LIVIVO - Search results -

Search results

Result 1 - 10 of total 22

Search options

Article ; Online: Advancing Fairness in Cardiac Care: Strategies for Mitigating Bias in Artificial Intelligence Models within Cardiology.

Nolin Lapalme, Alexis / Corbin, Denis / Tastet, Olivier / Avram, Robert / Hussin, Julie G

2024

Abstract: In the dynamic field of medical artificial intelligence (AI), cardiology stands out as a key area for its technological advancements and clinical application. This review explores the complex issue of data bias, specifically addressing those encountered ... ...

Abstract	In the dynamic field of medical artificial intelligence (AI), cardiology stands out as a key area for its technological advancements and clinical application. This review explores the complex issue of data bias, specifically addressing those encountered during the development and implementation of AI tools in cardiology. We dissect the origins and impacts of these biases, which challenge their reliability and widespread applicability in healthcare. Using a case study, we highlight the complexities involved in addressing these biases from a clinical viewpoint. The goal of this review is to equip researchers and clinicians with the practical knowledge needed to identify, understand, and mitigate these biases, advocating for the creation of AI solutions that are not just technologically sound, but also fair and effective for all patient demographics.
Language	English
Publishing date	2024-05-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	632813-1
ISSN	1916-7075 ; 0828-282X
ISSN (online)	1916-7075
ISSN	0828-282X
DOI	10.1016/j.cjca.2024.04.026
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 2150: 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 ▾

Article ; Online: Refining SARS-CoV-2 Intra-host Variation by Leveraging Large-scale Sequencing Data

Mostefai, Fatima / Grenier, Jean-Christophe / Poujol, Raphäel / Hussin, Julie G.

bioRxiv

Abstract: Understanding the evolution of viral genomes is essential for elucidating how viruses adapt and change over time. Analyzing intra-host single nucleotide variants (iSNVs) provides key insights into the mechanisms driving the emergence of new viral ... ...

Abstract	Understanding the evolution of viral genomes is essential for elucidating how viruses adapt and change over time. Analyzing intra-host single nucleotide variants (iSNVs) provides key insights into the mechanisms driving the emergence of new viral lineages, which is crucial for predicting and mitigating future viral threats. Despite the potential of next-generation sequencing (NGS) to capture these iSNVs, the process is fraught with challenges, particularly the risk of capturing sequencing artifacts that may result in false iSNVs. To tackle this issue, we developed a two-step workflow designed to enhance the reliability of iSNV detection in large heterogeneous collections of NGS libraries. We use over 130,000 publicly available SARS-CoV-2 NGS libraries to show how our comprehensive workflow effectively distinguishes emerging viral mutations from sequencing errors. This approach incorporates rigorous bioinformatics protocols, stringent quality control metrics, and innovative usage of dimensionality reduction methods to generate insightful representations of this high-dimensional dataset. We identified and mitigated notable batch effects linked to specific sequencing centers around the world and introduced quality control metrics such as the Strand Bias Likelihood that considers strand coverage imbalance, enhancing iSNV reliability. Additionally, we pioneer the application of the PHATE visualization approach to genomic data and introduce a methodology that quantifies how closely related groups of data points are within a two-dimensional space, enhancing our ability to explain clustering patterns based on their shared genetic characteristics. Our workflow not only sheds light on the complexities of viral genomic analysis with state-of-the-art sequencing technologies but also advances the detection of accurate intra-host mutations, opening the door for an enhanced understanding of viral adaptation mechanisms.
Keywords	covid19
Language	English
Publishing date	2024-05-01
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.04.26.591384
Database	COVID19

Full text online

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: Comparative Study of Protein Aggregation Propensity and Mutation Tolerance Between Naked Mole-Rat and Mouse.

Besse, Savandara / Poujol, Raphaël / Hussin, Julie G

Genome biology and evolution

2022 Volume 14, Issue 5

Abstract: The molecular mechanisms of aging and life expectancy have been studied in model organisms with short lifespans. However, long-lived species may provide insights into successful strategies for healthy aging, potentially opening the door for novel ... ...

Abstract	The molecular mechanisms of aging and life expectancy have been studied in model organisms with short lifespans. However, long-lived species may provide insights into successful strategies for healthy aging, potentially opening the door for novel therapeutic interventions in age-related diseases. Notably, naked mole-rats, the longest-lived rodent, present attenuated aging phenotypes compared with mice. Their resistance toward oxidative stress has been proposed as one hallmark of their healthy aging, suggesting their ability to maintain cell homeostasis, specifically their protein homeostasis. To identify the general principles behind their protein homeostasis robustness, we compared the aggregation propensity and mutation tolerance of naked mole-rat and mouse orthologous proteins. Our analysis showed no proteome-wide differential effects in aggregation propensity and mutation tolerance between these species, but several subsets of proteins with a significant difference in aggregation propensity. We found an enrichment of proteins with higher aggregation propensity in naked mole-rat, and these are functionally involved in the inflammasome complex and nucleic acid binding. On the other hand, proteins with lower aggregation propensity in naked mole-rat have a significantly higher mutation tolerance compared with the rest of the proteins. Among them, we identified proteins known to be associated with neurodegenerative and age-related diseases. These findings highlight the intriguing hypothesis about the capacity of the naked mole-rat proteome to delay aging through its proteomic intrinsic architecture.
MeSH term(s)	Animals ; Longevity/genetics ; Mice ; Mole Rats/genetics ; Mutation ; Protein Aggregates ; Proteome/genetics ; Proteomics
Chemical Substances	Protein Aggregates ; Proteome
Language	English
Publishing date	2022-04-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evac057
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Toward computing attributions for dimensionality reduction techniques.

Scicluna, Matthew / Grenier, Jean-Christophe / Poujol, Raphaël / Lemieux, Sébastien / Hussin, Julie G

Bioinformatics advances

2023 Volume 3, Issue 1, Page(s) vbad097

Abstract: Summary: We describe the problem of computing local feature attributions for dimensionality reduction methods. We use one such method that is well established within the context of supervised classification-using the gradients of target outputs with ... ...

Abstract	Summary: We describe the problem of computing local feature attributions for dimensionality reduction methods. We use one such method that is well established within the context of supervised classification-using the gradients of target outputs with respect to the inputs-on the popular dimensionality reduction technique t-SNE, widely used in analyses of biological data. We provide an efficient implementation for the gradient computation for this dimensionality reduction technique. We show that our explanations identify significant features using novel validation methodology; using synthetic datasets and the popular MNIST benchmark dataset. We then demonstrate the practical utility of our algorithm by showing that it can produce explanations that agree with domain knowledge on a SARS-CoV-2 sequence dataset. Throughout, we provide a road map so that similar explanation methods could be applied to other dimensionality reduction techniques to rigorously analyze biological datasets. Availability and implementation: We have created a Python package that can be installed using the following command: pip install interpretable_tsne. All code used can be found at github.com/MattScicluna/interpretable_tsne.
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad097
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: Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans.

Richard-St-Hilaire, Alex / Gamache, Isabel / Pelletier, Justin / Grenier, Jean-Christophe / Poujol, Raphaël / Hussin, Julie G

Genome biology and evolution

2023 Volume 16, Issue 1

Abstract: Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and ... ...

Abstract	Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.
MeSH term(s)	Animals ; Humans ; Cytochrome P-450 CYP3A/genetics ; Cytochrome P-450 CYP3A/metabolism ; Hominidae/metabolism ; Cytochrome P-450 Enzyme System/genetics ; Polymorphism, Genetic ; Selection, Genetic
Chemical Substances	Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evad236
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Study of effect modifiers of genetically predicted CETP reduction.

Legault, Marc-André / Barhdadi, Amina / Gamache, Isabel / Lemaçon, Audrey / Lemieux Perreault, Louis-Philippe / Grenier, Jean-Christophe / Sylvestre, Marie-Pierre / Hussin, Julie G / Rhainds, David / Tardif, Jean-Claude / Dubé, Marie-Pierre

Genetic epidemiology

2023 Volume 47, Issue 2, Page(s) 198–212

Abstract: Genetic variants in drug targets can be used to predict the long-term, on-target effect of drugs. Here, we extend this principle to assess how sex and body mass index may modify the effect of genetically predicted lower CETP levels on biomarkers and ... ...

Abstract	Genetic variants in drug targets can be used to predict the long-term, on-target effect of drugs. Here, we extend this principle to assess how sex and body mass index may modify the effect of genetically predicted lower CETP levels on biomarkers and cardiovascular outcomes. We found sex and body mass index (BMI) to be modifiers of the association between genetically predicted lower CETP and lipid biomarkers in UK Biobank participants. Female sex and lower BMI were associated with higher high-density lipoprotein cholesterol and lower low-density lipoprotein cholesterol for the same genetically predicted reduction in CETP concentration. We found that sex also modulated the effect of genetically lower CETP on cholesterol efflux capacity in samples from the Montreal Heart Institute Biobank. However, these modifying effects did not extend to sex differences in cardiovascular outcomes in our data. Our results provide insight into the clinical effects of CETP inhibitors in the presence of effect modification based on genetic data. The approach can support precision medicine applications and help assess the external validity of clinical trials.
MeSH term(s)	Humans ; Male ; Female ; Cholesterol Ester Transfer Proteins/genetics ; Cholesterol, HDL ; Cholesterol, LDL ; Biomarkers
Chemical Substances	Cholesterol Ester Transfer Proteins ; Cholesterol, HDL ; Cholesterol, LDL ; Biomarkers ; CETP protein, human
Language	English
Publishing date	2023-01-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605785-8
ISSN	1098-2272 ; 0741-0395
ISSN (online)	1098-2272
ISSN	0741-0395
DOI	10.1002/gepi.22514
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 1969: 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

Details ▾

Article ; Online: Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis.

Viruses

2024 Volume 16, Issue 3

Abstract: Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore ... ...

Abstract	Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Post-Acute COVID-19 Syndrome ; COVID-19 ; COVID-19 Serotherapy ; Immunocompromised Host ; Antibodies, Monoclonal ; Mutation ; Spike Glycoprotein, Coronavirus/genetics ; Antibodies, Viral ; Antibodies, Neutralizing
Chemical Substances	Antibodies, Monoclonal ; Spike Glycoprotein, Coronavirus ; Antibodies, Viral ; Antibodies, Neutralizing ; spike protein, SARS-CoV-2
Language	English
Publishing date	2024-02-23
Publishing country	Switzerland
Document type	Case Reports ; Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v16030342
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis.

N'Guessan, Arnaud / Kailasam, Senthilkumar / Mostefai, Fatima / Poujol, Raphaël / Grenier, Jean-Christophe / Ismailova, Nailya / Contini, Paola / De Palma, Raffaele / Haber, Carsten / Stadler, Volker / Bourque, Guillaume / Hussin, Julie G / Shapiro, B Jesse / Fritz, Jörg H / Piccirillo, Ciriaco A

iScience

2023 Volume 26, Issue 8, Page(s) 107394

Abstract: Here, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses. Applying a high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 ... ...

Abstract	Here, we exploit a deep serological profiling strategy coupled with an integrated, computational framework for the analysis of SARS-CoV-2 humoral immune responses. Applying a high-density peptide array (HDPA) spanning the entire proteomes of SARS-CoV-2 and endemic human coronaviruses allowed identification of B cell epitopes and relate them to their evolutionary and structural properties. We identify hotspots of pre-existing immunity and identify cross-reactive epitopes that contribute to increasing the overall humoral immune response to SARS-CoV-2. Using a public dataset of over 38,000 viral genomes from the early phase of the pandemic, capturing both inter- and within-host genetic viral diversity, we determined the evolutionary profile of epitopes and the differences across proteins, waves, and SARS-CoV-2 variants. Lastly, we show that mutations in spike and nucleocapsid epitopes are under stronger selection between than within patients, suggesting that most of the selective pressure for immune evasion occurs upon transmission between hosts.
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107394
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: Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results.

Baron, Cantin / Cherkaoui, Sarah / Therrien-Laperriere, Sandra / Ilboudo, Yann / Poujol, Raphaël / Mehanna, Pamela / Garrett, Melanie E / Telen, Marilyn J / Ashley-Koch, Allison E / Bartolucci, Pablo / Rioux, John D / Lettre, Guillaume / Des Rosiers, Christine / Ruiz, Matthieu / Hussin, Julie G

bioRxiv : the preprint server for biology

2023

Abstract: Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these ... ...

Abstract	Studies combining metabolomics and genetics, known as metabolite genome-wide association studies (mGWAS), have provided valuable insights into our understanding of the genetic control of metabolite levels. However, the biological interpretation of these associations remains challenging due to a lack of existing tools to annotate mGWAS gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we computed the shortest reactional distance (SRD) based on the curated knowledge of the KEGG database to explore its utility in enhancing the biological interpretation of results from three independent mGWAS, including a case study on sickle cell disease patients. Results show that, in reported mGWAS pairs, there is an excess of small SRD values and that SRD values and p-values significantly correlate, even beyond the standard conservative thresholds. The added-value of SRD annotation is shown for identification of potential false negative hits, exemplified by the finding of gene-metabolite associations with SRD ≤1 that did not reach standard genome-wide significance cut-off. The wider use of this statistic as an mGWAS annotation would prevent the exclusion of biologically relevant associations and can also identify errors or gaps in current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs that can be used to integrate statistical evidence to biological networks.
Language	English
Publishing date	2023-03-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.22.533869
Database	MEDical Literature Analysis and Retrieval System OnLINE

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 ▾

Article ; Online: Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results.

Baron, Cantin / Cherkaoui, Sarah / Therrien-Laperriere, Sandra / Ilboudo, Yann / Poujol, Raphaël / Mehanna, Pamela / Garrett, Melanie E / Telen, Marilyn J / Ashley-Koch, Allison E / Bartolucci, Pablo / Rioux, John D / Lettre, Guillaume / Rosiers, Christine Des / Ruiz, Matthieu / Hussin, Julie G

iScience

2023 Volume 26, Issue 12, Page(s) 108473

Abstract: Metabolite genome-wide association studies (mGWAS) have advanced our understanding of the genetic control of metabolite levels. However, interpreting these associations remains challenging due to a lack of tools to annotate gene-metabolite pairs beyond ... ...

Abstract	Metabolite genome-wide association studies (mGWAS) have advanced our understanding of the genetic control of metabolite levels. However, interpreting these associations remains challenging due to a lack of tools to annotate gene-metabolite pairs beyond the use of conservative statistical significance threshold. Here, we introduce the shortest reactional distance (SRD) metric, drawing from the comprehensive KEGG database, to enhance the biological interpretation of mGWAS results. We applied this approach to three independent mGWAS, including a case study on sickle cell disease patients. Our analysis reveals an enrichment of small SRD values in reported mGWAS pairs, with SRD values significantly correlating with mGWAS p values, even beyond the standard conservative thresholds. We demonstrate the utility of SRD annotation in identifying potential false negatives and inaccuracies within current metabolic pathway databases. Our findings highlight the SRD metric as an objective, quantitative and easy-to-compute annotation for gene-metabolite pairs, suitable to integrate statistical evidence to biological networks.
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.108473
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.

To top

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

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

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED