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  1. Article ; Online: Deep learning image analysis models pretrained on daily objects are useful for the preliminary characterization of particulate pharmaceutical samples.

    Salami, Hossein / Wood, Caitlin / Ouyang, Hanlin / Zhao, Xi / Skomski, Daniel

    Biotechnology and bioengineering

    2023  Volume 120, Issue 8, Page(s) 2175–2185

    Abstract: Visible and subvisible particles are a quality attribute in sterile pharmaceutical samples. A common method for characterizing and quantifying pharmaceutical samples containing particulates is imaging many individual particles using high-throughput ... ...

    Abstract Visible and subvisible particles are a quality attribute in sterile pharmaceutical samples. A common method for characterizing and quantifying pharmaceutical samples containing particulates is imaging many individual particles using high-throughput instrumentation and analyzing the populations data. The analysis includes conventional metrics such as the particle size distribution but can be more sophisticated by interpreting other visual/morphological features. To avoid the hurdles of building new image analysis models capable of extracting such relevant features from scratch, we propose using well-established pretrained deep learning image analysis models such as EfficientNet. We demonstrate that such models are useful as a prescreening tool for high-level characterization of biopharmaceutical particle image data. We show that although these models are originally trained for completely different tasks (such as the classification of daily objects in the ImageNet database), the visual feature vectors extracted by such models can be useful for studying different types of subvisible particles. This applicability is illustrated through multiple case studies: (i) particle risk assessment in prefilled syringe formulations containing different particle types such as silicone oil, (ii) method comparability with the example of accelerated forced degradation, and (iii) excipient influence on particle morphology with the example of Polysorbate 80 (PS80). As examples of agnostic applicability of pretrained models, we also elucidate the application to two high-throughput microscopy methods: microflow and background membrane imaging. We show that different particle populations with different morphological and visual features can be identified in different samples by leveraging out-of-the-box pretrained models to analyze images from each sample.
    MeSH term(s) Chemistry, Pharmaceutical/methods ; Particle Size ; Deep Learning ; Drug Compounding ; Excipients
    Chemical Substances Excipients
    Language English
    Publishing date 2023-07-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 280318-5
    ISSN 1097-0290 ; 0006-3592
    ISSN (online) 1097-0290
    ISSN 0006-3592
    DOI 10.1002/bit.28488
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Results From the POINT Pragmatic Randomized Trial: An Emergency Department-Based Peer Support Specialist Intervention to Increase Opioid Use Disorder Treatment Linkage and Reduce Recurrent Overdose.

    Watson, Dennis P / Tillson, Martha / Taylor, Lisa / Xu, Huiping / Ouyang, Fangqian / Beaudoin, Francesca L / O'Donnell, Daniel / McGuire, Alan B

    Substance use & addiction journal

    2024  , Page(s) 29767342231221054

    Abstract: Background: People with opioid use disorder (OUD) frequently present at the emergency department (ED), a potentially critical point for intervention and treatment linkage. Peer recovery support specialist (PRSS) interventions have expanded in US-based ... ...

    Abstract Background: People with opioid use disorder (OUD) frequently present at the emergency department (ED), a potentially critical point for intervention and treatment linkage. Peer recovery support specialist (PRSS) interventions have expanded in US-based EDs, although evidence supporting such interventions has not been firmly established.
    Methods: Researchers conducted a pragmatic trial of POINT (Project Planned Outreach, Intervention, Naloxone, and Treatment), an ED-initiated intervention for harm reduction and recovery coaching/treatment linkage in 2 Indiana EDs. Cluster randomization allocated patients to the POINT intervention (n 
    Results: POINT and standard care participants did not differ significantly on any outcomes measured. Participants who presented to the ED for overdose had significantly lower scores (3.5 vs 4.2,
    Conclusions: This is the first randomized trial investigating overdose outcomes for an ED peer recovery support specialist intervention. Though underpowered, results suggest no benefit of PRSS services over standard care. Given the scope of PRSS, future work in this area should assess more recovery- and harm reduction-oriented outcomes, as well as the potential benefits of integrating PRSS within multimodal ED-based interventions for OUD.
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Journal Article
    ISSN 2976-7350
    ISSN (online) 2976-7350
    DOI 10.1177/29767342231221054
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Causality-Inspired Single-Source Domain Generalization for Medical Image Segmentation.

    Ouyang, Cheng / Chen, Chen / Li, Surui / Li, Zeju / Qin, Chen / Bai, Wenjia / Rueckert, Daniel

    IEEE transactions on medical imaging

    2023  Volume 42, Issue 4, Page(s) 1095–1106

    Abstract: Deep learning models usually suffer from the domain shift issue, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep ... ...

    Abstract Deep learning models usually suffer from the domain shift issue, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data are only available from one source domain, which is common in medical imaging applications. We tackle this problem in the context of cross-domain medical image segmentation. In this scenario, domain shifts are mainly caused by different acquisition processes. We propose a simple causality-inspired data augmentation approach to expose a segmentation model to synthesized domain-shifted training examples. Specifically, 1) to make the deep model robust to discrepancies in image intensities and textures, we employ a family of randomly-weighted shallow networks. They augment training images using diverse appearance transformations. 2) Further we show that spurious correlations among objects in an image are detrimental to domain robustness. These correlations might be taken by the network as domain-specific clues for making predictions, and they may break on unseen domains. We remove these spurious correlations via causal intervention. This is achieved by resampling the appearances of potentially correlated objects independently. The proposed approach is validated on three cross-domain segmentation scenarios: cross-modality (CT-MRI) abdominal image segmentation, cross-sequence (bSSFP-LGE) cardiac MRI segmentation, and cross-site prostate MRI segmentation. The proposed approach yields consistent performance gains compared with competitive methods when tested on unseen domains.
    MeSH term(s) Male ; Humans ; Pelvis ; Prostate
    Language English
    Publishing date 2023-04-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 622531-7
    ISSN 1558-254X ; 0278-0062
    ISSN (online) 1558-254X
    ISSN 0278-0062
    DOI 10.1109/TMI.2022.3224067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Using Deep learning to Predict Cardiovascular Magnetic Resonance Findings from Echocardiography Videos.

    Sahashi, Yuki / Vukadinovic, Milos / Duffy, Grant / Li, Debiao / Cheng, Susan / Berman, Daniel S / Ouyang, David / Kwan, Alan C

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Background: Echocardiography is the most common modality for assessing cardiac structure and function. While cardiac magnetic resonance (CMR) imaging is less accessible, CMR can provide unique tissue characterization including late gadolinium ... ...

    Abstract Background: Echocardiography is the most common modality for assessing cardiac structure and function. While cardiac magnetic resonance (CMR) imaging is less accessible, CMR can provide unique tissue characterization including late gadolinium enhancement (LGE), T1 and T2 mapping, and extracellular volume (ECV) which are associated with tissue fibrosis, infiltration, and inflammation. While deep learning has been shown to uncover findings not recognized by clinicians, it is unknown whether CMR-based tissue characteristics can be derived from echocardiography videos using deep learning. We hypothesized that deep learning applied to echocardiography could predict CMR-based measurements.
    Methods: In a retrospective single-center study, adult patients with CMRs and echocardiography studies within 30 days were included. A video-based convolutional neural network was trained on echocardiography videos to predict CMR-derived labels including wall motion abnormality (WMA) presence, LGE presence, and abnormal T1, T2 or ECV across echocardiography views. The model performance was evaluated in a held-out test dataset not used for training.
    Results: The study population included 1,453 adult patients (mean age 56±18 years, 42% female) with 2,556 paired echocardiography studies occurring on average 2 days after CMR (interquartile range 2 days prior to 6 days after). The model had high predictive capability for presence of WMA (AUC 0.873 [95%CI 0.816-0.922]), however, the model was unable to reliably detect the presence of LGE (AUC 0.699 [0.613-0.780]), native T1 (AUC 0.614 [0.500-0.715]), T2 0.553 [0.420-0.692], or ECV 0.564 [0.455-0.691]).
    Conclusions: Deep learning applied to echocardiography accurately identified CMR-based WMA, but was unable to predict tissue characteristics, suggesting that signal for these tissue characteristics may not be present within ultrasound videos, and that the use of CMR for tissue characterization remains essential within cardiology.
    Clinical perspective: Tissue characterization of the heart muscle is useful for clinical diagnosis and prognosis by identifying myocardial fibrosis, inflammation, and infiltration, and can be measured using cardiac MRI. While echocardiography is highly accessible and provides excellent functional information, its ability to provide tissue characterization information is limited at this time. Our study using a deep learning approach to predict cardiac MRI-based tissue characteristics from echocardiography showed limited ability to do so, suggesting that alternative approaches, including non-deep learning methods should be considered in future research.
    Language English
    Publishing date 2024-04-19
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.16.24305936
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Single-use versus reusable metallic laryngoscopes for non-emergent intubation: A retrospective review of 72,672 intubations.

    Chang, Daniel R / Burnett, Garrett W / Chiu, Sophia / Ouyang, Yuxia / Lin, Hung-Mo / Hyman, Jaime B

    Journal of clinical anesthesia

    2023  Volume 89, Page(s) 111187

    Abstract: Study objective: Increased regulatory requirements for sterilization in recent years have prompted a widespread transition from reusable to single-use laryngoscopes. The purpose of this study was to determine if the transition from metallic reusable to ... ...

    Abstract Study objective: Increased regulatory requirements for sterilization in recent years have prompted a widespread transition from reusable to single-use laryngoscopes. The purpose of this study was to determine if the transition from metallic reusable to metallic single-use laryngoscopes impacted the performance of direct laryngoscopy at an academic medical center.
    Design: Single-site retrospective cohort study.
    Setting: General anesthetic cases requiring tracheal intubation.
    Patients: Adult patients undergoing non-emergent procedures.
    Interventions: Data were collected two years before and two years after a transition from metallic reusable to metallic single-use laryngoscopes.
    Measurements: The primary outcome was need for intubation rescue with an alternate device. Secondary outcomes were difficult laryngeal view (modified Cormack-Lehane grade ≥ 2b) and hypoxemia (SpO
    Main results: In total, 72,672 patients were included: 35,549 (48.9%) in the reusable laryngoscope cohort and 37,123 (51.1%) in the single-use laryngoscope cohort. Compared with reusable laryngoscopes, single-use laryngoscopes were associated with fewer rescue intubations with an alternate device (covariates-adjusted odds ratio [OR] 0.81 95% CI 0.66-0.99). Single-use laryngoscopes were also associated with lower odds of difficult laryngeal view (OR 0.86; 95% CI 0.80-0.93). Single use laryngoscopes were not associated with hypoxemia during the intubation attempt (OR 1.03; 95% CI 0.88-1.20). Similar results were observed for subgroup analyses including rapid sequence induction, Macintosh blades, Miller blades, and patients with difficult airway risk factors.
    Conclusions: Metallic single-use laryngoscopes were associated with less need for rescue intubation with alternate devices and lower incidence of poor laryngeal view compared to reusable metallic laryngoscopes.
    MeSH term(s) Adult ; Humans ; Laryngoscopes/adverse effects ; Retrospective Studies ; Laryngoscopy/methods ; Intubation, Intratracheal/methods ; Hypoxia/epidemiology ; Hypoxia/etiology ; Equipment Design
    Language English
    Publishing date 2023-06-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1011618-7
    ISSN 1873-4529 ; 0952-8180
    ISSN (online) 1873-4529
    ISSN 0952-8180
    DOI 10.1016/j.jclinane.2023.111187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: JDLL: a library to run deep learning models on Java bioimage informatics platforms.

    García López de Haro, Carlos / Dallongeville, Stéphane / Musset, Thomas / Gómez-de-Mariscal, Estibaliz / Sage, Daniel / Ouyang, Wei / Muñoz-Barrutia, Arrate / Tinevez, Jean-Yves / Olivo-Marin, Jean-Christophe

    Nature methods

    2024  Volume 21, Issue 1, Page(s) 7–8

    MeSH term(s) Deep Learning ; Indonesia ; Gene Library
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Letter
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-023-02129-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Resonant Mixing Dynamic Nuclear Polarization.

    Quan, Yifan / Ouyang, Yifu / Mardini, Michael / Palani, Ravi Shankar / Banks, Daniel / Kempf, James / Wenckebach, W Tom / Griffin, Robert G

    The journal of physical chemistry letters

    2023  Volume 14, Issue 31, Page(s) 7007–7013

    Abstract: We propose a mechanism for dynamic nuclear polarization that is different from the well-known Overhauser effect, solid effect, cross effect, and thermal mixing processes. We term ... ...

    Abstract We propose a mechanism for dynamic nuclear polarization that is different from the well-known Overhauser effect, solid effect, cross effect, and thermal mixing processes. We term it
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01869
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online: Predicting a Protein's Stability under a Million Mutations

    Ouyang-Zhang, Jeffrey / Diaz, Daniel J. / Klivans, Adam R. / Krähenbühl, Philipp

    2023  

    Abstract: Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has ... ...

    Abstract Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying promising mutations. Existing approaches, however, are computationally expensive, as the number of model inferences scales with the number of mutations queried. Our main contribution is a simple, parallel decoding algorithm. Our Mutate Everything is capable of predicting the effect of all single and double mutations in one forward pass. It is even versatile enough to predict higher-order mutations with minimal computational overhead. We build Mutate Everything on top of ESM2 and AlphaFold, neither of which were trained to predict thermodynamic stability. We trained on the Mega-Scale cDNA proteolysis dataset and achieved state-of-the-art performance on single and higher-order mutations on S669, ProTherm, and ProteinGym datasets. Code is available at https://github.com/jozhang97/MutateEverything

    Comment: NeurIPS 2023. Code available at https://github.com/jozhang97/MutateEverything
    Keywords Quantitative Biology - Biomolecules
    Publishing date 2023-10-19
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Stress-strain behaviour of unsaturated compacted coal rejects and tailings

    Buzzi Olivier / Li Jianping / Pineda Jubert / Payne Daniel / Ouyang Kaiwen / Wu Jinbiao

    E3S Web of Conferences, Vol 382, p

    2023  Volume 16001

    Abstract: The paper presents the results of an experimental study aimed at evaluating the stress-strain response of unsaturated tailings (Mixed Plant Reject and Dewatered Tailings) from a mine in Queensland, Australia, which can be applied to further optimise ... ...

    Abstract The paper presents the results of an experimental study aimed at evaluating the stress-strain response of unsaturated tailings (Mixed Plant Reject and Dewatered Tailings) from a mine in Queensland, Australia, which can be applied to further optimise current tailings disposal strategies of the mine. Triaxialtests at constant gravimetric water content were performed on specimens prepared at different compaction states using dynamic and static methods, to determine their shear strength. The dynamically compactedspecimens display a higher strength than that statically compacted ones, which highlights the significance of stress history for tailings strength. As-compacted and post-testing suction measurements, performed using a high-capacity tensiometer, showed a reduction in matric suction irrespective of the material type, which is caused by mechanical wetting. The strength envelope was found to be non-linear, partly because of suction changes during testing. Post-testing suction measurement showed spatial variability within each specimen, with the central part of the samples experiencing the maximum suction reduction. The paper concludes with a discussion on the interpretation of such results.
    Keywords Environmental sciences ; GE1-350
    Subject code 670
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Automated vs. manual case investigation and contact tracing for pandemic surveillance

    Cameron Raymond / Derek Ouyang / Alexis D'Agostino / Sarah L. Rudman / Daniel E. Ho

    EClinicalMedicine, Vol 55, Iss , Pp 101726- (2023)

    Evidence from a stepped wedge cluster randomized trialResearch in context

    1480  

    Abstract: Summary: Background: Case investigation and contact tracing (CICT) is an important tool for communicable disease control, both to proactively interrupt chains of transmission and to collect information for situational awareness. We run the first ... ...

    Abstract Summary: Background: Case investigation and contact tracing (CICT) is an important tool for communicable disease control, both to proactively interrupt chains of transmission and to collect information for situational awareness. We run the first randomized trial of COVID-19 CICT to investigate the utility of manual (i.e., call-based) vs. automated (i.e., survey-based) CICT for pandemic surveillance. Methods: Between December 15, 2021 and February 5, 2022, a stepped wedge cluster randomized trial was run in which Santa Clara County ZIP Codes progressively transitioned from manual to automated CICT. Eleven individual-level data fields on demographics and disease dynamics were observed for non-response. The data contains 106,522 positive cases across 29 ZIP Codes. Findings: Automated CICT reduced overall collected information by 29 percentage points (SE = 0.08, p < 0.01), as well as the response rate for individual fields. However, we find no evidence of differences in information loss by race or ethnicity. Interpretations: Automated CICT can serve as a useful alternative to manual CICT, with no substantial evidence of skewing data along racial or ethnic lines, but manual CICT improves completeness of key data for monitoring epidemiologic patterns. Funding: This research was supported in part by the Stanford Office of Community Engagement and the Stanford Institute for Human-Centered Artificial Intelligence.
    Keywords COVID-19 ; Contact tracing ; Health disparities ; Medicine (General) ; R5-920
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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