine learning infrastructure and expertise. While many of these methods have notable limitations, machine learning is expected to be the basis of modern LPI prediction algorithms.
Language	English
Publishing date	2021-06-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna7020033
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Audio / Video ; Online: Multi-omics data integration for the discovery of COVID-19 drug targets

Tyrone Chen / KIM-ANH LE CAO / Sonika Tyagi

2020

Abstract: The novel coronavirus SARS-Cov-2 continues to have adverse impacts on human health. Despite the volume of experiments performed and data available, its biology is not yet fully understood. Functional omics technologies such as high throughput sequencing ... ...

Abstract	The novel coronavirus SARS-Cov-2 continues to have adverse impacts on human health. Despite the volume of experiments performed and data available, its biology is not yet fully understood. Functional omics technologies such as high throughput sequencing and mass spectrometry allow users to capture large quantities of complex data. From these individual data modalities, it is possible to extract valuable information associated with a biological system under study, leading to new discoveries and a deeper knowledge of biology. However, combining these blocks of information can yield information that is not visible with a single data modality. To better understand this virus, we take a multi-omics integrative view of the data, combining both proteomics and translatome data. This is in contrast to existing studies which mostly focus on a single aspect of functional omics data, primarily the genome. As a result of this fragmented view, valuable information may be masked. Using a latent variable approach, our integrative pipeline unifies proteome and translatome. We compared the features of interest contributing to each biological outcome across the individual data blocks and the integrated omics data. This revealed previously invisible and potentially medically relevant features for drug development.
Keywords	Bioinformatics ; Virology ; Computational Biology ; Knowledge Representation and Machine Learning ; SARS-CoV-2 coronavirus ; genomics ; mitigation approaches ; drugs & medicinal substances repurposing ; COVID-19 virus (SARS-CoV-2) ; data integration ; Machine Learning ; Proteomics ; Translatomics ; covid19
Subject code	004
Publishing date	2020-07-23T03:36:48Z
Publishing country	au
Document type	Audio / Video ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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.

Article ; Online: A multi-modal data harmonisation approach for discovery of COVID-19 drug targets.

Chen, Tyrone / Philip, Melcy / Lê Cao, Kim-Anh / Tyagi, Sonika

Briefings in bioinformatics

2021 Volume 22, Issue 6

Abstract: Despite the volume of experiments performed and data available, the complex biology of coronavirus SARS-COV-2 is not yet fully understood. Existing molecular profiling studies have focused on analysing functional omics data of a single type, which ... ...

Abstract	Despite the volume of experiments performed and data available, the complex biology of coronavirus SARS-COV-2 is not yet fully understood. Existing molecular profiling studies have focused on analysing functional omics data of a single type, which captures changes in a small subset of the molecular perturbations caused by the virus. As the logical next step, results from multiple such omics analysis may be aggregated to comprehensively interpret the molecular mechanisms of SARS-CoV-2. An alternative approach is to integrate data simultaneously in a parallel fashion to highlight the inter-relationships of disease-driving biomolecules, in contrast to comparing processed information from each omics level separately. We demonstrate that valuable information may be masked by using the former fragmented views in analysis, and biomarkers resulting from such an approach cannot provide a systematic understanding of the disease aetiology. Hence, we present a generic, reproducible and flexible open-access data harmonisation framework that can be scaled out to future multi-omics analysis to study a phenotype in a holistic manner. The pipeline source code, detailed documentation and automated version as a R package are accessible. To demonstrate the effectiveness of our pipeline, we applied it to a drug screening task. We integrated multi-omics data to find the lowest level of statistical associations between data features in two case studies. Strongly correlated features within each of these two datasets were used for drug-target analysis, resulting in a list of 84 drug-target candidates. Further computational docking and toxicity analyses revealed seven high-confidence targets, amsacrine, bosutinib, ceritinib, crizotinib, nintedanib and sunitinib as potential starting points for drug therapy and development.
MeSH term(s)	Algorithms ; Biomarkers/chemistry ; COVID-19/drug therapy ; COVID-19/genetics ; COVID-19/pathology ; COVID-19/virology ; Computational Biology ; Databases, Genetic ; Genomics ; Humans ; Molecular Targeted Therapy ; SARS-CoV-2/chemistry ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; Software
Chemical Substances	Biomarkers
Language	English
Publishing date	2021-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbab185
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: 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)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Evaluation of Decision-Making for the Optimal Value of Sustainable Enterprise Development under Global 100 Index Thinking

Tyrone T. Lin / Shu-Yen Hsu / Chiao-Chen Chang

Sustainability, Vol 11, Iss 4, p

2019 Volume 1106

Abstract: This study seeks the best economic returns of a company’s sustainable business process, employs the Triple Bottom Line Model using the Global 100 Index as the decision variable, and follows the Geometric Brownian Motion, so as to determine the optimal ... ...

Abstract	This study seeks the best economic returns of a company’s sustainable business process, employs the Triple Bottom Line Model using the Global 100 Index as the decision variable, and follows the Geometric Brownian Motion, so as to determine the optimal timing for the input of environmental and social costs. The results of the sensitivity analysis show that when the average growth rate of the Global 100 Index is low, the optimal timing for the company’s input of environmental costs and social costs can be obtained. Analysis of the numerical example shows that, based on the financial value of the economic factor, companies should invest in environmental costs as soon as possible. This study replaces the conventional net present value model with the options evaluation model, uses the Global 100 Index as the threshold for decision-making evaluation to provide a more complete decision-making evaluation reference for enterprises, and makes up for the gap in recent research regarding investment time and decision variables. The study results introduce potential strategic value evaluations into the evaluation model of long-term uncertain sustainable operation value, which is more appropriate for the evaluation of the real sustainable operation value. It also provides implementation strategies for decision-makers to mitigate risks under uncertain environments and is the major difference and value of the Real Options Approach (ROA) to supplement Net Present Value (NPV) principles. The results of this study provide a reference for the sustainable development decision-making of corporate sustainability and feasibility and offer an important link in the value chain of food industry operations and management.
Keywords	triple bottom line ; corporate social responsibility ; environmental protection ; corporate sustainability ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	650
Language	English
Publishing date	2019-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

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.

Article ; Online: Single-cell analysis of lymphatic endothelial cell fate specification and differentiation during zebrafish development.

Grimm, Lin / Mason, Elizabeth / Yu, Hujun / Dudczig, Stefanie / Panara, Virginia / Chen, Tyrone / Bower, Neil I / Paterson, Scott / Rondon Galeano, Maria / Kobayashi, Sakurako / Senabouth, Anne / Lagendijk, Anne K / Powell, Joseph / Smith, Kelly A / Okuda, Kazuhide S / Koltowska, Katarzyna / Hogan, Benjamin M

The EMBO journal

2023 Volume 42, Issue 11, Page(s) e112590

Abstract: During development, the lymphatic vasculature forms as a second network derived chiefly from blood vessels. The transdifferentiation of embryonic venous endothelial cells (VECs) into lymphatic endothelial cells (LECs) is a key step in this process. ... ...

Abstract	During development, the lymphatic vasculature forms as a second network derived chiefly from blood vessels. The transdifferentiation of embryonic venous endothelial cells (VECs) into lymphatic endothelial cells (LECs) is a key step in this process. Specification, differentiation and maintenance of LEC fate are all driven by the transcription factor Prox1, yet the downstream mechanisms remain to be elucidated. We here present a single-cell transcriptomic atlas of lymphangiogenesis in zebrafish, revealing new markers and hallmarks of LEC differentiation over four developmental stages. We further profile single-cell transcriptomic and chromatin accessibility changes in zygotic prox1a mutants that are undergoing a LEC-VEC fate shift. Using maternal and zygotic prox1a/prox1b mutants, we determine the earliest transcriptomic changes directed by Prox1 during LEC specification. This work altogether reveals new downstream targets and regulatory regions of the genome controlled by Prox1 and presents evidence that Prox1 specifies LEC fate primarily by limiting blood vascular and haematopoietic fate. This extensive single-cell resource provides new mechanistic insights into the enigmatic role of Prox1 and the control of LEC differentiation in development.
MeSH term(s)	Animals ; Zebrafish/genetics ; Homeodomain Proteins/genetics ; Tumor Suppressor Proteins/genetics ; Endothelial Cells ; Cells, Cultured ; Cell Differentiation ; Lymphatic Vessels ; Lymphangiogenesis/genetics ; Transcription Factors/genetics ; Single-Cell Analysis
Chemical Substances	Homeodomain Proteins ; Tumor Suppressor Proteins ; Transcription Factors
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2022112590
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1808: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 100: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Curvature of the Retroviral Capsid Assembly Is Modulated by a Molecular Switch.

Thames, Tyrone / Bryer, Alexander J / Qiao, Xin / Jeon, Jaekyun / Weed, Ryan / Janicki, Kaylie / Hu, Bingwen / Gor'kov, Peter L / Hung, Ivan / Gan, Zhehong / Perilla, Juan R / Chen, Bo

The journal of physical chemistry letters

2021 Volume 12, Issue 32, Page(s) 7768–7776

Abstract: During the maturation step, the retroviral capsid proteins (CAs) assemble into polymorphic capsids. Their acute curvature is largely determined by 12 pentamers inserted into the hexameric lattice. However, how the CA switches its conformation to control ... ...

Abstract	During the maturation step, the retroviral capsid proteins (CAs) assemble into polymorphic capsids. Their acute curvature is largely determined by 12 pentamers inserted into the hexameric lattice. However, how the CA switches its conformation to control assembly curvature remains unclear. We report the high-resolution structural model of the Rous sarcoma virus (RSV) CA
MeSH term(s)	Capsid/chemistry ; Capsid Proteins/chemistry ; Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Pliability ; Protein Conformation ; Protein Domains ; Rous sarcoma virus/chemistry
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2021-08-10
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.1c01769
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Article ; Online: TGF-β uncouples glycolysis and inflammation in macrophages and controls survival during sepsis.

Gauthier, Thierry / Yao, Chen / Dowdy, Tyrone / Jin, Wenwen / Lim, Yun-Ji / Patiño, Liliana C / Liu, Na / Ohlemacher, Shannon I / Bynum, Andrew / Kazmi, Rida / Bewley, Carole A / Mitrovic, Mladen / Martin, Daniel / Morell, Robert J / Eckhaus, Michael / Larion, Mioara / Tussiwand, Roxane / O'Shea, John J / Chen, WanJun

Science signaling

2023 Volume 16, Issue 797, Page(s) eade0385

Abstract: Changes in metabolism of macrophages are required to sustain macrophage activation in response to different stimuli. We showed that the cytokine TGF-β (transforming growth factor-β) regulates glycolysis in macrophages independently of inflammatory ... ...

Abstract	Changes in metabolism of macrophages are required to sustain macrophage activation in response to different stimuli. We showed that the cytokine TGF-β (transforming growth factor-β) regulates glycolysis in macrophages independently of inflammatory cytokine production and affects survival in mouse models of sepsis. During macrophage activation, TGF-β increased the expression and activity of the glycolytic enzyme PFKL (phosphofructokinase-1 liver type) and promoted glycolysis but suppressed the production of proinflammatory cytokines. The increase in glycolysis was mediated by an mTOR-c-MYC-dependent pathway, whereas the inhibition of cytokine production was due to activation of the transcriptional coactivator SMAD3 and suppression of the activity of the proinflammatory transcription factors AP-1, NF-κB, and STAT1. In mice with LPS-induced endotoxemia and experimentally induced sepsis, the TGF-β-induced enhancement in macrophage glycolysis led to decreased survival, which was associated with increased blood coagulation. Analysis of septic patient cohorts revealed that the expression of
MeSH term(s)	Mice ; Animals ; Transforming Growth Factor beta/metabolism ; Lipopolysaccharides/toxicity ; COVID-19/metabolism ; Macrophages/metabolism ; Sepsis/metabolism ; Inflammation/metabolism ; Cytokines/metabolism ; Glycolysis
Chemical Substances	Transforming Growth Factor beta ; Lipopolysaccharides ; Cytokines
Language	English
Publishing date	2023-08-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2417226-1
ISSN	1937-9145 ; 1945-0877
ISSN (online)	1937-9145
ISSN	1945-0877
DOI	10.1126/scisignal.ade0385
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Evaluation of Decision-Making for the Optimal Value of Sustainable Enterprise Development under Global 100 Index Thinking

Lin, Tyrone T / Chang, Chiao-Chen / Hsu, Shu-Yen

Sustainability. 2019 Feb. 20, v. 11, no. 4

2019

Abstract	This study seeks the best economic returns of a company’s sustainable business process, employs the Triple Bottom Line Model using the Global 100 Index as the decision variable, and follows the Geometric Brownian Motion, so as to determine the optimal timing for the input of environmental and social costs. The results of the sensitivity analysis show that when the average growth rate of the Global 100 Index is low, the optimal timing for the company’s input of environmental costs and social costs can be obtained. Analysis of the numerical example shows that, based on the financial value of the economic factor, companies should invest in environmental costs as soon as possible. This study replaces the conventional net present value model with the options evaluation model, uses the Global 100 Index as the threshold for decision-making evaluation to provide a more complete decision-making evaluation reference for enterprises, and makes up for the gap in recent research regarding investment time and decision variables. The study results introduce potential strategic value evaluations into the evaluation model of long-term uncertain sustainable operation value, which is more appropriate for the evaluation of the real sustainable operation value. It also provides implementation strategies for decision-makers to mitigate risks under uncertain environments and is the major difference and value of the Real Options Approach (ROA) to supplement Net Present Value (NPV) principles. The results of this study provide a reference for the sustainable development decision-making of corporate sustainability and feasibility and offer an important link in the value chain of food industry operations and management.
Keywords	business enterprises ; costs and returns ; decision making ; economic factors ; food industry ; models ; risk ; supply chain ; sustainable development
Language	English
Dates of publication	2019-0220
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518383-7
ISSN	2071-1050
ISSN	2071-1050
DOI	10.3390/su11041106
Database	NAL-Catalogue (AGRICOLA)

Order via subito

To top

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

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

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

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito