A Deep Learning Framework for Predicting Patient Decannulation on Extracorporeal Membrane Oxygenation Devices: Development and Model Analysis Study.

BACKGROUND: Venovenous extracorporeal membrane oxygenation (VV-ECMO) is a therapy for patients with refractory respiratory failure. The decision to decannulate someone from extracorporeal membrane oxygenation (ECMO) often involves weaning trials and clinical intuition. To date, there are limited prognostication metrics to guide clinical decision-making to determine which patients will be successfully weaned and decannulated. OBJECTIVE: This study aims to assist clinicians with the decision to decannulate a patient from ECMO, using Continuous Evaluation of VV-ECMO Outcomes (CEVVO), a deep learning-based model for predicting success of decannulation in patients supported on VV-ECMO. The running metric may be applied daily to categorize patients into high-risk and low-risk groups. Using these data, providers may consider initiating a weaning trial based on their expertise and CEVVO. METHODS: Data were collected from 118 patients supported with VV-ECMO at the Columbia University Irving Medical Center. Using a long short-term memory-based network, CEVVO is the first model capable of integrating discrete clinical information with continuous data collected from an ECMO device. A total of 12 sets of 5-fold cross validations were conducted to assess the performance, which was measured using the area under the receiver operating characteristic curve (AUROC) and average precision (AP). To translate the predicted values into a clinically useful metric, the model results were calibrated and stratified into risk groups, ranging from 0 (high risk) to 3 (low risk). To further investigate the performance edge of CEVVO, 2 synthetic data sets were generated using Gaussian process regression. The first data set preserved the long-term dependency of the patient data set, whereas the second did not. RESULTS: CEVVO demonstrated consistently superior classification performance compared with contemporary models (P<.001 and P=.04 compared with the next highest AUROC and AP). Although the model's patient-by-patient predictive power may be too low to be integrated into a clinical setting (AUROC 95% CI 0.6822-0.7055; AP 95% CI 0.8515-0.8682), the patient risk classification system displayed greater potential. When measured at 72 hours, the high-risk group had a successful decannulation rate of 58% (7/12), whereas the low-risk group had a successful decannulation rate of 92% (11/12; P=.04). When measured at 96 hours, the high- and low-risk groups had a successful decannulation rate of 54% (6/11) and 100% (9/9), respectively (P=.01). We hypothesized that the improved performance of CEVVO was owing to its ability to efficiently capture transient temporal patterns. Indeed, CEVVO exhibited improved performance on synthetic data with inherent temporal dependencies (P<.001) compared with logistic regression and a dense neural network. CONCLUSIONS: The ability to interpret and integrate large data sets is paramount for creating accurate models capable of assisting clinicians in risk stratifying patients supported on VV-ECMO. Our framework may guide future incorporation of CEVVO into more comprehensive intensive care monitoring systems.

A heterogeneous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase.

Over-activation of the epidermal growth factor receptor (EGFR) is a hallmark of glioblastoma. However, EGFR-targeted therapies have led to minimal clinical response. While delivery of EGFR inhibitors (EGFRis) to the brain constitutes a major challenge, how additional drug-specific features alter efficacy remains poorly understood. We apply highly multiplex single-cell chemical genomics to define the molecular response of glioblastoma to EGFRis. Using a deep generative framework, we identify shared and drug-specific transcriptional programs that group EGFRis into distinct molecular classes. We identify programs that differ by the chemical properties of EGFRis, including induction of adaptive transcription and modulation of immunogenic gene expression. Finally, we demonstrate that pro-immunogenic expression changes associated with a subset of tyrphostin family EGFRis increase the ability of T-cells to target glioblastoma cells.

Sensory exotropia versus sensory esotropia: A comparative clinical features study.

PURPOSE: This study aimed to compare the preoperative clinical features of patients with sensory esotropia (ET) and sensory exotropia (XT). METHODS: In a retrospective study, the medical records of 13,252 patients who underwent strabismus surgery were reviewed at the Farabi Eye Hospital, Iran, from 2012 to March 2022. There were 1017 patients with sensory horizontal strabismus whose, in their worse eye, had corrected distance visual acuity (CDVA) equal to or <20/160 tested with the Snellen chart. RESULTS: The mean age of patients was 29.0 ± 12.4 years [574 (56.4%) males and 443 (43.6%) females]. Sensory XT and ET were observed in 717 (70.5%) and 300 (29.5%) patients, respectively (P<.001). The mean CDVA in the strabismic and non-strabismic eyes was 1.40 ± 0.75 and 0.05 ± 0.13, respectively (P<.001). Also, the CDVA in the strabismic eyes was significantly worse in the patients with sensory XT than in the patients with sensory ET (P<.001). Sphere and spherical equivalent (SE) components were more hyperopic in both eyes of patients with sensory ET than sensory XT (P<.001). In sensory ET group, the mean horizontal deviation at far and near was significantly higher than the sensory XT group (both P<.001). The prevalence of moderate and severe amblyopia among all patients with sensory strabismus was 274 (26.9%) and 727 (71.5%), respectively (P<.001). There were 398 (39.1%) patients who needed more than one surgery. CONCLUSION: The frequency of sensory XT was about 2.5 times more than the sensory ET. Most patients with sensory ET were operated at a younger age, had better CDVA, more hyperopic spherical and SE, and higher angle of deviation compared with patients with sensory XT. The chance of reoperation in patients with sensory strabismus was about 40%.

A comparison of Scansys and Sirius tomography in healthy eyes.

PURPOSE: To assess the level of agreement and evaluate the reliability of measurements between two Scheimpflug imaging modalities, Scansys (MediWorks, China) and Sirius (CSO, Italy), in quantifying the anterior segment parameters in healthy eyes. METHODS: In a cross-sectional study, the right eyes of 38 healthy participants without any ocular or systemic diseases were examined. A range of anterior segment parameters including anterior and posterior flat and steep keratometry, central corneal thickness (CCT), thinnest corneal thickness (TCT), anterior chamber depth (ACD), anterior chamber angle (ACA), corneal volume, anterior chamber volume, and horizontal white to white diameter, derived from the sagittal curvature maps were measured. To evaluate the reliability of the measurements, intraclass correlation coefficient (ICC) and correlation coefficient were measured. Additionally, Bland-Altman plots were employed to examine the agreement in mean (bias line) and 95% limits of agreement between the two devices. RESULTS: The mean age was 31.5 ± 6.9 (range: 19-47) years. The ICC indicated that the majority of anterior segment parameters had an excellent or good level of reliability, surpassing the threshold of 0.9. Nevertheless, CCT and ACA exhibited a moderate level of reliability, with ICC values of 0.794 and 0.728, respectively. The correlation analysis showed a strong correlation for all the variables tested. The Bland-Altman plots revealed that the bias line was near zero and the 95% limits of agreement were narrow for most variables, except for the anterior flat and steep keratometry, which were found to range from - 0.57 to 0.84 D and - 0.68 to 0.87 D, respectively. CONCLUSION: Scansys and Sirius devices can be effectively used interchangeably for the evaluation of most anterior segment parameters; however, for anterior corneal curvatures, CCT and ACA, their alternative use is not recommended.

Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.

Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for rigorous interpretation of cell states, mostly do not use associated histology images and are not capable of inferring shared neighborhoods across multiple tissues. Here we present Starfysh, a computational toolbox using a deep generative model that incorporates archetypal analysis and any known cell type markers to characterize known or new tissue-specific cell states without a single-cell reference. Starfysh improves the characterization of spatial dynamics in complex tissues using histology images and enables the comparison of niches as spatial hubs across tissues. Integrative analysis of primary estrogen receptor (ER)-positive breast cancer, triple-negative breast cancer (TNBC) and metaplastic breast cancer (MBC) tissues led to the identification of spatial hubs with patient- and disease-specific cell type compositions and revealed metabolic reprogramming shaping immunosuppressive hubs in aggressive MBC.

Sensory Strabismus; A Literature Review.

Persistent unilateral or bilateral visual deprivation at any age, particularly in children, can compromise sensory fusion and result in a type of strabismus known as sensory or secondary strabismus. There are several pathologies that can induce visual impairment, such as severe anisometropia, congenital unilateral cataract, corneal opacity, retinal diseases, and optic nerve anomalies. Sensory strabismus may be horizontal or vertical or a combination of them; however, most reports indicate the development of horizontal deviation as sensory strabismus. Regardless of the direction of the sensory strabismus, early diagnosis and management of the underlying pathology are important before strabismus treatment. The primary treatment approach for patients with sensory strabismus is surgery to correct ocular misalignment and straighten the eyes. This can help to improve the patients' symptoms and diminish the negative psychosocial impacts. In this article, we review the underlying etiologies and background pathologies associated with sensory strabismus. In addition, we investigate the determinant factors of the direction of sensory strabismus and its management strategies.

Brown syndrome: a literature review.

The current data on various aspects of Brown syndrome are limited and sporadic. This review provides a coherent and comprehensive review of basic features, etiology, classification, differential diagnosis, and different management strategies of patients with Brown syndrome. In this topical review, PubMed, Scopus, and Google Scholar search engines were searched for papers, published between 1950 and January 2023 based on the keywords of this article. The related articles were collected, summarized, categorized, assessed, concluded, and presented. Brown syndrome is identified by restricted passive and active elevation of the eye in adduction. The condition is divided into congenital and acquired causes. The clinical features result from a restricted motion of the superior oblique tendon sheath through the trochlea while trying to look up in adduction. The newest explanation of the underlying pathophysiology has been explained as the presence of a fibrotic strand in the superior oblique muscle tendon with variable insertion sites which creates various elevation deficits seen in Brown syndrome. The most common clinical features include the presence of an abnormal head posture, V-pattern strabismus, and hypotropia in the primary position. Management of Brown syndrome includes watchful observation, surgical, and non-surgical procedures. Some cases might resolve spontaneously without any intervention; however, some acquired cases might require systemic and/or intra-trochlear steroid administration to treat the underlying causes. Surgical procedures such as superior oblique tenectomy and using a silicon tendon expander are indicated in the presence of hypotropia and significant abnormal head posture in the primary position.

Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy.

Understanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular therapy, donor lymphocyte infusion (DLI), by analyzing 348,905 single-cell transcriptomes from 74 longitudinal bone-marrow samples of 25 patients with relapsed myeloid leukemia; a subset was evaluated by protein-based spatial analysis. In acute myelogenous leukemia (AML) responders, diverse immune cell types within the bone-marrow microenvironment (BME) were predicted to interact with a clonally expanded population of ZNF683 + GZMB + CD8+ cytotoxic T lymphocytes (CTLs) which demonstrated in vitro specificity for autologous leukemia. This population, originating predominantly from the DLI product, expanded concurrently with NK and B cells. AML nonresponder BME revealed a paucity of crosstalk and elevated TIGIT expression in CD8+ CTLs. Our study highlights recipient BME differences as a key determinant of effective anti-leukemia response and opens new opportunities to modulate cell-based leukemia-directed therapy.

Human vascular organoids with a mosaic AKT1 mutation recapitulate Proteus syndrome.

Vascular malformation, a key clinical phenotype of Proteus syndrome, lacks effective models for pathophysiological study and drug development due to limited patient sample access. To bridge this gap, we built a human vascular organoid model replicating Proteus syndrome's vasculature. Using CRISPR/Cas9 genome editing and gene overexpression, we created induced pluripotent stem cells (iPSCs) embodying the Proteus syndrome-specific AKTE17K point mutation for organoid generation. Our findings revealed that AKT overactivation in these organoids resulted in smaller sizes yet increased vascular connectivity, although with less stable connections. This could be due to the significant vasculogenesis induced by AKT overactivation. This phenomenon likely stems from boosted vasculogenesis triggered by AKT overactivation, leading to increased vascular sprouting. Additionally, a notable increase in dysfunctional PDGFRß+ mural cells, impaired in matrix secretion, was observed in these AKT-overactivated organoids. The application of AKT inhibitors (ARQ092, AZD5363, or GDC0068) reversed the vascular malformations; the inhibitors' effectiveness was directly linked to reduced connectivity in the organoids. In summary, our study introduces an innovative in vitro model combining organoid technology and gene editing to explore vascular pathophysiology in Proteus syndrome. This model not only simulates Proteus syndrome vasculature but also holds potential for mimicking vasculatures of other genetically driven diseases. It represents an advance in drug development for rare diseases, historically plagued by slow progress.

Longitudinal changes in crystalline lens thickness and power in children aged 6-12 years old.

OBJECTIVES: To determine the three-year changes in crystalline lens power (LP) and thickness (LT) in children and their associated factors. METHODS: Schoolchildren aged 6-12 years living in Shahroud, northeast Iran were examined in 2015 and 2018. The Bennett formula was used to calculate LP. Multiple generalized estimating equations (GEE) analysis was used for data analysis. RESULTS: Among the 8089 examined eyes, the mean LP in Phase 1 and 2, and the three-year change were 21.61 ± 1.47D, 21.00 ± 1.42D, and -0.61 ± 0.52D, respectively. The GEE model showed that negative shifts in LP were less pronounced with increasing age (ß = 0.176; p < 0.001), and were also less noticeable in hyperopes compared to emmetropes (ß = 0.120; p < 0.001). The changes in LP decreased when outdoor activity increased among urban residents (ß = 0.013; p = 0.039), while it increased in rural area (ß = -0.020; p = 0.047). Mean three-year change in LT was 0.002 ± 0.13 mm. Female sex and aging by one year increased the LT by 0.022 mm (P < 0.001). However, LT decreased in 6-8-year-olds, while it increased in 10-12-year-old children, both in a linear fashion. The change in LT was less in myopes than in emmetropes (ß = -0.018, P-value = 0.010). CONCLUSION: LP decreases after three years in 6 to 12-year-old children. LT increases slightly after three years in 6 to 12-year-old children. The changes in LP and LT were associated with the refractive errors, place of residence, age and gender and outdoor activity time.

Cellstitch: 3D cellular anisotropic image segmentation via optimal transport.

BACKGROUND: Spatial mapping of transcriptional states provides valuable biological insights into cellular functions and interactions in the context of the tissue. Accurate 3D cell segmentation is a critical step in the analysis of this data towards understanding diseases and normal development in situ. Current approaches designed to automate 3D segmentation include stitching masks along one dimension, training a 3D neural network architecture from scratch, and reconstructing a 3D volume from 2D segmentations on all dimensions. However, the applicability of existing methods is hampered by inaccurate segmentations along the non-stitching dimensions, the lack of high-quality diverse 3D training data, and inhomogeneity of image resolution along orthogonal directions due to acquisition constraints; as a result, they have not been widely used in practice. METHODS: To address these challenges, we formulate the problem of finding cell correspondence across layers with a novel optimal transport (OT) approach. We propose CellStitch, a flexible pipeline that segments cells from 3D images without requiring large amounts of 3D training data. We further extend our method to interpolate internal slices from highly anisotropic cell images to recover isotropic cell morphology. RESULTS: We evaluated the performance of CellStitch through eight 3D plant microscopic datasets with diverse anisotropic levels and cell shapes. CellStitch substantially outperforms the state-of-the art methods on anisotropic images, and achieves comparable segmentation quality against competing methods in isotropic setting. We benchmarked and reported 3D segmentation results of all the methods with instance-level precision, recall and average precision (AP) metrics. CONCLUSIONS: The proposed OT-based 3D segmentation pipeline outperformed the existing state-of-the-art methods on different datasets with nonzero anisotropy, providing high fidelity recovery of 3D cell morphology from microscopic images.

Deep generative model deciphers derailed trajectories in acute myeloid leukemia.

Single-cell genomics has the potential to map cell states and their dynamics in an unbiased way in response to perturbations like disease. However, elucidating the cell-state transitions from healthy to disease requires analyzing data from perturbed samples jointly with unperturbed reference samples. Existing methods for integrating and jointly visualizing single-cell datasets from distinct contexts tend to remove key biological differences or do not correctly harmonize shared mechanisms. We present Decipher, a model that combines variational autoencoders with deep exponential families to reconstruct derailed trajectories (https://github.com/azizilab/decipher). Decipher jointly represents normal and perturbed single-cell RNA-seq datasets, revealing shared and disrupted dynamics. It further introduces a novel approach to visualize data, without the need for methods such as UMAP or TSNE. We demonstrate Decipher on data from acute myeloid leukemia patient bone marrow specimens, showing that it successfully characterizes the divergence from normal hematopoiesis and identifies transcriptional programs that become disrupted in each patient when they acquire NPM1 driver mutations.

DIISCO: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data.

Characterizing cell-cell communication and tracking its variability over time is essential for understanding the coordination of biological processes mediating normal development, progression of disease, or responses to perturbations such as therapies. Existing tools lack the ability to capture time-dependent intercellular interactions, such as those influenced by therapy, and primarily rely on existing databases compiled from limited contexts. We present DIISCO, a Bayesian framework for characterizing the temporal dynamics of cellular interactions using single-cell RNA-sequencing data from multiple time points. Our method uses structured Gaussian process regression to unveil time-resolved interactions among diverse cell types according to their co-evolution and incorporates prior knowledge of receptor-ligand complexes. We show the interpretability of DIISCO in simulated data and new data collected from CAR-T cells co-cultured with lymphoma cells, demonstrating its potential to uncover dynamic cell-cell crosstalk.

Basic acquired nonaccommodative esotropia patients managed with surgery; a study of 2102 patients.

INTRODUCTION: Several studies investigated preoperative clinical features of patients with basic-acquired nonaccommodative esotropia (BANAET); however, their sample sizes were small, and they did not compare the clinical features among cases that needed different surgery times. The main purpose of this study is to compare the preoperative clinical features of patients with BANAET managed with one surgery with patients who underwent two or more strabismus surgery over 10 years. METHODS: This historical cohort study was performed on the hospital records of 13,252 Iranian strabismic patients who underwent surgery at Farabi eye hospital, Tehran, Iran, from 2012 to September 2022. Of those, 2102 cases with BANAET were selected as the sample size. Data collected included sex, age at the time of first surgery, corrected distance visual acuity (CDVA), refractive error, presence of amblyopia, angle of deviation, and times of surgery. RESULTS: The mean age was 18.9 ± 15.6 [1200 (57.1%) males and 902 (42.9%) females] and the median age was 14 years. In 1599 (76.1%) patients, esotropia was managed with one surgery; however, 342 (16.3%) cases were managed with two surgeries and 161 (7.6%) patients underwent three or more surgeries. The mean angle of horizontal deviation at distance and near in patients managed with two and ≥3 surgeries was significantly higher than in cases managed with one surgery (P < .001). Amblyopia was observed in 289 (18.1%) patients who were managed with one surgery, 69 (20.2%) patients with two surgeries and 43 (26.7%) patients with three or more surgeries (P < .001). Patients with BANAET managed successfully with only one surgery were younger, had better CDVA, lower astigmatism and less horizontal angle of deviation at distance and near than those who underwent two or more surgeries (all P < .001). DISCUSSION: The higher astigmatism, lower CDVA, greater angle of horizontal deviation, and higher frequency of amblyopia were found in the preoperative examinations of BANAET patients managed with two or more surgeries compared with cases managed with only one surgery.

Clinical features and refractive profile of Brown syndrome.

CLINICAL SIGNIFICANCE: Understanding the refractive profile, amblyopia prevalence, binocular status, and head position in patients with Brown syndrome help clinicians become more familiar with this syndrome. BACKGROUND: Brown syndrome is identified as an active and passive restricted elevation of the eye in adduction. There is little information on clinical features, including refractive status, amblyopia, abnormal head posture (AHP), and types of deviation in these patients. METHODS: This study retrospectively evaluated records of 100 Brown syndrome patients from 2015 to 2022 at Farabi Eye Hospital, Iran. RESULTS: The mean age was 6.99 ± 6.33 years, including 48 (48%) males. A congenital source was found in 74 (74%) and 96 (96%) patients had unilateral involvement. The mean CDVA for the affected and non-affected eyes were 0.05 ± 0.11 and 0.03 ± 0.06 logMAR, respectively (P = 0.31). In unilateral cases, hyperopia, myopia, and emmetropia were observed in 55 (57.29%), 2 (2.08%), and 39 (40.63%) affected eyes, respectively. The most common type of deviation was pure hypotropia, which was found in 53 (53%) cases, followed by 'combined exotropia and hypotropia' observed in 26 (26%) patients. The mean angle of hypotropia and horizontal deviation in the primary position at distance was 12.10 ± 8.50 and 8 ± 13.20 prism dioptre, respectively. A V-pattern was found in 76 (76%) patients. Amblyopia was observed in 13 (21.67%) of 60 cooperative patients, and AHP was noticed in 66 (66%) patients, in which "combined chin up and contralateral face turn" was the most common type. CONCLUSION: About 75% of cases were congenital, 50% had pure hypotropia, 75% showed V-pattern, 20% had amblyopia, and AHP was observed in 67% of patients. The remarkable prevalence of amblyopia alongside the high occurrence of AHP should alert clinicians to carefully assess patients with Brown syndrome for sensory fusion and amblyopia.

Modeling and countering the effects of cosmic radiation using bioengineered human tissues.

Cosmic radiation is the most serious risk that will be encountered during the planned missions to the Moon and Mars. There is a compelling need to understand the effects, safety thresholds, and mechanisms of radiation damage in human tissues, in order to develop measures for radiation protection during extended space travel. As animal models fail to recapitulate the molecular changes in astronauts, engineered human tissues and "organs-on-chips" are valuable tools for studying effects of radiation in vitro. We have developed a bioengineered tissue platform for studying radiation damage in individualized settings. To demonstrate its utility, we determined the effects of radiation using engineered models of two human tissues known to be radiosensitive: engineered cardiac tissues (eCT, a target of chronic radiation damage) and engineered bone marrow (eBM, a target of acute radiation damage). We report the effects of high-dose neutrons, a proxy for simulated galactic cosmic rays, on the expression of key genes implicated in tissue responses to ionizing radiation, phenotypic and functional changes in both tissues, and proof-of-principle application of radioprotective agents. We further determined the extent of inflammatory, oxidative stress, and matrix remodeling gene expression changes, and found that these changes were associated with an early hypertrophic phenotype in eCT and myeloid skewing in eBM. We propose that individualized models of human tissues have potential to provide insights into the effects and mechanisms of radiation during deep-space missions and allow testing of radioprotective measures.

MicroRNAs, small regulatory elements with significant effects on human implantation: a review.

Embryo implantation is a critical process for achieving a successful pregnancy and live birth. The proper implantation must have a synchronized interaction between blastocyst and a receptive endometrium. Many genes are involved in the modulation of precise molecular events during implantation. MicroRNAs (miRNAs) have been extensively reported as gene regulatory molecules on post-transcriptional levels involved in various biological processes such as gametogenesis, embryogenesis, and the quality of sperm, oocyte, and embryos. A plethora of evidence has demonstrated critical roles for miRNAs in regulating genes involved in the implantation process; hence, dysregulation of miRNAs could be associated with significant impairments in implantation, such as recurrent implantation failure. In addition to the indispensable role of miRNAs in the intracellular control of gene expression, they can also be secreted into extracellular fluid and circulation. Therefore, miRNAs in body fluids and blood may be exploited as non-invasive diagnostic biomarkers for different pathological and physiological conditions. Recently, several studies have focused on the discovery of miRNAs function in the implantation process by appraising miRNAs and their target genes in human embryos, endometrial tissue, and cell culture models. Moreover, it was revealed that there could be a significant association between endometrial receptivity or implantation status and the expression of miRNAs in human body fluids, reinforcing their role as non-invasive biomarkers. In the current work, we reviewed the studies concerning the role of intracellular and extracellular miRNAs in human implantation and the influence of their dysregulation on implantation disorders.

Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens.

Single-cell genomics enables dissection of tumor heterogeneity and molecular underpinnings of drug response at an unprecedented resolution1-11. However, broad clinical application of these methods remains challenging, due to several practical and preanalytical challenges that are incompatible with typical clinical care workflows, namely the need for relatively large, fresh tissue inputs. In the present study, we show that multimodal, single-nucleus (sn)RNA/T cell receptor (TCR) sequencing, spatial transcriptomics and whole-genome sequencing (WGS) are feasible from small, frozen tissues that approximate routinely collected clinical specimens (for example, core needle biopsies). Compared with data from sample-matched fresh tissue, we find a similar quality in the biological outputs of snRNA/TCR-seq data, while reducing artifactual signals and compositional biases introduced by fresh tissue processing. Profiling sequentially collected melanoma samples from a patient treated in the KEYNOTE-001 trial12, we resolved cellular, genomic, spatial and clonotype dynamics that represent molecular patterns of heterogeneous intralesional evolution during anti-programmed cell death protein 1 therapy. To demonstrate applicability to banked biospecimens of rare diseases13, we generated a single-cell atlas of uveal melanoma liver metastasis with matched WGS data. These results show that single-cell genomics from archival, clinical specimens is feasible and provides a framework for translating these methods more broadly to the clinical arena.

Outpatient Cardiovascular Rehabilitation Registry in Iran: The First Rehabilitation Registry Experience at EMR.

INTRODUCTION: The collected information includes demographic profile, medical history, physical examination, patient risk factors, anthropometric evaluation, medications, echocardiographic results, and exercise testing of all patients who participated in the outpatient cardiac rehabilitation program in Cardiac Rehabilitation Department since 1996 until now. Each patient was assigned an electronic code by which the patient's information could be identified. Subsequently, standard questionnaires were used, such as International physical activity questionnaire (IPAQ) to assess physical activity, MAC NEW to assess the quality of life, Spielberg to measure anxiety, Beck to assess depression, and nutritional questionnaires. RESULTS: The findings were recorded, and the data were analyzed by the web and SPSS software. For all patients, the forms were filled based on a number of variables including backgrounds, registration components, type of referral, diagnosis of underlying heart disease, methods of data collection and entry, details of the educational program, return to work, psychiatric condition, drug regimen, clinical condition, echocardiography findings, functional capacity and exercise test response, smoking status, nutritional habits, and finally their 5-year follow-up for events and re-hospitalization. CONCLUSION: It is necessary for the authors to establish a cardiac rehabilitation registration that can properly display care quality indicators and collect and report standard data from different nations to improve the quality of cardiac rehabilitation services and identify weaknesses.