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Article ; Online: G-quadruplex - Characterization of Functions and Potential Therapeutic Uses of Non-canonical DNA Structures.

Prosperi, Mattia

2019 Volume 26, Issue 16, Page(s) 2879–2880

MeSH term(s)	DNA/chemistry ; DNA/genetics ; G-Quadruplexes ; Gene Expression ; Genomic Instability ; Transcription, Genetic
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-09-17
Publishing country	United Arab Emirates
Document type	Editorial
ZDB-ID	1319315-6
ISSN	1875-533X ; 0929-8673
ISSN (online)	1875-533X
ISSN	0929-8673
DOI	10.2174/092986732616190820105842
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Article: Variational Temporal Deconfounder for Individualized Treatment Effect Estimation with Longitudinal Observational Data.

Feng, Zheng / Prosperi, Mattia / Guo, Yi / Bian, Jiang

Research square

2023

Abstract: Purpose: This paper proposes a new approach, Variational Temporal Deconfounder (VTD), for estimating individualized treatment effects (ITE) from longitudinal observational data, where we address the hidden confounding issues by using proxies (i.e., ... ...

Abstract	Purpose: This paper proposes a new approach, Variational Temporal Deconfounder (VTD), for estimating individualized treatment effects (ITE) from longitudinal observational data, where we address the hidden confounding issues by using proxies (i.e., surrogate variables that serve for unobservable variables). Methods: We build VTD by incorporating a variational recurrent autoencoder that learns the latent encodings of hidden confounders from observed proxies and an ITE estimation network that takes the learned hidden encodings to predict the probability of receiving treatments and potential outcomes. Results: We test VTD on both synthetic and real-world clinical data, and the results from synthetic data experiments demonstrate VTD's effectiveness in deconfounding by outperforming existing methods, while results from two real-world datasets (i.e., Medical Information Mart for Intensive Care version III [MIMIC-III] and the National Alzheimer's Coordinating Center [NACC] database) suggest that the performance of the VTD model outperforms existing baseline models, however, varies depending on the assumptions of underlying causal structures and availability of proxies for hidden confounders. Conclusion: The VTD offers a unique solution to address the confounding bias without the "unconfoundedness" assumption when estimating the ITE from longitudinal observational data. The elimination of the requirement for the "unconfoundedness" assumption makes the VTD more versatile and practical in real-world clinical applications of personalized medicine.
Language	English
Publishing date	2023-02-06
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2536079/v1
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Article: The

Marini, Simone / Boucher, Christina / Noyes, Noelle / Prosperi, Mattia

Frontiers in microbiology

2023 Volume 14, Page(s) 1060891

Abstract: Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e ... ...

Abstract	Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e.g., gene transfers, rearrangements) aspects. Curated ARG databases exist together with assorted ARG classification approaches (e.g., database alignment, machine learning). Besides ARGs that naturally occur in bacterial strains or are acquired through mobile elements, there are chromosomal genes that can render a bacterium resistant to antibiotics through point mutations, i.e., ARG variants (ARGVs). While ARG repositories also collect ARGVs, there are only a few tools that are able to identify ARGVs from metagenomics and high throughput sequencing data, with a number of limitations (e.g., pre-assembly,
Language	English
Publishing date	2023-03-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1060891
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Article: Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies.

Prosperi, Mattia / Rife, Brittany / Marini, Simone / Salemi, Marco

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine

2023 Volume 2022, Page(s) 2940–2944

Abstract: The SARS-CoV-2 pandemic has been presenting in periodic waves and multiple variants, of which some dominated over time with increased transmissibility. SARS-CoV-2 is still adapting in the human population, thus it is crucial to understand its ... ...

Abstract	The SARS-CoV-2 pandemic has been presenting in periodic waves and multiple variants, of which some dominated over time with increased transmissibility. SARS-CoV-2 is still adapting in the human population, thus it is crucial to understand its evolutionary patterns and dynamics ahead of time. In this work, we analyzed transmission clusters and topology of SARS-CoV-2 phylogenies at the global, regional (North America) and clade-specific (Delta and Omicron) epidemic scales. We used the Nextstrain's nCov open global all-time phylogeny (September 2022, 2,698 strains, 2,243 for North America, 499 for Delta21A, and 543 for Omicron20M), with Nextstrain's clade annotation and Pango lineages. Transmission clusters were identified using Phylopart, DYNAMITE, and several tree imbalance measures were calculated, including staircase-ness, Sackin and Colless index. We found that the phylogenetic clustering profiles of the global epidemic have highest diversification at a distance threshold of 3% (divergence of 10, where the tree sampled median is 49). Phylopart and DYNAMITE clusters moderately-to-highly agree with the Pango nomenclature and the Nextstrain's clade. At the regional and clade-specific scale, transmission clustering profiles tend to flatten and similar clusters are found at distance thresholds between 0.05% and 25%. All the considered phylogenies exhibit high tree imbalance with respect to what expected in random phylogenies, suggesting short infection times and antigenic drift, perhaps due to progressive transition from innate to adaptive immunity in the population.
Language	English
Publishing date	2023-01-02
Publishing country	United States
Document type	Journal Article
DOI	10.1109/bibm55620.2022.9995364
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Article: KARGA: Multi-platform Toolkit for

Prosperi, Mattia / Marini, Simone

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics

2021 Volume 2021

Abstract: High-throughput sequencing is widely used for strain detection and characterization of antibiotic resistance in microbial metagenomic samples. Current analytical tools use curated antibiotic resistance gene (ARG) databases to classify individual ... ...

Abstract	High-throughput sequencing is widely used for strain detection and characterization of antibiotic resistance in microbial metagenomic samples. Current analytical tools use curated antibiotic resistance gene (ARG) databases to classify individual sequencing reads or assembled contigs. However, identifying ARGs from raw read data can be time consuming (especially if assembly or alignment is required) and challenging, due to genome rearrangements and mutations. Here, we present the
Language	English
Publishing date	2021-08-10
Publishing country	United States
Document type	Journal Article
ISSN	2641-3590
ISSN	2641-3590
DOI	10.1109/bhi50953.2021.9508479
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Article ; Online: Assessing HIV-related stigma in the clinical setting: are providers in Florida interested?

Fisk-Hoffman, Rebecca J / Woody, Aislinn / Prosperi, Mattia / Cook, Robert L / Cook, Christa / Vaddiparti, Krishna

AIDS care

2024 Volume 36, Issue 2, Page(s) 248–254

Abstract: HIV-related stigma is a key contributor to poor HIV-related health outcomes. The purpose of this study is to explore implementing a stigma measure into routine HIV care focusing on the 10-item Medical Monitoring Project measure as a proposed measure. ... ...

Abstract	HIV-related stigma is a key contributor to poor HIV-related health outcomes. The purpose of this study is to explore implementing a stigma measure into routine HIV care focusing on the 10-item Medical Monitoring Project measure as a proposed measure. Healthcare providers engaged in HIV-related care in Florida were recruited. Participants completed an interview about their perceptions of measures to assess stigma during clinical care. The analysis followed a directed content approach. Fifteen participants completed the interviews (87% female, 47% non-Hispanic White, case manager 40%). Most providers thought that talking about stigma would be helpful (89%). Three major themes emerged from the analysis: acceptability, subscales of interest, and utility. In acceptability, participants mentioned that assessing stigma could encourage patient-centered care and serve as a conversation starter, but some mentioned not having enough time. Participants thought that the disclosure concerns and negative self-image subscales were most relevant. Some worried they would not have resources for patients or that some issues were beyond their influence. Participants were generally supportive of routinely addressing HIV-related stigma in clinical care, but were concerned that resources, especially to address concerns about disclosure and negative self-image, were not available.
MeSH term(s)	Humans ; Female ; Male ; Florida ; HIV Infections ; Social Stigma ; Anxiety ; Disclosure
Language	English
Publishing date	2024-01-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1012651-x
ISSN	1360-0451 ; 0954-0121
ISSN (online)	1360-0451
ISSN	0954-0121
DOI	10.1080/09540121.2023.2279981
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Article: Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.

Rancati, Simone / Nicora, Giovanna / Prosperi, Mattia / Bellazzi, Riccardo / Salemi, Marco / Marini, Simone

bioRxiv : the preprint server for biology

2024

Abstract: The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and lineages outcompeting previously circulating ones because of, among other factors, ... ...

Abstract	The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and lineages outcompeting previously circulating ones because of, among other factors, increased transmissibility and immune escape
Language	English
Publishing date	2024-02-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.24.563721
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Article ; Online: DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.

Sun, Chaoyue / Fang, Ruogu / Salemi, Marco / Prosperi, Mattia / Rife Magalis, Brittany

PLoS computational biology

2024 Volume 20, Issue 4, Page(s) e1011351

Abstract: In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in ... ...

Abstract	In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations. Moreover, tree topology and the incorporation of population parameters (phylodynamics) can be useful in reconstructing the evolutionary dynamics of an epidemic across space and time among individuals. We now demonstrate the utility of phylodynamic trees for transmission modeling and forecasting, developing a phylogeny-based deep learning system, referred to as DeepDynaForecast. Our approach leverages a primal-dual graph learning structure with shortcut multi-layer aggregation, which is suited for the early identification and prediction of transmission dynamics in emerging high-risk groups. We demonstrate the accuracy of DeepDynaForecast using simulated outbreak data and the utility of the learned model using empirical, large-scale data from the human immunodeficiency virus epidemic in Florida between 2012 and 2020. Our framework is available as open-source software (MIT license) at github.com/lab-smile/DeepDynaForcast.
MeSH term(s)	Deep Learning ; Phylogeny ; Humans ; Epidemics/statistics & numerical data ; Computational Biology/methods ; HIV Infections/transmission ; HIV Infections/epidemiology ; Software ; Florida/epidemiology ; Algorithms ; Computer Simulation ; Disease Outbreaks/statistics & numerical data
Language	English
Publishing date	2024-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; 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.1011351
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Article ; Online: Demographics, Trends, and Clinical Characteristics of HIV Pre-Exposure Prophylaxis Recipients and People Newly Diagnosed with HIV from Large Electronic Health Records in Florida.

Liu, Yiyang / Siddiqi, Khairul A / Cho, Hwayoung / Park, Haesuk / Prosperi, Mattia / Cook, Robert L

AIDS patient care and STDs

2024 Volume 38, Issue 1, Page(s) 14–22

Abstract: Florida is one of the HIV epicenters with high incidence and marked sociodemographic disparities. We analyzed a decade of statewide electronic health record/claims data-OneFlorida+-to identify and characterize pre-exposure prophylaxis (PrEP) recipients ... ...

Abstract	Florida is one of the HIV epicenters with high incidence and marked sociodemographic disparities. We analyzed a decade of statewide electronic health record/claims data-OneFlorida+-to identify and characterize pre-exposure prophylaxis (PrEP) recipients and newly diagnosed HIV cases in Florida. Refined computable phenotype algorithms were applied and a total of 2186 PrEP recipients and 7305 new HIV diagnoses were identified between January 2013 and April 2021. We examined patients' sociodemographic characteristics, stratified by self-reported sex, along with both frequency-driven and expert-selected descriptions of clinical conditions documented within 12 months before the first PrEP use or HIV diagnosis. PrEP utilization rate increased in both sexes; higher rates were observed among males with sex differences widening in recent years. HIV incidence peaked in 2016 and then decreased with minimal sex differences observed. Clinical characteristics were similar between the PrEP and new HIV diagnosis cohorts, characterized by a low prevalence of sexually transmitted infections (STIs) and a high prevalence of mental health and substance use conditions. Study limitations include the overrepresentation of Medicaid recipients, with over 96% of female PrEP users on Medicaid, and the inclusion of those engaged in regular health care. Although PrEP uptake increased in Florida, and HIV incidence decreased, sex disparity among PrEP recipients remained. Screening efforts beyond individuals with documented prior STI and high-risk behavior, especially for females, including integration of mental health care with HIV counseling and testing, are crucial to further equalize PrEP access and improve HIV prevention programs.
MeSH term(s)	United States ; Humans ; Female ; Male ; Florida/epidemiology ; Electronic Health Records ; Pre-Exposure Prophylaxis ; HIV Infections/diagnosis ; HIV Infections/epidemiology ; HIV Infections/prevention & control ; Demography
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1326868-5
ISSN	1557-7449 ; 0893-5068 ; 1087-2914
ISSN (online)	1557-7449
ISSN	0893-5068 ; 1087-2914
DOI	10.1089/apc.2023.0220
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Zs.A 2328: Show issues

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Article ; Online: Comorbidity Burden and Health Care Utilization by Substance use Disorder Patterns among People with HIV in Florida.

Liu, Yiyang / Manavalan, Preeti / Siddiqi, Khairul / Cook, Robert L / Prosperi, Mattia

AIDS and behavior

2024

Abstract: Substance use disorder (SUD), a common comorbidity among people with HIV (PWH), adversely affects HIV clinical outcomes and HIV-related comorbidities. However, less is known about the incidence of different chronic conditions, changes in overall ... ...

Abstract	Substance use disorder (SUD), a common comorbidity among people with HIV (PWH), adversely affects HIV clinical outcomes and HIV-related comorbidities. However, less is known about the incidence of different chronic conditions, changes in overall comorbidity burden, and health care utilization by SUD status and patterns among PWH in Florida, an area disproportionately affected by the HIV epidemic. We used electronic health records (EHR) from a large southeastern US consortium, the OneFlorida + clinical research data network. We identified a cohort of PWH with 3 + years of EHRs after the first visit with HIV diagnosis. International Classification of Diseases (ICD) codes were used to identify SUD and comorbidity conditions listed in the Charlson comorbidity index (CCI). A total of 42,271 PWH were included (mean age 44.5, 52% Black, 45% female). The prevalence SUD among PWH was 45.1%. Having a SUD diagnosis among PWH was associated with a higher incidence for most of the conditions listed on the CCI and faster increase in CCI score overtime (rate ratio = 1.45, 95%CI 1.42, 1.49). SUD in PWH was associated with a higher mean number of any care visits (21.7 vs. 14.8) and more frequent emergency department (ED, 3.5 vs. 2.0) and inpatient (8.5 vs. 24.5) visits compared to those without SUD. SUD among PWH was associated with a higher comorbidity burden and more frequent ED and inpatient visits than PWH without a diagnosis of SUD. The high SUD prevalence and comorbidity burden call for improved SUD screening, treatment, and integrated care among PWH.
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1339885-4
ISSN	1573-3254 ; 1090-7165
ISSN (online)	1573-3254
ISSN	1090-7165
DOI	10.1007/s10461-024-04325-y
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