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Article ; Online: Exploring the Promise and Challenges of Artificial Intelligence in Biomedical Research and Clinical Practice.

Altara, Raffaele / Basson, Cameron J / Biondi-Zoccai, Giuseppe / Booz, George W

2024

Abstract: Artificial intelligence (AI) is poised to revolutionize how science, and biomedical research in particular, are done. With AI, problem solving and complex tasks using massive data sets can be performed at a much higher rate and dimensionality level ... ...

Abstract	Artificial intelligence (AI) is poised to revolutionize how science, and biomedical research in particular, are done. With AI, problem solving and complex tasks using massive data sets can be performed at a much higher rate and dimensionality level compared to humans. With the ability to handle huge data sets and self-learn, AI is already being exploited in drug design, drug repurposing, toxicology, and material identification. AI could also be used in both basic and clinical research in study design, defining outcomes, analyzing data, interpreting findings, and even identifying the most appropriate areas of investigation and funding sources. State-of-the-art AI-based large language models (LLM), such as ChatGPT and Perplexity, are positioned to change forever how science is communicated and how scientists interact with one another and their profession, including post-publication appraisal and critique. Like all revolutions, upheaval will follow and not all outcomes can be predicted, necessitating guardrails at the onset, especially to minimize the untoward impact of the many drawbacks of LLMs, which include lack of confidentiality, risk of hallucinations, and propagation of mainstream albeit potentially mistaken opinions and perspectives. In this review, we highlight areas of biomedical research that are already being reshaped by AI and how AI is likely to impact it further in the near future. We discuss the potential benefits of AI in biomedical research and address possible risks, some surrounding the creative process, that warrant further reflection.
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	391970-5
ISSN	1533-4023 ; 0160-2446
ISSN (online)	1533-4023
ISSN	0160-2446
DOI	10.1097/FJC.0000000000001546
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Zs.A 1471: Show issues

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Article ; Online: Earthquake focal mechanisms with distributed acoustic sensing.

Li, Jiaxuan / Zhu, Weiqiang / Biondi, Ettore / Zhan, Zhongwen

Nature communications

2023 Volume 14, Issue 1, Page(s) 4181

Abstract: Earthquake focal mechanisms provide critical in-situ insights about the subsurface faulting geometry and stress state. For frequent small earthquakes (magnitude< 3.5), their focal mechanisms are routinely determined using first-arrival polarities picked ... ...

Abstract	Earthquake focal mechanisms provide critical in-situ insights about the subsurface faulting geometry and stress state. For frequent small earthquakes (magnitude< 3.5), their focal mechanisms are routinely determined using first-arrival polarities picked on the vertical component of seismometers. Nevertheless, their quality is usually limited by the azimuthal coverage of the local seismic network. The emerging distributed acoustic sensing (DAS) technology, which can convert pre-existing telecommunication cables into arrays of strain/strain-rate meters, can potentially fill the azimuthal gap and enhance constraints on the nodal plane orientation through its long sensing range and dense spatial sampling. However, determining first-arrival polarities on DAS is challenging due to its single-component sensing and low signal-to-noise ratio for direct body waves. Here, we present a data-driven method that measures P-wave polarities on a DAS array based on cross-correlations between earthquake pairs. We validate the inferred polarities using the regional network catalog on two DAS arrays, deployed in California and each comprising ~ 5000 channels. We demonstrate that a joint focal mechanism inversion combining conventional and DAS polarity picks improves the accuracy and reduces the uncertainty in the focal plane orientation. Our results highlight the significant potential of integrating DAS with conventional networks for investigating high-resolution earthquake source mechanisms.
MeSH term(s)	Humans ; Earthquakes ; Chromosome Inversion ; Problem Solving ; Signal-To-Noise Ratio ; Acoustics
Language	English
Publishing date	2023-07-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39639-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Feasibility of hepatitis C elimination by screening and treatment alone in high-income countries.

Tian, Feng / Forouzannia, Farinaz / Feng, Zeny / Biondi, Mia J / Mendlowitz, Andrew B / Feld, Jordan J / Sander, Beate / Wong, William W L

Hepatology (Baltimore, Md.)

2024

Abstract: Background and aims: Despite the availability of highly effective direct-acting antiviral therapy, chronic hepatitis C (CHC) continues to cause a major public health burden. In many high-income countries, treatment rates have been declining, which was ... ...

Abstract	Background and aims: Despite the availability of highly effective direct-acting antiviral therapy, chronic hepatitis C (CHC) continues to cause a major public health burden. In many high-income countries, treatment rates have been declining, which was exacerbated by the impact of the COVID-19 pandemic, threatening the ability to meet the World Health Organization (WHO)'s targets for eliminating HCV as a public health threat by 2030. We sought to model the impact of CHC in Canada, a resource-rich country with ongoing immigration from HCV-endemic regions; which relies exclusively on risk-based screening for case identification. Approach and results: We developed an agent-based model to characterize the HCV epidemic in a high-income country with ongoing immigration. Combinations of prevention such as harm reduction, screening, and treatment strategies were considered. Model parameters were estimated from the literature and calibrated against historical HCV data. Sensitivity analyses were performed to assess uncertainty. Under the current status quo of risk-based screening, we predict the incidence of CHC-induced decompensated cirrhosis, HCC, and liver-related deaths would decrease by 79.4%, 76.1%, and 62.1%, respectively, between 2015 and 2030, but CHC incidence would only decrease by 11.1%. The results were sensitive to HCV transmission rate and an annual number of people initiating treatment. Conclusions: Current risk-based screening, and subsequent treatment, will be inadequate to achieve WHO goals. With extensive scale-up in screening, and treatment, the mortality target may be achievable, but the target for preventing new CHC cases is unlikely reachable, highlighting the importance of developing enhanced harm-reduction strategies for HCV elimination.
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	604603-4
ISSN	1527-3350 ; 0270-9139
ISSN (online)	1527-3350
ISSN	0270-9139
DOI	10.1097/HEP.0000000000000779
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Zs.A 1660: Show issues

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Article ; Online: Seismic arrival-time picking on distributed acoustic sensing data using semi-supervised learning.

Zhu, Weiqiang / Biondi, Ettore / Li, Jiaxuan / Yin, Jiuxun / Ross, Zachary E / Zhan, Zhongwen

Nature communications

2023 Volume 14, Issue 1, Page(s) 8192

Abstract: Distributed Acoustic Sensing (DAS) is an emerging technology for earthquake monitoring and subsurface imaging. However, its distinct characteristics, such as unknown ground coupling and high noise level, pose challenges to signal processing. Existing ... ...

Abstract	Distributed Acoustic Sensing (DAS) is an emerging technology for earthquake monitoring and subsurface imaging. However, its distinct characteristics, such as unknown ground coupling and high noise level, pose challenges to signal processing. Existing machine learning models optimized for conventional seismic data struggle with DAS data due to its ultra-dense spatial sampling and limited manual labels. We introduce a semi-supervised learning approach to address the phase-picking task of DAS data. We use the pre-trained PhaseNet model to generate noisy labels of P/S arrivals in DAS data and apply the Gaussian mixture model phase association (GaMMA) method to refine these noisy labels and build training datasets. We develop PhaseNet-DAS, a deep learning model designed to process 2D spatio-temporal DAS data to achieve accurate phase picking and efficient earthquake detection. Our study demonstrates a method to develop deep learning models for DAS data, unlocking the potential of integrating DAS in enhancing earthquake monitoring.
Language	English
Publishing date	2023-12-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43355-3
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Article ; Online: An upper-crust lid over the Long Valley magma chamber.

Biondi, Ettore / Zhu, Weiqiang / Li, Jiaxuan / Williams, Ethan F / Zhan, Zhongwen

Science advances

2023 Volume 9, Issue 42, Page(s) eadi9878

Abstract: Geophysical characterization of calderas is fundamental in assessing their potential for future catastrophic volcanic eruptions. The mechanism behind the unrest of Long Valley Caldera in California remains highly debated, with recent periods of uplift ... ...

Abstract	Geophysical characterization of calderas is fundamental in assessing their potential for future catastrophic volcanic eruptions. The mechanism behind the unrest of Long Valley Caldera in California remains highly debated, with recent periods of uplift and seismicity driven either by the release of aqueous fluids from the magma chamber or by the intrusion of magma into the upper crust. We use distributed acoustic sensing data recorded along a 100-kilometer fiber-optic cable traversing the caldera to image its subsurface structure. Our images highlight a definite separation between the shallow hydrothermal system and the large magma chamber located at ~12-kilometer depth. The combination of the geological evidence with our results shows how fluids exsolved through second boiling provide the source of the observed uplift and seismicity.
Language	English
Publishing date	2023-10-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adi9878
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Article ; Online: Laparoscopic right hemicolectomy with complete mesocolic excision for a T4 caecal tumour adherent to the right iliac fossa and invading the lateral abdominal wall with associated phlegmon - a video vignette.

Afzal, Z / Stupalkowska, W / Davies, R J / Wheeler, J / Biondi, A / Di Saverio, S

Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland

2020 Volume 22, Issue 11, Page(s) 1783–1784

MeSH term(s)	Abdominal Wall ; Cecal Neoplasms/surgery ; Cellulitis ; Colectomy ; Colonic Neoplasms/surgery ; Humans ; Ilium ; Laparoscopy ; Lymph Node Excision ; Mesocolon/surgery
Language	English
Publishing date	2020-07-11
Publishing country	England
Document type	Letter ; Video-Audio Media
ZDB-ID	1440017-0
ISSN	1463-1318 ; 1462-8910
ISSN (online)	1463-1318
ISSN	1462-8910
DOI	10.1111/codi.15192
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Zs.A 5799: Show issues

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Article: Volatiles of fungal cultivars act as cues for host-selection in the fungus-farming ambrosia beetle

Gugliuzzo, Antonio / Kreuzwieser, Jürgen / Ranger, Christopher M / Tropea Garzia, Giovanna / Biondi, Antonio / Biedermann, Peter H W

Frontiers in microbiology

2023 Volume 14, Page(s) 1151078

Abstract: Many wood-boring insects use aggregation pheromones during mass colonization of host trees. Bark beetles (Curculionidae: Scolytinae) are a model system, but much less is known about the role of semiochemicals during host selection by ambrosia beetles. As ...

Abstract	Many wood-boring insects use aggregation pheromones during mass colonization of host trees. Bark beetles (Curculionidae: Scolytinae) are a model system, but much less is known about the role of semiochemicals during host selection by ambrosia beetles. As an ecological clade within the bark beetles, ambrosia beetles are obligately dependent on fungal mutualists for their sole source of nutrition. Mass colonization of trees growing in horticultural settings by exotic ambrosia beetles can occur, but aggregation cues have remained enigmatic. To elucidate this mechanism, we first characterized the fungal associates of the exotic, mass-aggregating ambrosia beetle
Language	English
Publishing date	2023-04-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1151078
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Article ; Online: Trypanosoma sp. infection in Boa constrictor snakes: morphological, hematological, clinical biochemistry, molecular, and phylogenetic characteristics.

Fonseca, Maisa S / Santos, Anderson J / Mendonça, Marcos A / Rodamilans, Gustavo M / Marques, Franciane S / Biondi, Ilka / Lira-da-Silva, Rejane M / Aburjaile, Flavia F / Sokolonski, Ana R / Soares, Rodrigo P / Meyer, Roberto / Portela, Ricardo W

Parasitology research

2023 Volume 123, Issue 1, Page(s) 21

Abstract: There are few reports of Trypanosoma in snakes, as well as little information about its pathogenicity in these animals. Thus, the present study aimed to characterize Trypanosoma found in Boa constrictor snakes, to verify the influence of the parasitism ... ...

Abstract	There are few reports of Trypanosoma in snakes, as well as little information about its pathogenicity in these animals. Thus, the present study aimed to characterize Trypanosoma found in Boa constrictor snakes, to verify the influence of the parasitism on hematological and clinical biochemistry parameters, and to perform a phylogenetic study of the isolates. Blood samples from sixty-one boas were analyzed for the presence of trypanosomatids and by hematological and clinical biochemistry assays. The flagellates that were found in this analysis were used for cell culture, morphometry, and molecular analysis. Later, molecular typing phylogenetic studies were performed. Nine positive animals (14.75%) were identified by microscopy analysis. The hematological results showed that parasitized animals presented significantly lower levels of packed cell volume, hemoglobin, mean corpuscular volume, and mean corpuscular hemoglobin. In the leukogram, eosinophils and heterophils counts were higher in parasitized animals. Considering the molecular analyses, the isolates presented a higher identity of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the 18S small subunit ribosomal RNA (SSU rRNA) gene fragments with Trypanosoma serpentis. The phylogenetic tree, using the GAPDH, clustered all isolates with T. serpentis and Trypanosoma cascavelli. This is the first description of T. serpentis parasitizing boas and of the clinical changes caused by trypanosomatid infection in snakes.
MeSH term(s)	Animals ; Boidae/genetics ; Phylogeny ; DNA, Ribosomal/genetics ; Trypanosoma ; RNA, Ribosomal, 18S/genetics ; Snakes ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; DNA, Protozoan
Chemical Substances	DNA, Ribosomal ; RNA, Ribosomal, 18S ; Glyceraldehyde-3-Phosphate Dehydrogenases (EC 1.2.1.-) ; DNA, Protozoan
Language	English
Publishing date	2023-12-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	284966-5
ISSN	1432-1955 ; 0932-0113 ; 0044-3255
ISSN (online)	1432-1955
ISSN	0932-0113 ; 0044-3255
DOI	10.1007/s00436-023-08023-x
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Article: Low‐Magnitude Seismicity With a Downhole Distributed Acoustic Sensing Array—Examples From the FORGE Geothermal Experiment

Lellouch, A. / Schultz, R. / Lindsey, N.J. / Biondi, B.L. / Ellsworth, W.L.

Journal of geophysical research. 2021 Jan., v. 126, no. 1

2021

Abstract: We show the capabilities of a downhole distributed acoustic sensing (DAS) array in detecting, locating, and characterizing low‐magnitude earthquakes occurring in the vicinity of the Frontier Observatory for Research in Geothermal Energy (FORGE) site in ... ...

Abstract	We show the capabilities of a downhole distributed acoustic sensing (DAS) array in detecting, locating, and characterizing low‐magnitude earthquakes occurring in the vicinity of the Frontier Observatory for Research in Geothermal Energy (FORGE) site in Utah. Continuous data for 10.5 days were acquired in a monitoring well at the FORGE geothermal site during the initial stimulation of an enhanced geothermal system in April–May 2019. Earthquake activity beneath Mineral Mountains, Utah also occurred within 10 km of the FORGE monitoring well. During the experiment, four earthquakes were cataloged by routine processing of the University of Utah Seismograph Stations. Our processing of DAS data finds 77 earthquakes during that period, of which 16 are visible on the regional network. Five additional events are found by template matching DAS data. The magnitude of completeness obtained by DAS processing is better by at least M = 0.5 than the dense surface array around the FORGE site. Depth estimation using DAS is more reliable than using a surface array. While a single vertical DAS array is limited in terms of event location due to its azimuthal ambiguity, multiple DAS wells or a combination of a downhole array with surface stations or near‐surface horizontal DAS could jointly resolve locations. All detected events probably originated from the two active source areas, located 3–5 and 8–10 km away from the FORGE site, respectively. Recorded events can be reliably clustered into several distinct families thanks to the spatial density and large number of DAS channels.
Keywords	acoustics ; earthquakes ; geophysics ; geothermal energy ; research ; Utah
Language	English
Dates of publication	2021-01
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ISSN	2169-9313
DOI	10.1029/2020JB020462
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023.

Sjaarda, Calvin P / Lau, Lynette / Simpson, Jared T / Fattouh, Ramzi / Biondi, Mia J / Maguire, Finlay / Campigotto, Aaron / Feng, Yujia / Tozer, Kyla / Wong, Henry / Sung, Wilson W L / Kim, Sean / Marshall, Christian R / Sheth, Prameet M / Kozak, Robert

JAMA network open

2023 Volume 6, Issue 7, Page(s) e2324963

Abstract: Importance: Nirmatrelvir-ritonavir is an oral antiviral medication that improves outcomes in SARS-CoV-2 infections. However, there is concern that antiviral resistance will develop and that these viruses could be selected for after treatment.: ... ...

Abstract	Importance: Nirmatrelvir-ritonavir is an oral antiviral medication that improves outcomes in SARS-CoV-2 infections. However, there is concern that antiviral resistance will develop and that these viruses could be selected for after treatment. Objective: To determine the prevalence of low-frequency SARS-CoV-2 variants in patient samples that could be selected for by nirmatrelvir-ritonavir. Design, setting, and participants: This retrospective cohort study was conducted at 4 laboratories that serve community hospitals, academic tertiary care centers, and COVID-19 assessment centers in Ontario, Canada. Participants included symptomatic or asymptomatic patients who tested positive for SARS-CoV-2 virus and submitted virus samples for diagnostic testing between March 2020 and January 2023. Exposure: SARS-CoV-2 infection. Main outcomes and measures: Samples with sufficient viral load underwent next-generation genome sequencing to identify low-frequency antiviral resistance variants that could not be identified through conventional sequencing. Results: This study included 78 866 clinical samples with next-generation whole-genome sequencing data for SARS-CoV-2. Low-frequency variants in the viral nsp5 gene were identified in 128 isolates (0.16%), and no single variant associated with antiviral resistance was predominate. Conclusions and relevance: This cohort study of low-frequency variants resistant to nirmatrelvir-ritonavir found that these variants were very rare in samples from patients with SARS-CoV-2, suggesting that selection of these variants by nirmatrelvir-ritonavir following the initiation of treatment may also be rare. Surveillance efforts that involve sequencing of viral isolates should continue to monitor for novel resistance variants as nirmatrelvir-ritonavir is used more broadly.
MeSH term(s)	Humans ; Ontario/epidemiology ; SARS-CoV-2/genetics ; Ritonavir/therapeutic use ; Prevalence ; Cohort Studies ; Retrospective Studies ; COVID-19/epidemiology ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19 Drug Treatment
Chemical Substances	nirmatrelvir (7R9A5P7H32) ; Ritonavir (O3J8G9O825) ; Antiviral Agents
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2023.24963
Database	MEDical Literature Analysis and Retrieval System OnLINE

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