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Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures.
Tumor hypoxia drives metabolic shifts, cancer progression, and therapeutic resistance. Challenges in quantifying hypoxia have hindered the exploitation of this potential "Achilles' heel." While gene expression signatures have shown promise as surrogate measures of hypoxia, signature usage is heterogeneous and debated. Here, we present a systematic pan-cancer evaluation of 70 hypoxia signatures and 14 summary scores in 104 cell lines and 5,407 tumor samples using 472 million length-matched random gene signatures. Signature and score choice strongly influenced the prediction of hypoxia in vitro and in vivo. In cell lines, the Tardon signature was highly accurate in both bulk and single-cell data (94% accuracy, interquartile mean). In tumors, the Buffa and Ragnum signatures demonstrated superior performance, with Buffa/mean and Ragnum/interquartile mean emerging as the most promising for prospective clinical trials. This work delivers recommendations for experimental hypoxia detection and patient stratification for hypoxia-targeting therapies, alongside a generalizable framework for signature evaluation.
Association Between Patient Perception of Disease Status and Different Components of the Minimal Disease Activity Criteria in Psoriatic Arthritis.
OBJECTIVE: The aim of this study was to evaluate whether meeting minimal disease activity (MDA) as measured by the MDA criteria was perceived as good disease control by patients with psoriatic arthritis (PsA) regardless of which MDA components were not met. METHODS: We analyzed data from the Remission/Flare in PsA (ReFlaP) study (ClinicalTrials.gov: NCT03119805), a cross-sectional international study of adult patients with PsA. Patients self-reported if they felt their PsA was in remission (REM), low disease activity (LDA), or neither. The relationship between patient-reported status and the MDA components met was analyzed using point-biserial correlation, chi-square test, odds ratios, and specificity. RESULTS: Of the study participants who met MDA, 88.4% reported good disease status (REM/LDA). Pain was the most commonly unmet component. A moderate to strong correlation was found between meeting more MDA components and patient-reported good status irrespective of component unmet. On individual component testing, MDA state and patient-reported REM/LDA were significantly associated irrespective of unmet component, with the exception of entheses. Specificity of the MDA score irrespective of the unmet component was > 90%. The odds of MDA patients reporting poor disease status were significant only for when pain visual analog score (VAS) < 1 was the unmet component. This significance was not supported by the sensitivity analysis. CONCLUSION: This study suggests strong agreement between MDA status and patient-reported good status irrespective of unmet component. Pain < 1 or 2 on a 0-10 VAS was the hardest component to meet. The high specificity regardless of the unmet MDA component suggests patients who feel their disease is active are minimally misclassified by the score.
Years of life lost to COVID-19 in 81 countries.
Understanding the mortality impact of COVID-19 requires not only counting the dead, but analyzing how premature the deaths are. We calculate years of life lost (YLL) across 81 countries due to COVID-19 attributable deaths, and also conduct an analysis based on estimated excess deaths. We find that over 20.5 million years of life have been lost to COVID-19 globally. As of January 6, 2021, YLL in heavily affected countries are 2-9 times the average seasonal influenza; three quarters of the YLL result from deaths in ages below 75 and almost a third from deaths below 55; and men have lost 45% more life years than women. The results confirm the large mortality impact of COVID-19 among the elderly. They also call for heightened awareness in devising policies that protect vulnerable demographics losing the largest number of life-years.
Expanding the OMOP Common Data Model to Support Perinatal Research in Network Studies.
OBJECTIVES: The Observational Medical Outcomes Partnership common data model (OMOP-CDM) is a useful tool for large-scale network analysis but currently lacks a structured approach to pregnancy episodes. We aimed to develop and implement a perinatal expansion for the OMOP-CDM to facilitate perinatal network research. METHODS: We collaboratively developed a perinatal expansion with input from domain experts and stakeholders to reach consensus. The structure and vocabularies followed the OMOP-CDM ontological framework principles. We tested the expansion using SIDIAP and Norwegian databases. We developed a diagnostics package for quality control assessment and conducted a descriptive analysis on the captured perinatal data mapped to the OMOP-CDM. RESULTS: The perinatal expansion consists of a pregnancy table and an infant table, each with required and optional variables incorporated into standardized vocabularies. Quality assessment of the perinatal expansion table in SIDIAP and Norwegian databases demonstrated accurate capture of perinatal characteristics. Descriptive analysis measured the number of pregnancies (SIDIAP: 646 530; Norway: 746 671), pregnancy outcomes (e.g., 0.5% stillbirths in SIDIAP and 0.4% in Norway), gestational length (median [IQR] in days, SIDIAP: 273 [56-280]; Norway: 280 [273-286]), number of infants (Norway: 758 806), and birth weight (median [IQR] in grams, Norway: 3520 [3175-3860)], among other relevant variables. DISCUSSION AND CONCLUSION: We developed and implemented a perinatal expansion that captures important variables for perinatal research and allows interoperability with existing tables in the OMOP-CDM, which is expected to facilitate future network studies. The publicly available diagnostics package enables testing the implementation of the extension table and the quality and completeness of available data on pregnancy and pregnancy-related outcomes in databases mapped to the OMOP CDM.
Aligning, autoencoding and prompting large language models for novel disease reporting
Given radiology images, automatic radiology report generation aims to produce informative text that reports diseases. It can benefit current clinical practice in diagnostic radiology. Existing methods typically rely on large-scale medical datasets annotated by clinicians to train desirable models. However, for novel diseases, sufficient training data are typically not available. We propose a prompt-based deep learning framework, i.e., PromptLLM, to align, autoencode, and prompt the (large) language model to generate reports for novel diseases accurately and efficiently. Our method includes three major steps: (1) aligning visual images and textual reports to learn general knowledge across modalities from diseases where labeled data are sufficient, (2) autoencoding the LLM using unlabeled data of novel diseases to learn the specific knowledge and writing styles of the novel disease, and (3) prompting the LLM with learned knowledge and writing styles to report the novel diseases contained in the radiology images. Through the above three steps, with limited labels on novel diseases, we show that PromptLLM can rapidly learn the corresponding knowledge for accurate novel disease reporting. The experiments on COVID-19 and diverse thorax diseases show that our approach, utilizing 1% of the training data, achieves desirable performance compared to previous methods. It shows that our approach allows us to relax the reliance on labeled data that is common to existing methods. It could have a real-world impact on data analysis during the early stages of novel diseases. Our code and data are available at https://github.com/ai-in-health/PromptLLM.
MAIT cells protect against sterile lung injury.
Mucosal-associated invariant T (MAIT) cells, the most abundant unconventional T cells in the lung, can exhibit a wide range of functional responses to different triggers via their T cell receptor (TCR) and/or cytokines. Their role, especially in sterile lung injury, is unknown. Using single-cell RNA sequencing (scRNA-seq), spectral analysis, and adoptive transfer in a bleomycin-induced sterile lung injury, we found that bleomycin activates murine pulmonary MAIT cells and is associated with a protective role against bleomycin-induced lung injury. MAIT cells drive the accumulation of type 1 conventional dendritic cells (cDC1s), limiting tissue damage in a DNGR-1-dependent manner. Human scRNA-seq data revealed that MAIT cells were activated, with increased cDC populations in idiopathic pulmonary fibrosis patients. Thus, MAIT cells enhance defense against sterile lung injury by fostering cDC1-driven anti-fibrotic pathways.
Patient and parent perspectives on being invited to join a trial of night-time only versus full-time bracing for adolescent idiopathic scoliosis : a qualitative study.
AIMS: The Bracing Adolescent Idiopathic Scoliosis (BASIS) study is a randomized controlled non-inferiority pragmatic trial of 'full-time bracing' (FTB) compared to 'night-time bracing' (NTB) for the treatment of adolescent idiopathic scoliosis (AIS). We anticipated that recruiting patients to BASIS would be challenging, as it is a paediatric trial comparing two markedly different bracing pathways. No previous studies have compared the experiences of AIS patients treated with FTB to those treated with NTB. This qualitative study was embedded in BASIS to explore families' perspectives of BASIS, to inform trial communication, and to identify strategies to support patients treated in a brace. METHODS: Semi-structured interviews were conducted with parents (n = 26) and young people (n = 21) who had been invited to participate in BASIS at ten of the 22 UK paediatric spine services in hospitals recruiting to BASIS. Audio-recorded interviews were transcribed and analyzed thematically. RESULTS: Families viewed their interactions with BASIS recruiters positively, but were often confused about core aspects of BASIS, such as the aims, expectations of bracing, and the process of randomization. Participants typically expressed a preference for NTB, but recruiters may have framed NTB more favourably. Patients and parents reported challenges wearing a brace, such as physical discomfort, feelings of self-consciousness, difficulty participating in physical activities, and strain on financial resources to support brace use. Patients in FTB reported more pronounced challenges. While families valued health professional support, they felt there was a lack of social, emotional, and school support, and relied on online resources, as well private counselling services to address this need. CONCLUSION: The findings informed the development of resources and strategies, including guidance for schools and the recommendations in this paper, to support patients to wear NTB and FTB as prescribed. The results indicated opportunities for recruiters to enhance trial communication in ways that could improve informed consent and recruitment to BASIS, and inform future trials of bracing.
Impact of the COVID-19 pandemic on paediatric patients with cancer in low-income, middle-income and high-income countries: protocol for a multicentre, international, observational cohort study.
INTRODUCTION: Childhood cancers are a leading cause of non-communicable disease deaths for children around the world. The COVID-19 pandemic may have impacted on global children's cancer services, which can have consequences for childhood cancer outcomes. The Global Health Research Group on Children's Non-Communicable Diseases is currently undertaking the first international cohort study to determine the variation in paediatric cancer management during the COVID-19 pandemic, and the short-term to medium-term impacts on childhood cancer outcomes. METHODS AND ANALYSIS: This is a multicentre, international cohort study that will use routinely collected hospital data in a deidentified and anonymised form. Patients will be recruited consecutively into the study, with a 12-month follow-up period. Patients will be included if they are below the age of 18 years and undergoing anticancer treatment for the following cancers: acute lymphoblastic leukaemia, Burkitt lymphoma, Hodgkin lymphoma, Wilms tumour, sarcoma, retinoblastoma, gliomas, medulloblastomas and neuroblastomas. Patients must be newly presented or must be undergoing active anticancer treatment from 12 March 2020 to 12 December 2020. The primary objective of the study was to determine all-cause mortality rates of 30 days, 90 days and 12 months. This study will examine the factors that influenced these outcomes. χ2 analysis will be used to compare mortality between low-income and middle-income countries and high-income countries. Multilevel, multivariable logistic regression analysis will be undertaken to identify patient-level and hospital-level factors affecting outcomes with adjustment for confounding factors. ETHICS AND DISSEMINATION: At the host centre, this study was deemed to be exempt from ethical committee approval due to the use of anonymised registry data. At other centres, participating collaborators have gained local approvals in accordance with their institutional ethical regulations. Collaborators will be encouraged to present the results locally, nationally and internationally. The results will be submitted for publication in a peer-reviewed journal.
Twelve-month observational study of children with cancer in 41 countries during the COVID-19 pandemic.
INTRODUCTION: Childhood cancer is a leading cause of death. It is unclear whether the COVID-19 pandemic has impacted childhood cancer mortality. In this study, we aimed to establish all-cause mortality rates for childhood cancers during the COVID-19 pandemic and determine the factors associated with mortality. METHODS: Prospective cohort study in 109 institutions in 41 countries. INCLUSION CRITERIA: children <18 years who were newly diagnosed with or undergoing active treatment for acute lymphoblastic leukaemia, non-Hodgkin's lymphoma, Hodgkin lymphoma, retinoblastoma, Wilms tumour, glioma, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, medulloblastoma and neuroblastoma. Of 2327 cases, 2118 patients were included in the study. The primary outcome measure was all-cause mortality at 30 days, 90 days and 12 months. RESULTS: All-cause mortality was 3.4% (n=71/2084) at 30-day follow-up, 5.7% (n=113/1969) at 90-day follow-up and 13.0% (n=206/1581) at 12-month follow-up. The median time from diagnosis to multidisciplinary team (MDT) plan was longest in low-income countries (7 days, IQR 3-11). Multivariable analysis revealed several factors associated with 12-month mortality, including low-income (OR 6.99 (95% CI 2.49 to 19.68); p<0.001), lower middle income (OR 3.32 (95% CI 1.96 to 5.61); p<0.001) and upper middle income (OR 3.49 (95% CI 2.02 to 6.03); p<0.001) country status and chemotherapy (OR 0.55 (95% CI 0.36 to 0.86); p=0.008) and immunotherapy (OR 0.27 (95% CI 0.08 to 0.91); p=0.035) within 30 days from MDT plan. Multivariable analysis revealed laboratory-confirmed SARS-CoV-2 infection (OR 5.33 (95% CI 1.19 to 23.84); p=0.029) was associated with 30-day mortality. CONCLUSIONS: Children with cancer are more likely to die within 30 days if infected with SARS-CoV-2. However, timely treatment reduced odds of death. This report provides crucial information to balance the benefits of providing anticancer therapy against the risks of SARS-CoV-2 infection in children with cancer.
Use of oxygen-loaded nanobubbles to improve tissue oxygenation: Bone-relevant mechanisms of action and effects on osteoclast differentiation.
Gas-loaded nanobubbles have potential as a method of oxygen delivery to increase tumour oxygenation and therapeutically alleviate tumour hypoxia. However, the mechanism(s) whereby oxygen-loaded nanobubbles increase tumour oxygenation are unknown; with their calculated oxygen-carrying capacity being insufficient to explain this effect. Intra-tumoural hypoxia is a prime therapeutic target, at least partly due to hypoxia-dependent stimulation of the formation and function of bone-resorbing osteoclasts which establish metastatic cells in bone. This study aims to investigate potential mechanism(s) of oxygen delivery and in particular the possible use of oxygen-loaded nanobubbles in preventing bone metastasis via effects on osteoclasts. Lecithin-based nanobubbles preferentially interacted with phagocytic cells (monocytes, osteoclasts) via a combination of lipid transfer, clathrin-dependent endocytosis and phagocytosis. This interaction caused general suppression of osteoclast differentiation via inhibition of cell fusion. Additionally, repeat exposure to oxygen-loaded nanobubbles inhibited osteoclast formation to a greater extent than nitrogen-loaded nanobubbles. This gas-dependent effect was driven by differential effects on the fusion of mononuclear precursor cells to form pre-osteoclasts, partly due to elevated potentiation of RANKL-induced ROS by nitrogen-loaded nanobubbles. Our findings suggest that oxygen-loaded nanobubbles could represent a promising therapeutic strategy for cancer therapy; reducing osteoclast formation and therefore bone metastasis via preferential interaction with monocytes/macrophages within the tumour and bone microenvironment, in addition to known effects of directly improving tumour oxygenation.
Postpartum-specific vital sign reference ranges
The majority of maternal deaths occur in the postpartum period (57% in the United States), compared with the antenatal and intrapartum periods. However, maternal deaths in the postpartum period have not been studied as extensively as the antenatal and intrapartum periods. Venous thromboembolism, hemorrhage, sepsis, and gestational hypertensive disorders are the leading causes of death during postpartum. Little data exists describing normal postpartum vital signs. This study aimed to estimate maternal postpartum vital sign ranges.