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  1. Article ; Online: Effective Communication of Personalized Risks and Patient Preferences During Surgical Informed Consent Using Data Visualization: Qualitative Semistructured Interview Study With Patients After Surgery.

    Gisladottir, Undina / Nakikj, Drashko / Jhunjhunwala, Rashi / Panton, Jasmine / Brat, Gabriel / Gehlenborg, Nils

    JMIR human factors

    2022  Volume 9, Issue 2, Page(s) e29118

    Abstract: Background: There is no consensus on which risks to communicate to a prospective surgical patient during informed consent or how. Complicating the process, patient preferences may diverge from clinical assumptions and are often not considered for ... ...

    Abstract Background: There is no consensus on which risks to communicate to a prospective surgical patient during informed consent or how. Complicating the process, patient preferences may diverge from clinical assumptions and are often not considered for discussion. Such discrepancies can lead to confusion and resentment, raising the potential for legal action. To overcome these issues, we propose a visual consent tool that incorporates patient preferences and communicates personalized risks to patients using data visualization. We used this platform to identify key effective visual elements to communicate personalized surgical risks.
    Objective: Our main focus is to understand how to best communicate personalized risks using data visualization. To contextualize patient responses to the main question, we examine how patients perceive risks before surgery (research question 1), how suitably the visual consent tool is able to present personalized surgical risks (research question 2), how well our visualizations convey those personalized surgical risks (research question 3), and how the visual consent tool could improve the informed consent process and how it can be used (research question 4).
    Methods: We designed a visual consent tool to meet the objectives of our study. To calculate and list personalized surgical risks, we used the American College of Surgeons risk calculator. We created multiple visualization mock-ups using visual elements previously determined to be well-received for risk communication. Semistructured interviews were conducted with patients after surgery, and each of the mock-ups was presented and evaluated independently and in the context of our visual consent tool design. The interviews were transcribed, and thematic analysis was performed to identify major themes. We also applied a quantitative approach to the analysis to assess the prevalence of different perceptions of the visualizations presented in our tool.
    Results: In total, 20 patients were interviewed, with a median age of 59 (range 29-87) years. Thematic analysis revealed factors that influenced the perception of risk (the surgical procedure, the cognitive capacity of the patient, and the timing of consent; research question 1); factors that influenced the perceived value of risk visualizations (preference for rare event communication, preference for risk visualization, and usefulness of comparison with the average; research question 3); and perceived usefulness and use cases of the visual consent tool (research questions 2 and 4). Most importantly, we found that patients preferred the visual consent tool to current text-based documents and had no unified preferences for risk visualization. Furthermore, our findings suggest that patient concerns were not often represented in existing risk calculators.
    Conclusions: We identified key elements that influence effective visual risk communication in the perioperative setting and pointed out the limitations of the existing calculators in addressing patient concerns. Patient preference is highly variable and should influence choices regarding risk presentation and visualization.
    Language English
    Publishing date 2022-04-29
    Publishing country Canada
    Document type Journal Article
    ISSN 2292-9495
    ISSN (online) 2292-9495
    DOI 10.2196/29118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: ATXN3 deubiquitinates YAP1 to promote tumor growth.

    Wang, Shengnan / Liu, Kun / Han, Xiaohua / Cheng, Yang / Zhao, Emily / Brat, Daniel J / Sun, Zhaolin / Fang, Deyu

    American journal of cancer research

    2023  Volume 13, Issue 9, Page(s) 4222–4234

    Abstract: The ubiquitin-specific peptidase Ataxin-3 (ATXN3) has emerged as a potential oncogene in a variety of human cancers. However, the molecular mechanisms underlying how ATXN3 achieves its tumorigenic functions remain largely undefined. Herein, we report ... ...

    Abstract The ubiquitin-specific peptidase Ataxin-3 (ATXN3) has emerged as a potential oncogene in a variety of human cancers. However, the molecular mechanisms underlying how ATXN3 achieves its tumorigenic functions remain largely undefined. Herein, we report that targeted deletion of the ATXN3 gene in cancer cells by the CRISPR-Cas9 system resulted in decreased protein expression of Yes-associated protein 1 (YAP1) without altering its mRNA transcription. Interestingly, genetic ATXN3 suppression selectively inhibited the expression levels of YAP1 target genes including the connective tissue growth factor (
    Language English
    Publishing date 2023-09-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2589522-9
    ISSN 2156-6976
    ISSN 2156-6976
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: How surgeons use risk calculators and non-clinical factors for informed consent and shared decision making: A qualitative study.

    Panton, Jasmine / Beaulieu-Jones, Brendin R / Marwaha, Jayson S / Woods, Alison P / Nakikj, Drashko / Gehlenborg, Nils / Brat, Gabriel A

    American journal of surgery

    2023  Volume 226, Issue 5, Page(s) 660–667

    Abstract: Background: The discussion of risks, benefits, and alternatives to surgery with patients is a defining component of informed consent. As shared-decision making has become central to surgeon-patient communication, risk calculators have emerged as a tool ... ...

    Abstract Background: The discussion of risks, benefits, and alternatives to surgery with patients is a defining component of informed consent. As shared-decision making has become central to surgeon-patient communication, risk calculators have emerged as a tool to aid communication and decision-making. To optimize informed consent, it is necessary to understand how surgeons assess and communicate risk, and the role of risk calculators in this process.
    Methods: We conducted interviews with 13 surgeons from two institutions to understand how surgeons assess risk, the role of risk calculators in decision-making, and how surgeons approach risk communication during informed consent. We performed a qualitative analysis of interviews based on SRQR guidelines.
    Results: Our analysis yielded insights regarding (a) the landscape and approach to obtaining surgical consent; (b) detailed perceptions regarding the value and design of assessing and communicating risk; and (c) practical considerations regarding the future of personalized risk communication in decision-making. Above all, we found that non-clinical factors such as health and risk literacy are changing how surgeons assess and communicate risk, which diverges from traditional risk calculators.
    Conclusion: Principally, we found that surgeons incorporate a range of clinical and non-clinical factors to risk stratify patients and determine how to optimally frame and discuss risk with individual patients. We observed that surgeons' perception of risk communication, and the importance of eliciting patient preferences to direct shared-decision making, did not consistently align with patient priorities. This study underscored criticisms of risk calculators and novel decision-aids - which must be addressed prior to greater adoption.
    MeSH term(s) Humans ; Decision Making, Shared ; Surgeons ; Informed Consent ; Decision Making
    Language English
    Publishing date 2023-07-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2953-1
    ISSN 1879-1883 ; 0002-9610
    ISSN (online) 1879-1883
    ISSN 0002-9610
    DOI 10.1016/j.amjsurg.2023.07.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Comparing Rationale for Opioid Prescribing Decisions after Surgery with Subsequent Patient Consumption: A Survey of the Highest Quartile of Prescribers.

    Beaulieu-Jones, Brendin R / Marwaha, Jayson S / Kennedy, Chris J / Le, Danny / Berrigan, Margaret T / Nathanson, Larry A / Brat, Gabriel A

    Journal of the American College of Surgeons

    2023  Volume 237, Issue 6, Page(s) 835–843

    Abstract: Background: Opioid prescribing patterns, including those after surgery, have been implicated as a significant contributor to the US opioid crisis. A plethora of interventions-from nudges to reminders-have been deployed to improve prescribing behavior, ... ...

    Abstract Background: Opioid prescribing patterns, including those after surgery, have been implicated as a significant contributor to the US opioid crisis. A plethora of interventions-from nudges to reminders-have been deployed to improve prescribing behavior, but reasons for persistent outlier behavior are often unknown.
    Study design: Our institution employs multiple prescribing resources and a near real-time, feedback-based intervention to promote appropriate opioid prescribing. Since 2019, an automated system has emailed providers when a prescription exceeds the 75th percentile of typical opioid consumption for a given procedure-as defined by institutional data collection. Emails include population consumption metrics and an optional survey on rationale for prescribing. Responses were analyzed to understand why providers choose to prescribe atypically large discharge opioid prescriptions. We then compared provider prescriptions against patient consumption.
    Results: During the study period, 10,672 eligible postsurgical patients were discharged; 2,013 prescriptions (29.4% of opioid prescriptions) exceeded our institutional guideline. Surveys were completed by outlier prescribers for 414 (20.6%) encounters. Among patients where both consumption data and prescribing rationale surveys were available, 35.2% did not consume any opioids after discharge and 21.5% consumed <50% of their prescription. Only 93 (39.9%) patients receiving outlier prescriptions were outlier consumers. Most common reasons for prescribing outlier amounts were attending preference (34%) and prescriber analysis of patient characteristics (34%).
    Conclusions: The top quartile of opioid prescriptions did not align with, and often far exceeded, patient postdischarge opioid consumption. Providers cite assessment of patient characteristics as a common driver of decision-making, but this did not align with patient usage for approximately 50% of patients.
    MeSH term(s) Humans ; Analgesics, Opioid/therapeutic use ; Aftercare ; Practice Patterns, Physicians' ; Patient Discharge ; Benchmarking
    Chemical Substances Analgesics, Opioid
    Language English
    Publishing date 2023-09-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1181115-8
    ISSN 1879-1190 ; 1072-7515
    ISSN (online) 1879-1190
    ISSN 1072-7515
    DOI 10.1097/XCS.0000000000000861
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Image texture, low contrast liver lesion detectability and impact on dose: Deep learning algorithm compared to partial model-based iterative reconstruction.

    Racine, D / Brat, H G / Dufour, B / Steity, J M / Hussenot, M / Rizk, B / Fournier, D / Zanca, F

    European journal of radiology

    2021  Volume 141, Page(s) 109808

    Abstract: Objectives: To compare deep learning (True Fidelity, TF) and partial model based Iterative Reconstruction (ASiR-V) algorithm for image texture, low contrast lesion detectability and potential dose reduction.: Methods: Anthropomorphic phantoms ( ... ...

    Abstract Objectives: To compare deep learning (True Fidelity, TF) and partial model based Iterative Reconstruction (ASiR-V) algorithm for image texture, low contrast lesion detectability and potential dose reduction.
    Methods: Anthropomorphic phantoms (mimicking non-overweight and overweight patient), containing lesions of 6 mm in diameter with 20HU contrast, were scanned at five different dose levels (2,6,10,15,20 mGy) on a CT system, using clinical routine protocols for liver lesion detection. Images were reconstructed using ASiR-V 0% (surrogate for FBP), 60 % and TF at low, medium and high strength. Noise texture was characterized by computing a normalized Noise Power Spectrum filtered by an eye filter. The similarity against FBP texture was evaluated using peak frequency difference (PFD) and root mean square deviation (RMSD). Low contrast detectability was assessed using a channelized Hotelling observer and the area under the ROC curve (AUC) was used as figure of merit. Potential dose reduction was calculated to obtain the same AUC for TF and ASiR-V.
    Results: FBP-like noise texture was more preserved with TF (PFD from -0.043mm-1 to -0.09mm-1, RMSD from 0.12mm-1 to 0.21mm-1) than with ASiR-V (PFD equal to 0.12 mm-1, RMSD equal to 0.53mm-1), resulting in a sharper image. AUC was always higher with TF than ASIR-V. In average, TF compared to ASiR-V, enabled a radiation dose reduction potential of 7%, 25 % and 33 % for low, medium and high strength respectively.
    Conclusion: Compared to ASIR-V, TF at high strength does not impact noise texture and maintains low contrast liver lesions detectability at significant lower dose.
    MeSH term(s) Algorithms ; Deep Learning ; Humans ; Liver Neoplasms/diagnostic imaging ; Phantoms, Imaging ; Radiation Dosage ; Radiographic Image Interpretation, Computer-Assisted ; Tomography, X-Ray Computed
    Language English
    Publishing date 2021-06-03
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 138815-0
    ISSN 1872-7727 ; 0720-048X
    ISSN (online) 1872-7727
    ISSN 0720-048X
    DOI 10.1016/j.ejrad.2021.109808
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An integrative web-based software tool for multi-dimensional pathology whole-slide image analytics.

    Shen, Alice / Wang, Fusheng / Paul, Saptarshi / Bhuvanapalli, Divya / Alayof, Jacob / Farris, Alton B / Teodoro, George / Brat, Daniel J / Kong, Jun

    Physics in medicine and biology

    2022  Volume 67, Issue 22

    Abstract: Objective. ...

    Abstract Objective.
    MeSH term(s) Humans ; Image Processing, Computer-Assisted/methods ; Software ; Algorithms ; Computers ; Internet
    Language English
    Publishing date 2022-11-09
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 208857-5
    ISSN 1361-6560 ; 0031-9155
    ISSN (online) 1361-6560
    ISSN 0031-9155
    DOI 10.1088/1361-6560/ac8fde
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Immune checkpoint blockade in glioblastoma: from tumor heterogeneity to personalized treatment.

    Arrieta, Víctor A / Dmello, Crismita / McGrail, Daniel J / Brat, Daniel J / Lee-Chang, Catalina / Heimberger, Amy B / Chand, Dhan / Stupp, Roger / Sonabend, Adam M

    The Journal of clinical investigation

    2023  Volume 133, Issue 2

    Abstract: Immune checkpoint blockade (ICB) has revolutionized modern cancer therapy, arousing great interest in the neuro-oncology community. While several reports show that subsets of patients with glioma exhibit durable responses to immunotherapy, the efficacy ... ...

    Abstract Immune checkpoint blockade (ICB) has revolutionized modern cancer therapy, arousing great interest in the neuro-oncology community. While several reports show that subsets of patients with glioma exhibit durable responses to immunotherapy, the efficacy of this treatment has not been observed for unselected patient populations, preventing its broad clinical implementation for gliomas and glioblastoma (GBM). To exploit the maximum therapeutic potential of ICB for patients with glioma, understanding the different aspects of glioma-related tumor immune responses is of critical importance. In this Review, we discuss contributing factors that distinguish subsets of patients with glioma who may benefit from ICB. Specifically, we discuss (a) the complex interaction between the tumor immune microenvironment and glioma cells as a potential influence on immunotherapy responses; (b) promising biomarkers for responses to immune checkpoint inhibitors; and (c) the potential contributions of peripheral immune cells to therapeutic responses.
    MeSH term(s) Humans ; Glioblastoma/drug therapy ; Immune Checkpoint Inhibitors/pharmacology ; Immune Checkpoint Inhibitors/therapeutic use ; Precision Medicine ; Glioma ; Immunotherapy ; Tumor Microenvironment
    Chemical Substances Immune Checkpoint Inhibitors
    Language English
    Publishing date 2023-01-17
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 3067-3
    ISSN 1558-8238 ; 0021-9738
    ISSN (online) 1558-8238
    ISSN 0021-9738
    DOI 10.1172/JCI163447
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Cardiopulmonary exercise testing for identification of patients with hyperventilation syndrome.

    Brat, Kristian / Stastna, Nela / Merta, Zdenek / Olson, Lyle J / Johnson, Bruce D / Cundrle, Ivan

    PloS one

    2019  Volume 14, Issue 4, Page(s) e0215997

    Abstract: Introduction: Measurement of ventilatory efficiency, defined as minute ventilation per unit carbon dioxide production (VE/VCO2), by cardiopulmonary exercise testing (CPET) has been proposed as a screen for hyperventilation syndrome (HVS). However, ... ...

    Abstract Introduction: Measurement of ventilatory efficiency, defined as minute ventilation per unit carbon dioxide production (VE/VCO2), by cardiopulmonary exercise testing (CPET) has been proposed as a screen for hyperventilation syndrome (HVS). However, increased VE/VCO2 may be associated with other disorders which need to be distinguished from HVS. A more specific marker of HVS by CPET would be clinically useful. We hypothesized ventilatory control during exercise is abnormal in patients with HVS.
    Methods: Patients who underwent CPET from years 2015 through 2017 were retrospectively identified and formed the study group. HVS was defined as dyspnea with respiratory alkalosis (pH >7.45) at peak exercise with absence of acute or chronic respiratory, heart or psychiatric disease. Healthy patients were selected as controls. For comparison the Student t-test or Mann-Whitney U test were used. Data are summarized as mean ± SD or median (IQR); p<0.05 was considered significant.
    Results: Twenty-nine patients with HVS were identified and 29 control subjects were selected. At rest, end-tidal carbon dioxide (PETCO2) was 27 mmHg (25-30) for HVS patients vs. 30 mmHg (28-32); in controls (p = 0.05). At peak exercise PETCO2 was also significantly lower (27 ± 4 mmHg vs. 35 ± 4 mmHg; p<0.01) and VE/VCO2 higher ((38 (35-43) vs. 31 (27-34); p<0.01)) in patients with HVS. In contrast to controls, there were minimal changes of PETCO2 (0.50 ± 5.26 mmHg vs. 6.2 ± 4.6 mmHg; p<0.01) and VE/VCO2 ((0.17 (-4.24-6.02) vs. -6.6 (-11.4-(-2.8)); p<0.01)) during exercise in patients with HVS. The absence of VE/VCO2 and PETCO2 change during exercise was specific for HVS (83% and 93%, respectively).
    Conclusion: Absence of VE/VCO2 and PETCO2 change during exercise may identify patients with HVS.
    MeSH term(s) Adult ; Carbon Dioxide/metabolism ; Dyspnea/physiopathology ; Exercise Test ; Exercise Tolerance ; Female ; Heart Failure/physiopathology ; Humans ; Hyperventilation/diagnosis ; Hyperventilation/physiopathology ; Male ; Middle Aged ; Oxygen Consumption/physiology
    Chemical Substances Carbon Dioxide (142M471B3J)
    Language English
    Publishing date 2019-04-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0215997
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  9. Article ; Online: Analyzing Surgical Technique in Diverse Open Surgical Videos With Multitask Machine Learning.

    Goodman, Emmett D / Patel, Krishna K / Zhang, Yilun / Locke, William / Kennedy, Chris J / Mehrotra, Rohan / Ren, Stephen / Guan, Melody / Zohar, Orr / Downing, Maren / Chen, Hao Wei / Clark, Jevin Z / Berrigan, Margaret T / Brat, Gabriel A / Yeung-Levy, Serena

    JAMA surgery

    2023  Volume 159, Issue 2, Page(s) 185–192

    Abstract: Objective: To overcome limitations of open surgery artificial intelligence (AI) models by curating the largest collection of annotated videos and to leverage this AI-ready data set to develop a generalizable multitask AI model capable of real-time ... ...

    Abstract Objective: To overcome limitations of open surgery artificial intelligence (AI) models by curating the largest collection of annotated videos and to leverage this AI-ready data set to develop a generalizable multitask AI model capable of real-time understanding of clinically significant surgical behaviors in prospectively collected real-world surgical videos.
    Design, setting, and participants: The study team programmatically queried open surgery procedures on YouTube and manually annotated selected videos to create the AI-ready data set used to train a multitask AI model for 2 proof-of-concept studies, one generating surgical signatures that define the patterns of a given procedure and the other identifying kinematics of hand motion that correlate with surgeon skill level and experience. The Annotated Videos of Open Surgery (AVOS) data set includes 1997 videos from 23 open-surgical procedure types uploaded to YouTube from 50 countries over the last 15 years. Prospectively recorded surgical videos were collected from a single tertiary care academic medical center. Deidentified videos were recorded of surgeons performing open surgical procedures and analyzed for correlation with surgical training.
    Exposures: The multitask AI model was trained on the AI-ready video data set and then retrospectively applied to the prospectively collected video data set.
    Main outcomes and measures: Analysis of open surgical videos in near real-time, performance on AI-ready and prospectively collected videos, and quantification of surgeon skill.
    Results: Using the AI-ready data set, the study team developed a multitask AI model capable of real-time understanding of surgical behaviors-the building blocks of procedural flow and surgeon skill-across space and time. Through principal component analysis, a single compound skill feature was identified, composed of a linear combination of kinematic hand attributes. This feature was a significant discriminator between experienced surgeons and surgical trainees across 101 prospectively collected surgical videos of 14 operators. For each unit increase in the compound feature value, the odds of the operator being an experienced surgeon were 3.6 times higher (95% CI, 1.67-7.62; P = .001).
    Conclusions and relevance: In this observational study, the AVOS-trained model was applied to analyze prospectively collected open surgical videos and identify kinematic descriptors of surgical skill related to efficiency of hand motion. The ability to provide AI-deduced insights into surgical structure and skill is valuable in optimizing surgical skill acquisition and ultimately improving surgical care.
    MeSH term(s) Humans ; Artificial Intelligence ; Retrospective Studies ; Video Recording/methods ; Machine Learning ; Academic Medical Centers
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Observational Study ; Journal Article
    ZDB-ID 2701841-6
    ISSN 2168-6262 ; 2168-6254
    ISSN (online) 2168-6262
    ISSN 2168-6254
    DOI 10.1001/jamasurg.2023.6262
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  10. Article ; Online: TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

    Hou, Yue / Konen, Jessica / Brat, Daniel J / Marcus, Adam I / Cooper, Lee A D

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 7248

    Abstract: Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of ...

    Abstract Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.
    MeSH term(s) Carcinoma, Non-Small-Cell Lung/diagnostic imaging ; Carcinoma, Non-Small-Cell Lung/pathology ; Cell Culture Techniques ; Cell Proliferation/genetics ; Humans ; Neoplasm Invasiveness/genetics ; Neoplasm Invasiveness/pathology ; Software ; Spheroids, Cellular/pathology
    Language English
    Publishing date 2018-05-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-25337-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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