ADAM9 promotes type I interferon-mediated innate immunity during encephalomyocarditis virus infection.

Viral myocarditis, an inflammatory disease of the heart, causes significant morbidity and mortality. Type I interferon (IFN)-mediated antiviral responses protect against myocarditis, but the mechanisms are poorly understood. We previously identified A Disintegrin And Metalloproteinase domain 9 (ADAM9) as an important factor in viral pathogenesis. ADAM9 is implicated in a range of human diseases, including inflammatory diseases; however, its role in viral infection is unknown. Here, we demonstrate that mice lacking ADAM9 are more susceptible to encephalomyocarditis virus (EMCV)-induced death and fail to mount a characteristic type I IFN response. This defect in type I IFN induction is specific to positive-sense, single-stranded RNA (+ ssRNA) viruses and involves melanoma differentiation-associated protein 5 (MDA5)-a key receptor for +ssRNA viruses. Mechanistically, ADAM9 binds to MDA5 and promotes its oligomerization and thereby downstream mitochondrial antiviral-signaling protein (MAVS) activation in response to EMCV RNA stimulation. Our findings identify a role for ADAM9 in the innate antiviral response, specifically MDA5-mediated IFN production, which protects against virus-induced cardiac damage, and provide a potential therapeutic target for treatment of viral myocarditis.

Spatial distribution of tumor-associated macrophages in an orthotopic prostate cancer mouse model.

Mounting evidence suggests that the immune landscape within prostate tumors influences progression, metastasis, treatment response, and patient outcomes. In this study, we investigated the spatial density of innate immune cell populations within NOD.SCID orthotopic prostate cancer xenografts following microinjection of human DU145 prostate cancer cells. Our laboratory has previously developed nanoscale liposomes that attach to leukocytes via conjugated E-selectin (ES) and kill cancer cells via TNF-related apoptosis inducing ligand (TRAIL). Immunohistochemistry (IHC) staining was performed on tumor samples to identify and quantify leukocyte infiltration for different periods of tumor growth and E-selectin/TRAIL (EST) liposome treatments. We examined the spatial-temporal dynamics of three different immune cell types infiltrating tumors using QuPath image analysis software. IHC staining revealed that F4/80+ tumor-associated macrophages (TAMs) were the most abundant immune cells in all groups, irrespective of time or treatment. The density of TAMs decreased over the course of tumor growth and decreased in response to EST liposome treatments. Intratumoral versus marginal analysis showed a greater presence of TAMs in the marginal regions at 3 weeks of tumor growth which became more evenly distributed over time and in tumors treated with EST liposomes. TUNEL staining indicated that EST liposomes significantly increased cell apoptosis in treated tumors. Additionally, confocal microscopy identified liposome-coated TAMs in both the core and periphery of tumors, highlighting the ability of liposomes to infiltrate tumors by "piggybacking" on macrophages. The results of this study indicate that TAMs represent the majority of innate immune cells within NOD.SCID orthotopic prostate tumors, and spatial density varies widely as a function of tumor size, duration of tumor growth, and treatment of EST liposomes.

Smoking out Australia's growing illicit tobacco market: Current trends and future challenges.

Data from the Australian Taxation Office and Australian Border Force show notable recent increases in illicit tobacco seizures across Australia. The illicit tobacco market results in substantial losses in tax revenue, funds organised crime, and perpetuates tobacco use, threatening to undermine Australia's ability to achieve its national commercial tobacco endgame goal of 5 % or less smoking prevalence by 2030. This commentary discusses recent trends in Australia's illicit tobacco trade, reasons why this is of concern, potential drivers of Australians' illicit tobacco use, and policy measures that could be implemented to mitigate increasing illicit tobacco trade such as implementing a track and trace system, increased investment in the Australian Border Force to enhance detection of illicit tobacco shipments at Australia's borders, and encouraging public tip-offs of illicit tobacco sales.

Incorporation of ChatGPT and Other Large Language Models into a Graduate Level Computational Bioengineering Course.

The remarkable capabilities of generative artificial intelligence and large language models (LLMs) such as ChatGPT have delighted users around the world. Educators have regarded these tools as either a cause for great concern, an opportunity to educate students on cutting-edge technology, or often some combination of the two. Throughout the Fall 2023 semester, we explored the use of ChatGPT (and Bard, among other LLMs) in a graduate level numerical and statistical methods course for PhD-level bioengineers. In this article we share examples of this ChatGPT content, our observations on what worked best in our course, and speculate on how bioengineering students may be best served by this technology in the future.

Talent identification in soccer: The influence of technical, physical and maturity-related characteristics on a national selection process.

The present study examines the influence of technical, physical, and relative age characteristics on players selection success within the Scottish Performance School trials. Ninety adolescent players (81 males, 9 females; mean ± standard deviation: age = 11.3 ± 0.4 years, height = 149.6 ± 6.9 cm, mass 38.1 ± 4.7 kg) performed a battery of physical fitness (20m Sprint, CMJ, 5-0-5 agility test), anthropometric, and 8 small-sided games (SSG; 9v9) as part of a talent identification (TID) programme. Players technical (ball touches, time on the ball, high-speed releases) and locomotor activities (high-speed running distance, sprint distance, accelerations, and decelerations) were monitored using foot-mounted inertial measurements units during SSG's. The data was analysed using independent sample T-tests. Mann-Whitney U analyses were conducted to examine the differences between groups whose data was determined as being (non)parametric, with Cohen effect sizes applied. Successful players performed significantly better during physical tests (Effect size ± confidence limits: Left 5-0-5 = -0.89±0.13, Right 5-0-5 = -0.51±0.11), had significantly higher locomotor activities during SSG (high-intensity distance = 0.4±26.6, horizontal accelerations = 0.59±1.19) and significantly higher technical outputs during SSG (touches = 0.71±6.1, releases = 0.49±2.5, high-speed releases = 0.59±2.7, time on the ball = 0.52±3.4) compared to unsuccessful players. Successful players had significantly higher locomotor activities and technical outputs during SSG than their unsuccessful counterparts. Monitoring technical and locomotor activities during SSG may compliment or replace physical testing batteries for assessing TID processes in soccer.

Between loss and restoration: The role of liminality in advancing theories of grief and bereavement.

A recent national survey of bereaved partners found high levels of complicated grief and psychological distress, with evidence that loneliness and isolation may contribute to these outcomes. However, the mechanisms of action for this have not been explored. To advance grief theory this paper reports analysis of the survey free-text data to examine the relationship between social support and emotional responses to bereavement. Individuals bereaved of a civil partner or spouse 6-10 months previously were identified through death registration data. 569/1945 (29 %) completed surveys were received. Of those, 311 participants (55 %) provided responses to two free-text questions which asked about their 'feelings since the death of their partner or spouse', and 'about the support around' them. Data were analysed using corpus-assisted discourse analysis and the discourse dynamics approach for figurative language. Participants described diverse emotional responses to the bereavement (e.g. sadness, anger, denial, acceptance), and the value of formal and informal bereavement support. Although many of the experiences described are accounted for in existing grief theory, some participants described a liminal experience not recognised within these theories. They felt trapped, unable to engage with loss or restoration, and unable to move forward as their planned future no longer existed. They sought out 'communitas' (solidarity in experiences), but often found support from their social networks had diminished. Metaphors were used to describe this liminality, with partner grief expressed as a dark agentic force, a monster, an abyss, and as water. The findings of this study offer original insights into experiences and trajectories of bereavement, and our understandings of prolonged or complicated grief. A novel model 'Between Loss and Restoration' is presented to include these experiences. Recognition of the place for liminality within the spectrum of grief experiences could enhance grief literacy and improve formal and informal bereavement support provision.

Grand Challenges at the Interface of Engineering and Medicine.

Over the past two decades Biomedical Engineering has emerged as a major discipline that bridges societal needs of human health care with the development of novel technologies. Every medical institution is now equipped at varying degrees of sophistication with the ability to monitor human health in both non-invasive and invasive modes. The multiple scales at which human physiology can be interrogated provide a profound perspective on health and disease. We are at the nexus of creating "avatars" (herein defined as an extension of "digital twins") of human patho/physiology to serve as paradigms for interrogation and potential intervention. Motivated by the emergence of these new capabilities, the IEEE Engineering in Medicine and Biology Society, the Departments of Biomedical Engineering at Johns Hopkins University and Bioengineering at University of California at San Diego sponsored an interdisciplinary workshop to define the grand challenges that face biomedical engineering and the mechanisms to address these challenges. The Workshop identified five grand challenges with cross-cutting themes and provided a roadmap for new technologies, identified new training needs, and defined the types of interdisciplinary teams needed for addressing these challenges. The themes presented in this paper include: 1) accumedicine through creation of avatars of cells, tissues, organs and whole human; 2) development of smart and responsive devices for human function augmentation; 3) exocortical technologies to understand brain function and treat neuropathologies; 4) the development of approaches to harness the human immune system for health and wellness; and 5) new strategies to engineer genomes and cells.

How manufacturing won or lost the COVID-19 vaccine race.

The development of vaccines for COVID-19 occurred at an unprecedented pace, and 32 vaccines using a broad range of technologies had received authorization for use on an emergency basis by the end of 2021, from either a national regulatory authority or the World Health Organization. However, 27 of those 32 vaccines had little impact on the global course of the pandemic. Only five vaccines, from AstraZeneca, Pfizer/BioNTech, Sinovac, Moderna, and Sinopharm, were manufactured, authorized, and distributed in time to significantly impact the number of deaths worldwide. Together, these five vaccines averted an estimated 17 million deaths in the first year of the vaccination campaign. The shared characteristic of these five manufacturers was their ability to rapidly develop and scale up vaccine production to deliver the large manufacturing volumes required to immunize large segments of the global population. Because the development and manufacturing of these vaccines was generally on the critical path to authorization and supply, the technical activities involved with development, scale-up, testing, technology transfer, and full-scale manufacturing, as well as aspects of the Chemistry, Manufacturing, and Controls (CMC) regulatory interactions, are examined for each vaccine and technology for which information is available in the public domain to provide lessons learned and recommendations on proactive actions to better prepare us for a future pandemic response. The critical success factors include prior experience with commercialization and approval, robust quality systems, rigorous process development strategies, flexible manufacturing facilities with a skilled workforce, collaboration, access to consumables, reagents, and adjuvants (if relevant), and an equitable distribution of the global vaccine manufacturing network.

Tuning of TRAIL clustering on the surface of nanoscale liposomes by phase separation.

Phase-separated liposomes were used to formulate tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), a protein that selectively kills cancer cells while sparing most healthy ones. By controlling the average number of TRAIL molecules per liposome, we demonstrate the ability to tune the formation of TRAIL clusters and their resulting apoptotic activity.

Tumor nano-lysate activates dendritic cells to evoke a preventative immune response.

A tumor nano-lysate "TNL" vaccine comprised of sonicated 4T1 cells was developed, characterized and implemented for the prevention of triple-negative breast cancer. This study aimed to gain a better understanding of the immune response behind the success of the vaccine in vivo, through use of ex vivo and in vivo assays. Here, we analyze the activation of various immune cells isolated from healthy mouse spleens and find that antigen-presenting cells (APCs) such as dendritic cells (DCs) are being activated following 24 h incubation with 1:10 mg TNL/mg splenocytes. These cells were further explored to determine the pathway by which activation is occurring, and it was observed that TNL are phagocytosed by DCs to activate NF-kB and c-Fos pathways, resulting in enhanced cytokine release after 24 h. An in vivo temporal analysis was performed in mice to understand the immune response at 1, 3, 7 and 10 days after one 100 µL dose of TNL consisting of 105 sonicated 4T1 cells via cardiac puncture and splenocyte and peripheral blood mononuclear cell (PBMC) analysis. Changes were observed for up to one week. A multiple dose study was performed comparing mice that were vaccinated with one dose of TNL administered every ten days for 3 doses total, as well as a PBS vehicle control. Survival for TNL-vaccinated mice was enhanced compared to the PBS control, and there was an average delay of 10 days in the onset of metastasis. The differences between the groups at the end of the study demonstrate the potential for TNL as a preventative therapeutic.

Respiratory signal estimation for cardiac perfusion SPECT using deep learning.

BACKGROUND: Respiratory motion induces artifacts in reconstructed cardiac perfusion SPECT images. Correction for respiratory motion often relies on a respiratory signal describing the heart displacements during breathing. However, using external tracking devices to estimate respiratory signals can add cost and operational complications in a clinical setting. PURPOSE: We aim to develop a deep learning (DL) approach that uses only SPECT projection data for respiratory signal estimation. METHODS: A modified U-Net was implemented that takes temporally finely sampled SPECT sub-projection data (100 ms) as input. These sub-projections are obtained by reframing the 20-s list-mode data, resulting in 200 sub-projections, at each projection angle for each SPECT camera head. The network outputs a 200-time-point motion signal for each projection angle, which was later aggregated over all angles to give a full respiratory signal. The target signal for DL model training was from an external stereo-camera visual tracking system (VTS). In addition to comparing DL and VTS, we also included a data-driven approach based on the center-of-mass (CoM) strategy. This CoM method estimates respiratory signals by monitoring the axial changes of CoM for counts in the heart region of the sub-projections. We utilized 900 subjects with stress cardiac perfusion SPECT studies, with 302 subjects for testing and the remaining 598 subjects for training and validation. RESULTS: The Pearson's correlation coefficient between the DL respiratory signal and the reference VTS signal was 0.90, compared to 0.70 between the CoM signal and the reference. For respiratory motion correction on SPECT images, all VTS, DL, and CoM approaches partially de-blured the heart wall, resulting in a thinner wall thickness and increased recovered maximal image intensity within the wall, with VTS reducing blurring the most followed by the DL approach. Uptake quantification for the combined anterior and inferior segments of polar maps showed a mean absolute difference from the reference VTS of 1.7% for the DL method for patients with motion >12 mm, compared to 2.6% for the CoM method and 8.5% for no correction. CONCLUSION: We demonstrate the capability of a DL approach to estimate respiratory signal from SPECT projection data for cardiac perfusion imaging. Our results show that the DL based respiratory motion correction reduces artefacts and achieves similar regional quantification to that obtained using the stereo-camera VTS signals. This may enable fully automatic data-driven respiratory motion correction without relying on external motion tracking devices.

Early post-treatment MRI predicts long-term hepatocellular carcinoma response to radiation segmentectomy.

OBJECTIVES: Radiation segmentectomy using yttrium-90 plays an emerging role in the management of early-stage HCC. However, the value of early post-treatment MRI for response assessment is uncertain. We assessed the value of response criteria obtained early after radiation segmentectomy in predicting long-term response in patients with HCC. MATERIALS AND METHODS: Patients with HCC who underwent contrast-enhanced MRI before, early, and 12 months after radiation segmentectomy were included in this retrospective single-center study. Three independent radiologists reviewed images at baseline and 1st follow-up after radiation segmentectomy and assessed lesion-based response according to mRECIST, LI-RADS treatment response algorithm (TRA), and image subtraction. The endpoint was response at 12 months based on consensus readout of two separate radiologists. Diagnostic accuracy for predicting complete response (CR) at 12 months based on the 1st post-treatment MRI was calculated. RESULTS: Eighty patients (M/F 60/20, mean age 67.7 years) with 80 HCCs were assessed (median size baseline, 1.8 cm [IQR, 1.4-2.9 cm]). At 12 months, 74 patients were classified as CR (92.5%), 5 as partial response (6.3%), and 1 as progressive disease (1.2%). Diagnostic accuracy for predicting CR was fair to good for all readers with excellent positive predictive value (PPV): mRECIST (range between 3 readers, accuracy: 0.763-0.825, PPV: 0.966-1), LI-RADS TRA (accuracy: 0.700-0.825, PPV: 0.983-1), and subtraction (accuracy: 0.775-0.825, PPV: 0.967-1), with no difference in accuracy between criteria (p range 0.053 to > 0.9). CONCLUSION: mRECIST, LI-RADS TRA, and subtraction obtained on early post-treatment MRI show similar performance for predicting long-term response in patients with HCC treated with radiation segmentectomy. CLINICAL RELEVANCE STATEMENT: Response assessment extracted from early post-treatment MRI after radiation segmentectomy predicts complete response in patients with HCC with high PPV (≥ 0.96). KEY POINTS: • Early post-treatment response assessment on MRI predicts response in patients with HCC treated with radiation segmentectomy with fair to good accuracy and excellent positive predictive value. • There was no difference in diagnostic accuracy between mRECIST, LI-RADS, and subtraction for predicting HCC response to radiation segmentectomy.

The association of intraoperative opioid dose with postanesthesia care unit outcomes in children: a retrospective study.

PURPOSE: In children, the relationship between the dose of intraoperative opioid and postoperative outcomes is unclear. We examined the relationship between intraoperative opioid dose and postanesthesia care unit (PACU) pain scores and opioid and antiemetic administrations. METHODS: We performed a single-institution retrospective cohort study. Patients who were aged < 19 yr, had an American Society of Anesthesiologists Physical Status of I-III, were undergoing one of 11 procedures under general anesthesia and without regional anesthesia, and who were admitted to the PACU were included. Patients were analyzed by quartiles of total intraoperative opioid dose using multivariable regression, adjusting for confounders including procedure. An exploratory analysis of opioid-free anesthetics was also performed. RESULTS: Three thousand, seven hundred and thirty-three cases were included, and the mean age of included patients was 8.3 yr. After adjustment, there were no significant differences between the lowest and higher quartiles for first conscious pain score, mean pain score, PACU opioid dose, or PACU length of stay; in addition, estimated differences were small. Patients in higher quartiles were estimated to be more likely to receive antiemetics, significantly so for those in the second quartile. Patients in the lowest quartile received significantly more intraoperative nonopioid analgesics. In the exploratory analysis, no significant difference in PACU pain scores was found in cases without intraoperative opioids. CONCLUSIONS: Children who received lower doses of intraoperative opioids did not have worse PACU pain outcomes but required fewer antiemetics and received greater numbers of nonopioid analgesics intraoperatively. These findings suggest that lower doses of intraoperative opioids may be administered to children as long as other analgesics are used.

RéSUMé: OBJECTIF: Chez les enfants, la relation entre la dose peropératoire d'opioïdes et les issues postopératoires n'est pas claire. Nous avons examiné la relation entre la dose peropératoire d'opioïdes, les scores de douleur en salle de réveil, et les administrations d'opioïdes et d'antiémétiques. MéTHODE: Nous avons réalisé une étude de cohorte rétrospective dans un seul établissement. Nous avons inclus les patient·es âgé·es < 19 ans ayant un statut physique ASA de I-III et bénéficiant de l'une de 11 interventions sous anesthésie générale et sans anesthésie régionale, et qui avaient été admis·es en salle de réveil. Les patient·es ont été analysé·es par quartiles de la dose totale d'opioïdes peropératoires en utilisant une régression multivariée, en ajustant les données pour tenir compte des facteurs de confusion, notamment de l'intervention. Une analyse exploratoire des anesthésiques sans opioïdes a également été réalisée. RéSULTATS: Au total 3733 cas ont été inclus, et l'âge moyen des enfants était de 8,3 ans. Après ajustement, il n'y avait pas de différences significatives entre les quartiles inférieur et supérieur pour le premier score de douleur chez l'enfant conscient·e, le score de douleur moyen, la dose d'opioïdes en salle de réveil ou la durée du séjour en salle de réveil; de plus, les différences estimées étaient faibles. On a estimé que les patient·es des quartiles supérieurs étaient plus susceptibles de recevoir des antiémétiques et ce, de manière significative pour ceux et celles du deuxième quartile. Les patient·es du quartile inférieur ont reçu significativement plus d'analgésiques non opioïdes peropératoires. Dans l'analyse exploratoire, aucune différence significative dans les scores de douleur en salle de réveil n'a été trouvée dans les cas sans opioïdes peropératoires. CONCLUSION: Les enfants qui ont reçu des doses plus faibles d'opioïdes peropératoires n'ont pas eu de pires issues de douleur en salle de réveil, mais ont eu besoin de moins d'antiémétiques et ont reçu un plus grand nombre d'analgésiques non opioïdes en peropératoire. Ces résultats suggèrent que des doses plus faibles d'opioïdes peropératoires peuvent être administrées aux enfants tant que d'autres analgésiques sont utilisés.

TRAIL-conjugated liposomes that bind natural killer cells to induce colorectal cancer cell apoptosis.

Natural killer (NK) cell functionality is a strong indicator of favorable prognosis in cancer patients, making NK cells an appealing therapeutic target to prevent lymph node dissemination. We engineered liposomes that are conjugated with anti-CD335 antibodies for NK cell targeting, and the apoptotic ligand TRAIL to kill cancer cells. Liposomes were made using a thin film hydration method followed by extrusion to approximately 100 nm in diameter and conjugation of proteins via thiol-maleimide click chemistry. TRAIL/anti-CD335 liposomes successfully bound to isolated NK cells. Once piggybacked to the surface of NK cells, these "Super Natural Killer Cells" were able to more effectively kill oxaliplatin-resistant SW620 cells and metastatic COLO205 colorectal cancer cells via TRAIL-mediated apoptosis compared to NK cells alone. Importantly, Super NK cells were more effective under physiological levels of fluid shear stress found in the lymphatics. Liposome biodistribution after intravenous administration confirmed the sustained presence of liposomes within the spleen and tumor draining mesenteric lymph nodes for at least 4 days. These results demonstrate the enhanced apoptotic effects of NK cells armored with liposomal TRAIL against clinically relevant colorectal cancer cells, providing the groundwork for in vivo treatment studies in mouse models of colorectal cancer metastasis.

Activation of Dendritic Cells Isolated from the Blood of Patients with Prostate Cancer by Ex Vivo Fluid Shear Stress Stimulation.

Prostate cancer is one of the most common cancers among men in the United States and a leading cause of cancer-related death in men. Treatment options for patients with advanced prostate cancer include hormone therapies, chemotherapies, radioligand therapies, and immunotherapies. Provenge (sipuleucel-T) is an autologous cancer-vaccine-based immunotherapy approved for men with asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC). Administration of sipuleucel-T involves leukapheresis of patient blood to isolate antigen-presenting cells (APCs), including dendritic cells (DCs), and subsequent incubation of isolated APCs with both an antigen, prostatic acid phosphatase (PAP), and granulocyte macrophage-colony stimulating factor (GM-CSF) before their infusion back into the patient. Although sipuleucel-T has been shown to improve overall survival, other meaningful outcomes, such as prostate-specific antigen (PSA) levels and radiographic response, are inconsistent. This lack of robust response may be due to limited ex vivo activation of DCs using current protocols. Earlier studies have shown that many cell types can be activated ex vivo by external forces such as fluid shear stress (FSS). We hypothesize that novel fluid shear stress technologies and methods can be used to improve ex vivo efficacy of prostate cancer DC activation in prostate cancer. Herein, we report a new protocol for activating DCs from patients with prostate cancer using ex vivo fluid shear stress. Ultimately, the goal of these studies is to improve DC activation to expand the efficacy of therapies such as sipuleucel-T. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample collection and DC isolation Basic Protocol 2: Determination and application of fluid shear stress Basic Protocol 3: Flow cytometry analysis of DCs after FSS stimulation.

Dual Affinity Nanoparticles for the Transport of Therapeutics from Carrier Cells to Target Cells under Physiological Flow Conditions.

In this study, a novel two-stage nanoparticle delivery platform was developed based on the dual functionalization of a liposome with moieties that have fundamentally different strengths of adhesion and binding kinetics. The essential concept of this system is that the nanoparticles are designed to loosely bind to the carrier cell until they come into contact with the target cell, to which they bind with greater strength. This allows the nanoparticle to be transferred from one cell to another, circulating for longer periods of time in the blood and delivering the therapeutic agent to the target circulating tumor cell. Liposomes were prepared using the lipid cake and extrusion technique, then functionalized with E-selectin (ES), anti-cell surface vimentin antibody fragments, and TRAIL via click chemistry. The binding of dual affinity (DA) liposomes was confirmed with the neutrophil-like cell line PLB985, the colorectal cancer cell line HCT116, and healthy granulocytes isolated from peripheral whole blood under physiologically relevant fluid shear stress (FSS) in a cone-and-plate viscometer. Transfer of the DA liposomes from PLB985 to HCT116 cells under FSS was greater compared to all of the control liposome formulations. Additionally, DA liposomes demonstrated enhanced apoptotic effects on HCT116 cells in whole blood under FSS, surpassing the efficacy of the ES/TRAIL liposomes previously developed by the King Lab.

Benign and Malignant Ovarian Teratomas: Multimodality Imaging Findings With Histopathologic Correlation.

ABSTRACT: The purpose of this article is to provide a comprehensive review of the imaging findings along with histopathologic correlation of mature (benign) teratomas and malignant ovarian teratomas, which include both immature teratomas and malignant degeneration of mature teratomas. The radiologist's ability to provide an accurate diagnosis plays an essential role in guiding the interdisciplinary care of patients with malignant teratomas and improving their outcomes.

Graph-based multi-modality integration for prediction of cancer subtype and severity.

Personalised cancer screening before therapy paves the way toward improving diagnostic accuracy and treatment outcomes. Most approaches are limited to a single data type and do not consider interactions between features, leaving aside the complementary insights that multimodality and systems biology can provide. In this project, we demonstrate the use of graph theory for data integration via individual networks where nodes and edges are individual-specific. We showcase the consequences of early, intermediate, and late graph-based fusion of RNA-Seq data and histopathology whole-slide images for predicting cancer subtypes and severity. The methodology developed is as follows: (1) we create individual networks; (2) we compute the similarity between individuals from these graphs; (3) we train our model on the similarity matrices; (4) we evaluate the performance using the macro F1 score. Pros and cons of elements of the pipeline are evaluated on publicly available real-life datasets. We find that graph-based methods can increase performance over methods that do not study interactions. Additionally, merging multiple data sources often improves classification compared to models based on single data, especially through intermediate fusion. The proposed workflow can easily be adapted to other disease contexts to accelerate and enhance personalized healthcare.

Regulation of gene expression downstream of a novel Fgf/Erk pathway during Xenopus development.

Activation of Map kinase/Erk signalling downstream of fibroblast growth factor (Fgf) tyrosine kinase receptors regulates gene expression required for mesoderm induction and patterning of the anteroposterior axis during Xenopus development. We have proposed that a subset of Fgf target genes are activated in the embyo in response to inhibition of a transcriptional repressor. Here we investigate the hypothesis that Cic (Capicua), which was originally identified as a transcriptional repressor negatively regulated by receptor tyrosine kinase/Erk signalling in Drosophila, is involved in regulating Fgf target gene expression in Xenopus. We characterise Xenopus Cic and show that it is widely expressed in the embryo. Fgf overexpression or ectodermal wounding, both of which potently activate Erk, reduce Cic protein levels in embryonic cells. In keeping with our hypothesis, we show that Cic knockdown and Fgf overexpression have overlapping effects on embryo development and gene expression. Transcriptomic analysis identifies a cohort of genes that are up-regulated by Fgf overexpression and Cic knockdown. We investigate two of these genes as putative targets of the proposed Fgf/Erk/Cic axis: fos and rasl11b, which encode a leucine zipper transcription factor and a ras family GTPase, respectively. We identify Cic consensus binding sites in a highly conserved region of intron 1 in the fos gene and Cic sites in the upstream regions of several other Fgf/Cic co-regulated genes, including rasl11b. We show that expression of fos and rasl11b is blocked in the early mesoderm when Fgf and Erk signalling is inhibited. In addition, we show that fos and rasl11b expression is associated with the Fgf independent activation of Erk at the site of ectodermal wounding. Our data support a role for a Fgf/Erk/Cic axis in regulating a subset of Fgf target genes during gastrulation and is suggestive that Erk signalling is involved in regulating Cic target genes at the site of ectodermal wounding.