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1.
Article in English | MEDLINE | ID: mdl-38082806

ABSTRACT

Commercial ultrasound vascular phantoms lack the anatomic diversity required for robust pre-clinical interventional device testing. We fabricated individualized phantoms to test an artificial intelligence enabled ultrasound-guided surgical robotic system (AI-GUIDE) which allows novices to cannulate deep vessels. After segmenting vessels on computed tomography scans, vessel cores, bony anatomy, and a mold tailored to the skin contour were 3D-printed. Vessel cores were coated in silicone, surrounded in tissue-mimicking gel tailored for ultrasound and needle insertion, and dissolved with water. One upper arm and four inguinal phantoms were constructed. Operators used AI-GUIDE to deploy needles into phantom vessels. Two groin phantoms were tested due to imaging artifacts in the other two phantoms. Six operators (medical experience: none, 3; 1-5 years, 2; 5+ years, 1) inserted 27 inguinal needles with 81% (22/27) success in a median of 48 seconds. Seven operators performed 24 arm injections, without tuning the AI for arm anatomy, with 71% (17/24) success. After excluding failures due to motor malfunction and a defective needle, success rate was 100% (22/22) in the groin and 85% (17/20) in the arm. Individualized 3D-printed phantoms permit testing of surgical robotics across a large number of operators and different anatomic sites. AI-GUIDE operators rapidly and reliably inserted a needle into target vessels in the upper arm and groin, even without prior medical training. Virtual device trials in individualized 3-D printed phantoms may improve rigor of results and expedite translation.Clinical Relevance- Individualized phantoms enable rigorous and efficient evaluation of interventional devices and reduce the need for animal and human subject testing.


Subject(s)
Artificial Intelligence , Needles , Animals , Humans , Ultrasonography , Phantoms, Imaging , Ultrasonography, Interventional/methods
2.
Nat Commun ; 14(1): 5983, 2023 09 26.
Article in English | MEDLINE | ID: mdl-37752135

ABSTRACT

Resistance mechanisms to immune checkpoint blockade therapy (ICBT) limit its response duration and magnitude. Paradoxically, Interferon γ (IFNγ), a key cytokine for cellular immunity, can promote ICBT resistance. Using syngeneic mouse tumour models, we confirm that chronic IFNγ exposure confers resistance to immunotherapy targeting PD-1 (α-PD-1) in immunocompetent female mice. We observe upregulation of poly-ADP ribosyl polymerase 14 (PARP14) in chronic IFNγ-treated cancer cell models, in patient melanoma with elevated IFNG expression, and in melanoma cell cultures from ICBT-progressing lesions characterised by elevated IFNγ signalling. Effector T cell infiltration is enhanced in tumours derived from cells pre-treated with IFNγ in immunocompetent female mice when PARP14 is pharmacologically inhibited or knocked down, while the presence of regulatory T cells is decreased, leading to restoration of α-PD-1 sensitivity. Finally, we determine that tumours which spontaneously relapse in immunocompetent female mice following α-PD-1 therapy upregulate IFNγ signalling and can also be re-sensitised upon receiving PARP14 inhibitor treatment, establishing PARP14 as an actionable target to reverse IFNγ-driven ICBT resistance.


Subject(s)
Immune Checkpoint Inhibitors , Melanoma , Female , Humans , Animals , Mice , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Programmed Cell Death 1 Receptor , Interferon-gamma , Neoplasm Recurrence, Local , Disease Models, Animal , Poly(ADP-ribose) Polymerases
3.
Cancer Res Commun ; 2(3): 131-145, 2022 03 10.
Article in English | MEDLINE | ID: mdl-36466034

ABSTRACT

Targeting the human epidermal growth factor receptor 2 (HER2) became a landmark in the treatment of HER2-driven breast cancer. Nonetheless, the clinical efficacy of anti-HER2 therapies can be short-lived and a significant proportion of patients ultimately develop metastatic disease and die. One striking consequence of oncogenic activation of HER2 in breast cancer cells is the constitutive activation of the extracellular-regulated protein kinase 5 (ERK5) through its hyperphosphorylation. In this study, we sought to decipher the significance of this unique molecular signature in promoting therapeutic resistance to anti-HER2 agents. We found that a small-molecule inhibitor of ERK5 suppressed the phosphorylation of the retinoblastoma protein (RB) in HER2 positive breast cancer cells. As a result, ERK5 inhibition enhanced the anti-proliferative activity of single-agent anti-HER2 therapy in resistant breast cancer cell lines by causing a G1 cell cycle arrest. Moreover, ERK5 knockdown restored the anti-tumor activity of the anti-HER2 agent lapatinib in human breast cancer xenografts. Taken together, these findings support the therapeutic potential of ERK5 inhibitors to improve the clinical benefit that patients receive from targeted HER2 therapies.


Subject(s)
Antineoplastic Agents , Breast Neoplasms , Humans , Female , Breast Neoplasms/drug therapy , Antineoplastic Agents/pharmacology , Protein Kinases/therapeutic use , Quinazolines/pharmacology , Cell Cycle
4.
Biosensors (Basel) ; 12(12)2022 Dec 14.
Article in English | MEDLINE | ID: mdl-36551134

ABSTRACT

Hemorrhage is the leading cause of preventable death from trauma. Accurate monitoring of hemorrhage and resuscitation can significantly reduce mortality and morbidity but remains a challenge due to the low sensitivity of traditional vital signs in detecting blood loss and possible hemorrhagic shock. Vital signs are not reliable early indicators because of physiological mechanisms that compensate for blood loss and thus do not provide an accurate assessment of volume status. As an alternative, machine learning (ML) algorithms that operate on an arterial blood pressure (ABP) waveform have been shown to provide an effective early indicator. However, these ML approaches lack physiological interpretability. In this paper, we evaluate and compare the performance of ML models trained on nine ABP-derived features that provide physiological insight, using a database of 13 human subjects from a lower-body negative pressure (LBNP) model of progressive central hypovolemia and subsequent progressive restoration to normovolemia (i.e., simulated hemorrhage and whole blood resuscitation). Data were acquired at multiple repressurization rates for each subject to simulate varying resuscitation rates, resulting in 52 total LBNP collections. This work is the first to use a single ABP-based algorithm to monitor both simulated hemorrhage and resuscitation. A gradient-boosted regression tree model trained on only the half-rise to dicrotic notch (HRDN) feature achieved a root-mean-square error (RMSE) of 13%, an R2 of 0.82, and area under the receiver operating characteristic curve of 0.97 for detecting decompensation. This single-feature model's performance compares favorably to previously reported results from more-complex black box machine learning models. This model further provides physiological insight because HRDN represents an approximate measure of the delay between the ABP ejected and reflected wave and therefore is an indication of cardiac and peripheral vascular mechanisms that contribute to the compensatory response to blood loss and replacement.


Subject(s)
Blood Volume , Hemorrhage , Humans , Blood Pressure/physiology , Blood Volume/physiology , Hemorrhage/complications , Hemorrhage/diagnosis , Hypovolemia/diagnosis , Hypovolemia/etiology , Vital Signs
5.
Annu Int Conf IEEE Eng Med Biol Soc ; 2022: 1747-1752, 2022 07.
Article in English | MEDLINE | ID: mdl-36086009

ABSTRACT

Hemorrhage is the leading cause of preventable death from trauma. Traditionally, vital signs have been used to detect blood loss and possible hemorrhagic shock. However, vital signs are not sensitive for early detection because of physiological mechanisms that compensate for blood loss. As an alternative, machine learning algorithms that operate on an arterial blood pressure (ABP) waveform acquired via photoplethysmography have been shown to provide an effective early indicator. However, these machine learning approaches lack physiological interpretability. In this paper, we evaluate the importance of nine ABP-derived features that provide physiological insight, using a database of 40 human subjects from a lower-body negative pressure model of progressive central hypovolemia. One feature was found to be considerably more important than any other. That feature, the half-rise to dicrotic notch (HRDN), measures an approximate time delay between the ABP ejected and reflected wave components. This delay is an indication of compensatory mechanisms such as reduced arterial compliance and vasoconstriction. For a scale of 0% to 100%, with 100% representing normovolemia and 0% representing decompensation, linear regression of the HRDN feature results in root-mean-squared error of 16.9%, R2 of 0.72, and an area under the receiver operating curve for detecting decompensation of 0.88. These results are comparable to previously reported results from the more complex black box machine learning models. Clinical Relevance- A single physiologically interpretable feature measured from an arterial blood pressure waveform is shown to be effective in monitoring for blood loss and impending hemorrhagic shock based on data from a human lower-body negative pressure model of progressive central hypolemia.


Subject(s)
Cardiovascular Diseases , Shock, Hemorrhagic , Blood Pressure/physiology , Cardiovascular Diseases/complications , Hemorrhage , Humans , Hypovolemia/diagnosis , Lower Body Negative Pressure/adverse effects , Shock, Hemorrhagic/complications , Shock, Hemorrhagic/diagnosis
6.
Annu Int Conf IEEE Eng Med Biol Soc ; 2022: 1675-1681, 2022 07.
Article in English | MEDLINE | ID: mdl-36086232

ABSTRACT

Lung ultrasound (LUS) as a diagnostic tool is gaining support for its role in the diagnosis and management of COVID-19 and a number of other lung pathologies. B-lines are a predominant feature in COVID-19, however LUS requires a skilled clinician to interpret findings. To facilitate the interpretation, our main objective was to develop automated methods to classify B-lines as pathologic vs. normal. We developed transfer learning models based on ResNet networks to classify B-lines as pathologic (at least 3 B-lines per lung field) vs. normal using COVID-19 LUS data. Assessment of B-line severity on a 0-4 multi-class scale was also explored. For binary B-line classification, at the frame-level, all ResNet models pretrained with ImageNet yielded higher performance than the baseline nonpretrained ResNet-18. Pretrained ResNet-18 has the best Equal Error Rate (EER) of 9.1% vs the baseline of 11.9%. At the clip-level, all pretrained network models resulted in better Cohen's kappa agreement (linear-weighted) and clip score accuracy, with the pretrained ResNet-18 having the best Cohen's kappa of 0.815 [95% CI: 0.804-0.826], and ResNet-101 the best clip scoring accuracy of 93.6%. Similar results were shown for multi-class scoring, where pretrained network models outperformed the baseline model. A class activation map is also presented to guide clinicians in interpreting LUS findings. Future work aims to further improve the multi-class assessment for severity of B-lines with a more diverse LUS dataset.


Subject(s)
COVID-19 , Deep Learning , COVID-19/diagnostic imaging , Humans , Lung/diagnostic imaging , Thorax , Ultrasonography
7.
Cell Rep ; 39(12): 110995, 2022 06 21.
Article in English | MEDLINE | ID: mdl-35732120

ABSTRACT

Dysregulated cellular metabolism is a cancer hallmark for which few druggable oncoprotein targets have been identified. Increased fatty acid (FA) acquisition allows cancer cells to meet their heightened membrane biogenesis, bioenergy, and signaling needs. Excess FAs are toxic to non-transformed cells but surprisingly not to cancer cells. Molecules underlying this cancer adaptation may provide alternative drug targets. Here, we demonstrate that diacylglycerol O-acyltransferase 1 (DGAT1), an enzyme integral to triacylglyceride synthesis and lipid droplet formation, is frequently up-regulated in melanoma, allowing melanoma cells to tolerate excess FA. DGAT1 over-expression alone transforms p53-mutant zebrafish melanocytes and co-operates with oncogenic BRAF or NRAS for more rapid melanoma formation. Antagonism of DGAT1 induces oxidative stress in melanoma cells, which adapt by up-regulating cellular reactive oxygen species defenses. We show that inhibiting both DGAT1 and superoxide dismutase 1 profoundly suppress tumor growth through eliciting intolerable oxidative stress.


Subject(s)
Diacylglycerol O-Acyltransferase , Melanoma , Animals , Diacylglycerol O-Acyltransferase/genetics , Diacylglycerol O-Acyltransferase/metabolism , Oncogene Proteins/metabolism , Oxidative Stress , Reactive Oxygen Species , Triglycerides , Zebrafish/metabolism
8.
Sci Rep ; 12(1): 3463, 2022 03 02.
Article in English | MEDLINE | ID: mdl-35236896

ABSTRACT

Early detection of diseases such as COVID-19 could be a critical tool in reducing disease transmission by helping individuals recognize when they should self-isolate, seek testing, and obtain early medical intervention. Consumer wearable devices that continuously measure physiological metrics hold promise as tools for early illness detection. We gathered daily questionnaire data and physiological data using a consumer wearable (Oura Ring) from 63,153 participants, of whom 704 self-reported possible COVID-19 disease. We selected 73 of these 704 participants with reliable confirmation of COVID-19 by PCR testing and high-quality physiological data for algorithm training to identify onset of COVID-19 using machine learning classification. The algorithm identified COVID-19 an average of 2.75 days before participants sought diagnostic testing with a sensitivity of 82% and specificity of 63%. The receiving operating characteristic (ROC) area under the curve (AUC) was 0.819 (95% CI [0.809, 0.830]). Including continuous temperature yielded an AUC 4.9% higher than without this feature. For further validation, we obtained SARS CoV-2 antibody in a subset of participants and identified 10 additional participants who self-reported COVID-19 disease with antibody confirmation. The algorithm had an overall ROC AUC of 0.819 (95% CI [0.809, 0.830]), with a sensitivity of 90% and specificity of 80% in these additional participants. Finally, we observed substantial variation in accuracy based on age and biological sex. Findings highlight the importance of including temperature assessment, using continuous physiological features for alignment, and including diverse populations in algorithm development to optimize accuracy in COVID-19 detection from wearables.


Subject(s)
Body Temperature , COVID-19/diagnosis , Wearable Electronic Devices , Adolescent , Adult , Aged , Aged, 80 and over , Algorithms , COVID-19/virology , Female , Humans , Male , Middle Aged , SARS-CoV-2/isolation & purification , Young Adult
10.
Br J Sports Med ; 56(8): 446-451, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35022161

ABSTRACT

OBJECTIVE: Exertional heat stroke (EHS), characterised by a high core body temperature (Tcr) and central nervous system (CNS) dysfunction, is a concern for athletes, workers and military personnel who must train and perform in hot environments. The objective of this study was to determine whether algorithms that estimate Tcr from heart rate and gait instability from a trunk-worn sensor system can forward predict EHS onset. METHODS: Heart rate and three-axis accelerometry data were collected from chest-worn sensors from 1806 US military personnel participating in timed 4/5-mile runs, and loaded marches of 7 and 12 miles; in total, 3422 high EHS-risk training datasets were available for analysis. Six soldiers were diagnosed with heat stroke and all had rectal temperatures of >41°C when first measured and were exhibiting CNS dysfunction. Estimated core temperature (ECTemp) was computed from sequential measures of heart rate. Gait instability was computed from three-axis accelerometry using features of pattern dispersion and autocorrelation. RESULTS: The six soldiers who experienced heat stroke were among the hottest compared with the other soldiers in the respective training events with ECTemps ranging from 39.2°C to 40.8°C. Combining ECTemp and gait instability measures successfully identified all six EHS casualties at least 3.5 min in advance of collapse while falsely identifying 6.1% (209 total false positives) examples where exertional heat illness symptoms were neither observed nor reported. No false-negative cases were noted. CONCLUSION: The combination of two algorithms that estimate Tcr and ataxic gate appears promising for real-time alerting of impending EHS.


Subject(s)
Heat Stress Disorders , Heat Stroke , Gait , Heat Stress Disorders/diagnosis , Heat Stroke/diagnosis , Hot Temperature , Humans , Temperature
11.
Biosensors (Basel) ; 11(12)2021 Dec 18.
Article in English | MEDLINE | ID: mdl-34940279

ABSTRACT

Hemorrhage is a leading cause of trauma death, particularly in prehospital environments when evacuation is delayed. Obtaining central vascular access to a deep artery or vein is important for administration of emergency drugs and analgesics, and rapid replacement of blood volume, as well as invasive sensing and emerging life-saving interventions. However, central access is normally performed by highly experienced critical care physicians in a hospital setting. We developed a handheld AI-enabled interventional device, AI-GUIDE (Artificial Intelligence Guided Ultrasound Interventional Device), capable of directing users with no ultrasound or interventional expertise to catheterize a deep blood vessel, with an initial focus on the femoral vein. AI-GUIDE integrates with widely available commercial portable ultrasound systems and guides a user in ultrasound probe localization, venous puncture-point localization, and needle insertion. The system performs vascular puncture robotically and incorporates a preloaded guidewire to facilitate the Seldinger technique of catheter insertion. Results from tissue-mimicking phantom and porcine studies under normotensive and hypotensive conditions provide evidence of the technique's robustness, with key performance metrics in a live porcine model including: a mean time to acquire femoral vein insertion point of 53 ± 36 s (5 users with varying experience, in 20 trials), a total time to insert catheter of 80 ± 30 s (1 user, in 6 trials), and a mean number of 1.1 (normotensive, 39 trials) and 1.3 (hypotensive, 55 trials) needle insertion attempts (1 user). These performance metrics in a porcine model are consistent with those for experienced medical providers performing central vascular access on humans in a hospital.


Subject(s)
Catheterization, Central Venous , Robotic Surgical Procedures , Ultrasonography, Interventional , Animals , Artificial Intelligence , Femoral Vein/diagnostic imaging , Humans , Swine
12.
Oncogene ; 40(23): 3929-3941, 2021 06.
Article in English | MEDLINE | ID: mdl-33981002

ABSTRACT

There is overwhelming clinical evidence that the extracellular-regulated protein kinase 5 (ERK5) is significantly dysregulated in human breast cancer. However, there is no definite understanding of the requirement of ERK5 in tumor growth and metastasis due to very limited characterization of the pathway in disease models. In this study, we report that a high level of ERK5 is a predictive marker of metastatic breast cancer. Mechanistically, our in vitro data revealed that ERK5 was critical for maintaining the invasive capability of triple-negative breast cancer (TNBC) cells through focal adhesion protein kinase (FAK) activation. Specifically, we found that phosphorylation of FAK at Tyr397 was controlled by a kinase-independent function of ERK5. Accordingly, silencing ERK5 in mammary tumor grafts impaired FAK phosphorylation at Tyr397 and suppressed TNBC cell metastasis to the lung without preventing tumor growth. Collectively, these results establish a functional relationship between ERK5 and FAK signaling in promoting malignancy. Thus, targeting the oncogenic ERK5-FAK axis represents a promising therapeutic strategy for breast cancer exhibiting aggressive clinical behavior.


Subject(s)
Focal Adhesion Kinase 1/metabolism , Mitogen-Activated Protein Kinase 7/metabolism , Triple Negative Breast Neoplasms/enzymology , Animals , Antigens, CD/biosynthesis , Antigens, CD/genetics , Antigens, CD/metabolism , Cadherins/biosynthesis , Cadherins/genetics , Cadherins/metabolism , Cell Adhesion/physiology , Cell Line, Tumor , Disease Progression , Female , Heterografts , Humans , Lung Neoplasms/enzymology , Lung Neoplasms/genetics , Lung Neoplasms/secondary , Mice , Mice, Nude , Mitogen-Activated Protein Kinase 7/biosynthesis , Mitogen-Activated Protein Kinase 7/genetics , Neoplasm Invasiveness , Phosphorylation , Prognosis , Triple Negative Breast Neoplasms/genetics , Triple Negative Breast Neoplasms/pathology
13.
Sensors (Basel) ; 21(6)2021 Mar 14.
Article in English | MEDLINE | ID: mdl-33799420

ABSTRACT

Parkinson's disease (PD) is a chronic movement disorder that produces a variety of characteristic movement abnormalities. The ubiquity of wrist-worn accelerometry suggests a possible sensor modality for early detection of PD symptoms and subsequent tracking of PD symptom severity. As an initial proof of concept for this technological approach, we analyzed the U.K. Biobank data set, consisting of one week of wrist-worn accelerometry from a population with a PD primary diagnosis and an age-matched healthy control population. Measures of movement dispersion were extracted from automatically segmented gait data, and measures of movement dimensionality were extracted from automatically segmented low-movement data. Using machine learning classifiers applied to one week of data, PD was detected with an area under the curve (AUC) of 0.69 on gait data, AUC = 0.84 on low-movement data, and AUC = 0.85 on a fusion of both activities. It was also found that classification accuracy steadily improved across the one-week data collection, suggesting that higher accuracy could be achievable from a longer data collection. These results suggest the viability of using a low-cost and easy-to-use activity sensor for detecting movement abnormalities due to PD and motivate further research on early PD detection and tracking of PD symptom severity.


Subject(s)
Accelerometry/instrumentation , Parkinson Disease/diagnosis , Tremor/diagnosis , Wearable Electronic Devices , Accelerometry/methods , Adult , Aged , Biological Specimen Banks , Gait/physiology , Humans , Machine Learning , Middle Aged , Monitoring, Physiologic , Parkinson Disease/physiopathology , Wrist
14.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 4636-4639, 2020 07.
Article in English | MEDLINE | ID: mdl-33019027

ABSTRACT

Breathing rate was estimated from chest-worn accelerometry collected from 1,522 servicemembers during training by a wearable physiological monitor. A total of 29,189 hours of training and sleep data were analyzed. The primary purpose of the monitor was to assess thermal-work strain and avoid heat injuries. The monitor design was thus not optimized to estimate breathing rate. Since breathing rate cannot be accurately estimated during periods of high activity, a qualifier was applied to identify sedentary time periods, totaling 8,867 hours. Breathing rate was estimated for a total of 4,179 hours, or 14% of the total collection and 47% of the sedentary total, primarily during periods of sleep. The breathing rate estimation method was compared to an FDA 510(K)-cleared criterion breathing rate sensor (Zephyr, Annapolis MD, USA) in a controlled laboratory experiment, which showed good agreement between the two techniques. Contributions of this paper are to: 1) provide the first analysis of accelerometry-derived breathing rate on free-living data including periods of high activity as well as sleep, along with a qualifier that effectively identifies sedentary periods appropriate for estimating breathing rate; 2) test breathing rate estimation on a data set with a total duration that is more than 60 times longer than that of the largest previously reported study, 3) test breathing rate estimation on data from a physiological monitor that has not been expressly designed for that purpose.


Subject(s)
Accelerometry , Respiratory Rate , Humans , Monitoring, Physiologic , Sleep , Thorax
15.
Int J Mol Sci ; 21(15)2020 Jul 23.
Article in English | MEDLINE | ID: mdl-32717819

ABSTRACT

Osteosarcomas (OSs) are bone tumors most commonly found in pediatric and adolescent patients characterized by high risk of metastatic progression and recurrence after therapy. Effective therapeutic management of this disease still remains elusive as evidenced by poor patient survival rates. To achieve a more effective therapeutic management regimen, and hence patient survival, there is a need to identify more focused targeted therapies for OSs treatment in the clinical setting. The role of the OS tumor stroma microenvironment plays a significant part in the development and dissemination of this disease. Important components, and hence potential targets for treatment, are the tumor-infiltrating macrophages that are known to orchestrate many aspects of OS stromal signaling and disease progression. In particular, increased infiltration of M2-like tumor-associated macrophages (TAMs) has been associated with OS metastasis and poor patient prognosis despite currently used aggressive therapies regimens. This review aims to provide a summary update of current macrophage-centered knowledge and to discuss the possible roles that macrophages play in the process of OS metastasis development focusing on the potential influence of stromal cross-talk signaling between TAMs, cancer-stem cells and additional OSs tumoral microenvironment factors.


Subject(s)
Bone Neoplasms , Osteosarcoma , Signal Transduction/immunology , Tumor Microenvironment/immunology , Tumor-Associated Macrophages , Bone Neoplasms/immunology , Bone Neoplasms/metabolism , Bone Neoplasms/pathology , Bone Neoplasms/therapy , Humans , Neoplasm Metastasis , Osteosarcoma/immunology , Osteosarcoma/metabolism , Osteosarcoma/pathology , Osteosarcoma/therapy , Tumor-Associated Macrophages/immunology , Tumor-Associated Macrophages/metabolism , Tumor-Associated Macrophages/pathology
16.
Ultrasound Med Biol ; 46(10): 2667-2676, 2020 10.
Article in English | MEDLINE | ID: mdl-32622685

ABSTRACT

The purpose of this study was to develop an automated method for classifying liver fibrosis stage ≥F2 based on ultrasound shear wave elastography (SWE) and to assess the system's performance in comparison with a reference manual approach. The reference approach consists of manually selecting a region of interest from each of eight or more SWE images, computing the mean tissue stiffness within each of the regions of interest and computing a resulting stiffness value as the median of the means. The 527-subject database consisted of 5526 SWE images and pathologist-scored biopsies, with data collected from a single system at a single site. The automated method integrates three modules that assess SWE image quality, select a region of interest from each SWE measurement and perform machine learning-based, multi-image SWE classification for fibrosis stage ≥F2. Several classification methods were developed and tested using fivefold cross-validation with training, validation and test sets partitioned by subject. Performance metrics were area under receiver operating characteristic curve (AUROC), specificity at 95% sensitivity and number of SWE images required. The final automated method yielded an AUROC of 0.93 (95% confidence interval: 0.90-0.94) versus 0.69 (95% confidence interval: 0.65-0.72) for the reference method, 71% specificity with 95% sensitivity versus 5% and four images per decision versus eight or more. In conclusion, the automated method reported in this study significantly improved the accuracy for ≥F2 classification of SWE measurements as well as reduced the number of measurements needed, which has the potential to reduce clinical workflow.


Subject(s)
Elasticity Imaging Techniques/methods , Image Processing, Computer-Assisted , Liver Cirrhosis/classification , Liver Cirrhosis/diagnostic imaging , Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Retrospective Studies , Young Adult
17.
Cancer Res ; 80(16): 3319-3330, 2020 08 15.
Article in English | MEDLINE | ID: mdl-32561530

ABSTRACT

The presence of immunosuppressive macrophages that become activated in the tumor microenvironment constitutes a major factor responsible for tumor growth and malignancy. In line with this knowledge, we report here that macrophage proliferation is a significant feature of advanced stages of cancer. Moreover, we have found that a high proportion of proliferating macrophages in human tumors express ERK5. ERK5 was required for supporting the proliferation of macrophages in tumor grafts in mice. Furthermore, myeloid ERK5 deficiency negatively impacted the proliferation of both resident and infiltrated macrophages in metastatic lung nodules. ERK5 maintained the capacity of macrophages to proliferate by suppressing p21 expression to halt their differentiation program. Collectively, these data provide insight into the mechanism underpinning macrophage proliferation to support malignant tumor development, thereby strengthening the value of ERK5-targeted therapies to restore antitumor immunity through the blockade of protumorigenic macrophage activation. SIGNIFICANCE: These findings offer a new rationale for anti-ERK5 therapy to improve cancer patient outcomes by blocking the proliferative activity of tumor macrophages.


Subject(s)
Cell Proliferation , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Mitogen-Activated Protein Kinase 7/metabolism , Neoplasms/metabolism , Neoplasms/pathology , Tumor-Associated Macrophages/metabolism , Animals , Cell Differentiation , Humans , Ki-67 Antigen/analysis , Melanoma/secondary , Mice , Mice, Inbred C57BL , Mitogen-Activated Protein Kinase 7/antagonists & inhibitors , Mitogen-Activated Protein Kinase 7/deficiency , Tumor-Associated Macrophages/cytology
18.
Pigment Cell Melanoma Res ; 33(5): 695-708, 2020 09.
Article in English | MEDLINE | ID: mdl-32145051

ABSTRACT

A major challenge for managing melanoma is its tumour heterogeneity based on individual co-existing melanoma cell phenotypes. These phenotypes display variable responses to standard therapies, and they drive individual steps of melanoma progression; hence, understanding their behaviour is imperative. Melanoma phenotypes are defined by distinct transcriptional states, which relate to different melanocyte lineage development phases, ranging from a mesenchymal, neural crest-like to a proliferative, melanocytic phenotype. It is thought that adaptive phenotype plasticity based on transcriptional reprogramming drives melanoma progression, but at which stage individual phenotypes dominate and moreover, how they interact is poorly understood. We monitored melanocytic and mesenchymal phenotypes throughout melanoma progression and detected transcriptional reprogramming at different stages, with a gain in mesenchymal traits in circulating melanoma cells (CTCs) and proliferative features in metastatic tumours. Intriguingly, we found that distinct phenotype populations interact in a cooperative manner, which generates tumours of greater "fitness," supports CTCs and expands organotropic cues in metastases. Fibronectin, expressed in mesenchymal cells, acts as key player in cooperativity and promotes survival of melanocytic cells. Our data reveal an important role for inter-phenotype communications at various stages of disease progression, suggesting these communications could act as therapeutic target.


Subject(s)
Adaptation, Physiological , Cell Communication , Disease Progression , Melanoma/pathology , Animals , Cell Line, Tumor , Cell Proliferation , Fibronectins/metabolism , Humans , Melanocytes/pathology , Mesoderm/pathology , Mice , Neoplasm Metastasis , Neoplastic Cells, Circulating/pathology , Phenotype
19.
Health Secur ; 17(6): 468-476, 2019.
Article in English | MEDLINE | ID: mdl-31859569

ABSTRACT

The type of host that a virus can infect, referred to as host specificity or tropism, influences infectivity and thus is important for disease diagnosis, epidemic response, and prevention. Advances in DNA sequencing technology have enabled rapid metagenomic analyses of viruses, but the prediction of virus phenotype from genome sequences is an active area of research. As such, automatic prediction of host tropism from analysis of genomic information is of considerable utility. Previous research has applied machine learning methods to accomplish this task, although deep learning (particularly deep convolutional neural network, CNN) techniques have not yet been applied. These techniques have the ability to learn how to recognize critical hierarchical structures within the genome in a data-driven manner. We designed deep CNN models to identify host tropism for human and avian influenza A viruses based on protein sequences and performed a detailed analysis of the results. Our findings show that deep CNN techniques work as well as existing approaches (with 99% mean accuracy on the binary prediction task) while performing end-to-end learning of the prediction model (without the need to specify handcrafted features). The findings also show that these models, combined with standard principal component analysis, can be used to quantify and visualize viral strain similarity.


Subject(s)
Influenza A virus/physiology , Influenza in Birds/virology , Influenza, Human/virology , Machine Learning , Neural Networks, Computer , Viral Tropism , Animals , Birds , Computer Simulation , Genotype , Humans , Influenza A virus/genetics , Models, Biological , Phenotype
20.
J Neuroinflammation ; 16(1): 25, 2019 Feb 05.
Article in English | MEDLINE | ID: mdl-30722781

ABSTRACT

BACKGROUND: Chimeric mouse models generated via adoptive bone marrow transfer are the foundation for immune cell tracking in neuroinflammation. Chimeras that exhibit low chimerism levels, blood-brain barrier disruption and pro-inflammatory effects prior to the progression of the pathological phenotype, make it difficult to distinguish the role of immune cells in neuroinflammatory conditions. Head-shielded irradiation overcomes many of the issues described and replaces the recipient bone marrow system with donor haematopoietic cells expressing a reporter gene or different pan-leukocyte antigen, whilst leaving the blood-brain barrier intact. However, our previous work with full body irradiation suggests that this may generate a pro-inflammatory peripheral environment which could impact on the brain's immune microenvironment. Our aim was to compare non-myeloablative busulfan conditioning against head-shielded irradiation bone marrow chimeras prior to implantation of glioblastoma, a malignant brain tumour with a pro-inflammatory phenotype. METHODS: Recipient wild-type/CD45.1 mice received non-myeloablative busulfan conditioning (25 mg/kg), full intensity head-shielded irradiation, full intensity busulfan conditioning (125 mg/kg) prior to transplant with whole bone marrow from CD45.2 donors and were compared against untransplanted controls. Half the mice from each group were orthotopically implanted with syngeneic GL-261 glioblastoma cells. We assessed peripheral blood, bone marrow and spleen chimerism, multi-organ pro-inflammatory cytokine profiles at 12 weeks and brain chimerism and immune cell infiltration by whole brain flow cytometry before and after implantation of glioblastoma at 12 and 14 weeks respectively. RESULTS: Both non-myeloablative conditioning and head-shielded irradiation achieve equivalent blood and spleen chimerism of approximately 80%, although bone marrow engraftment is higher in the head-shielded irradiation group and highest in the fully conditioned group. Head-shielded irradiation stimulated pro-inflammatory cytokines in the blood and spleen but not in the brain, suggesting a systemic response to irradiation, whilst non-myeloablative conditioning showed no cytokine elevation. Non-myeloablative conditioning achieved higher donor chimerism in the brain after glioblastoma implantation than head-shielded irradiation with an altered immune cell profile. CONCLUSION: Our data suggest that non-myeloablative conditioning generates a more homeostatic peripheral inflammatory environment than head-shielded irradiation to allow a more consistent evaluation of immune cells in glioblastoma and can be used to investigate the roles of peripheral immune cells and bone marrow-derived subsets in other neurological diseases.


Subject(s)
Antineoplastic Agents, Alkylating/pharmacology , Bone Marrow Cells/drug effects , Bone Marrow Cells/radiation effects , Brain Neoplasms/immunology , Busulfan/pharmacology , Chimera , Immunity, Cellular/drug effects , Immunity, Cellular/radiation effects , Inflammation/pathology , Radiation Chimera , Animals , Bone Marrow Cells/immunology , Cell Line, Tumor , Cytokines/blood , Female , Glioblastoma/pathology , Inflammation/chemically induced , Leukocyte Common Antigens/genetics , Mice , Mice, Inbred C57BL , Neoplasm Transplantation
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