Interactive Isosurface Visualization in Memory Constrained Environments Using Deep Learning and Speculative Raycasting.

New web technologies have enabled the deployment of powerful GPU-based computational pipelines that run entirely in the web browser, opening a new frontier for accessible scientific visualization applications. However, these new capabilities do not address the memory constraints of lightweight end-user devices encountered when attempting to visualize the massive data sets produced by today's simulations and data acquisition systems. We propose a novel implicit isosurface rendering algorithm for interactive visualization of massive volumes within a small memory footprint. We achieve this by progressively traversing a wavefront of rays through the volume and decompressing blocks of the data on-demand to perform implicit ray-isosurface intersections, displaying intermediate results each pass. We improve the quality of these intermediate results using a pretrained deep neural network that reconstructs the output of early passes, allowing for interactivity with better approximates of the final image. To accelerate rendering and increase GPU utilization, we introduce speculative ray-block intersection into our algorithm, where additional blocks are traversed and intersected speculatively along rays to exploit additional parallelism in the workload. Our algorithm is able to trade-off image quality to greatly decrease rendering time for interactive rendering even on lightweight devices. Our entire pipeline is run in parallel on the GPU to leverage the parallel computing power that is available even on lightweight end-user devices. We compare our algorithm to the state of the art in low-overhead isosurface extraction and demonstrate that it achieves 1.7×- 5.7× reductions in memory overhead and up to 8.4× reductions in data decompressed.

Accelerated motion correction with deep generative diffusion models.

PURPOSE: The aim of this work is to develop a method to solve the ill-posed inverse problem of accelerated image reconstruction while correcting forward model imperfections in the context of subject motion during MRI examinations. METHODS: The proposed solution uses a Bayesian framework based on deep generative diffusion models to jointly estimate a motion-free image and rigid motion estimates from subsampled and motion-corrupt two-dimensional (2D) k-space data. RESULTS: We demonstrate the ability to reconstruct motion-free images from accelerated two-dimensional (2D) Cartesian and non-Cartesian scans without any external reference signal. We show that our method improves over existing correction techniques on both simulated and prospectively accelerated data. CONCLUSION: We propose a flexible framework for retrospective motion correction of accelerated MRI based on deep generative diffusion models, with potential application to other forward model corruptions.

Explorative Discovery of Gene Signatures and Clinotypes in Glioblastoma Cancer Through GeneTerrain Knowledge Map Representation.

This study introduces the GeneTerrain Knowledge Map Representation (GTKM), a novel method for visualizing gene expression data in cancer research. GTKM leverages protein-protein interactions to graphically display differentially expressed genes (DEGs) on a 2-dimensional contour plot, offering a more nuanced understanding of gene interactions and expression patterns compared to traditional heatmap methods. The research demonstrates GTKM's utility through four case studies on glioblastoma (GBM) datasets, focusing on survival analysis, subtype identification, IDH1 mutation analysis, and drug sensitivities of different tumor cell lines. Additionally, a prototype website has been developed to showcase these findings, indicating the method's adaptability for various cancer types. The study reveals that GTKM effectively identifies gene patterns associated with different clinical outcomes in GBM, and its profiles enable the identification of sub-gene signature patterns crucial for predicting survival. The methodology promises significant advancements in precision medicine, providing a powerful tool for understanding complex gene interactions and identifying potential therapeutic targets in cancer treatment.

Correcting synthetic MRI contrast-weighted images using deep learning.

Synthetic magnetic resonance imaging (MRI) offers a scanning paradigm where a fast multi-contrast sequence can be used to estimate underlying quantitative tissue parameter maps, which are then used to synthesize any desirable clinical contrast by retrospectively changing scan parameters in silico. Two benefits of this approach are the reduced exam time and the ability to generate arbitrary contrasts offline. However, synthetically generated contrasts are known to deviate from the contrast of experimental scans. The reason for contrast mismatch is the necessary exclusion of some unmodeled physical effects such as partial voluming, diffusion, flow, susceptibility, magnetization transfer, and more. The inclusion of these effects in signal encoding would improve the synthetic images, but would make the quantitative imaging protocol impractical due to long scan times. Therefore, in this work, we propose a novel deep learning approach that generates a multiplicative correction term to capture unmodeled effects and correct the synthetic contrast images to better match experimental contrasts for arbitrary scan parameters. The physics inspired deep learning model implicitly accounts for some unmodeled physical effects occurring during the scan. As a proof of principle, we validate our approach on synthesizing arbitrary inversion recovery fast spin-echo scans using a commercially available 2D multi-contrast sequence. We observe that the proposed correction visually and numerically reduces the mismatch with experimentally collected contrasts compared to conventional synthetic MRI. Finally, we show results of a preliminary reader study and find that the proposed method statistically significantly improves in contrast and SNR as compared to synthetic MR images.

The robustness of persistent homology of brain networks to data acquisition-related non-neural variability in resting state fMRI.

There is increasing interest in investigating brain function based on functional connectivity networks (FCN) obtained from resting-state functional magnetic resonance imaging (fMRI). FCNs, typically obtained using measures of time series association such as Pearson's correlation, are sensitive to data acquisition parameters such as sampling period. This introduces non-neural variability in data pooled from different acquisition protocols and MRI scanners, negating the advantages of larger sample sizes in pooled data. To address this, we hypothesize that the topology or shape of brain networks must be preserved irrespective of how densely it is sampled, and metrics which capture this topology may be statistically similar across sampling periods, thereby alleviating this source of non-neural variability. Accordingly, we present an end-to-end pipeline that uses persistent homology (PH), a branch of topological data analysis, to demonstrate similarity across FCNs acquired at different temporal sampling periods. PH, as a technique, extracts topological features by capturing the network organization across all continuous threshold values, as opposed to graph theoretic methods, which fix a discrete network topology by thresholding the connectivity matrix. The extracted topological features are encoded in the form of persistent diagrams that can be compared against one another using the earth-moving metric, also popularly known as the Wasserstein distance. We extract topological features from three data cohorts, each acquired at different temporal sampling periods and demonstrate that these features are statistically the same, hence, empirically showing that PH may be robust to changes in data acquisition parameters such as sampling period.

Using digital phenotyping to understand health-related outcomes: A scoping review.

BACKGROUND: Digital phenotyping may detect changes in health outcomes and potentially lead to proactive measures to mitigate health declines and avoid major medical events. While health-related outcomes have traditionally been acquired through self-report measures, those approaches have numerous limitations, such as recall bias, and social desirability bias. Digital phenotyping may offer a potential solution to these limitations. OBJECTIVES: The purpose of this scoping review was to identify and summarize how passive smartphone data are processed and evaluated analytically, including the relationship between these data and health-related outcomes. METHODS: A search of PubMed, Scopus, Compendex, and HTA databases was conducted for all articles in April 2021 using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Scoping Review (PRISMA-ScR) guidelines. RESULTS: A total of 40 articles were included and went through an analysis based on data collection approaches, feature extraction, data analytics, behavioral markers, and health-related outcomes. This review demonstrated a layer of features derived from raw sensor data that can then be integrated to estimate and predict behaviors, emotions, and health-related outcomes. Most studies collected data from a combination of sensors. GPS was the most used digital phenotyping data. Feature types included physical activity, location, mobility, social activity, sleep, and in-phone activity. Studies involved a broad range of the features used: data preprocessing, analysis approaches, analytic techniques, and algorithms tested. 55% of the studies (n = 22) focused on mental health-related outcomes. CONCLUSION: This scoping review catalogued in detail the research to date regarding the approaches to using passive smartphone sensor data to derive behavioral markers to correlate with or predict health-related outcomes. Findings will serve as a central resource for researchers to survey the field of research designs and approaches performed to date and move this emerging domain of research forward towards ultimately providing clinical utility in patient care.

An untrained deep learning method for reconstructing dynamic MR images from accelerated model-based data.

PURPOSE: To implement physics-based regularization as a stopping condition in tuning an untrained deep neural network for reconstructing MR images from accelerated data. METHODS: The ConvDecoder (CD) neural network was trained with a physics-based regularization term incorporating the spoiled gradient echo equation that describes variable-flip angle data. Fully-sampled variable-flip angle k-space data were retrospectively accelerated by factors of R = {8, 12, 18, 36} and reconstructed with CD, CD with the proposed regularization (CD + r), locally low-rank (LR) reconstruction, and compressed sensing with L1-wavelet regularization (L1). Final images from CD + r training were evaluated at the "argmin" of the regularization loss; whereas the CD, LR, and L1 reconstructions were chosen optimally based on ground truth data. The performance measures used were the normalized RMS error, the concordance correlation coefficient, and the structural similarity index. RESULTS: The CD + r reconstructions, chosen using the stopping condition, yielded structural similarity indexs that were similar to the CD (p = 0.47) and LR structural similarity indexs (p = 0.95) across R and that were significantly higher than the L1 structural similarity indexs (p = 0.04). The concordance correlation coefficient values for the CD + r T1 maps across all R and subjects were greater than those corresponding to the L1 (p = 0.15) and LR (p = 0.13) T1 maps, respectively. For R ≥ 12 (≤4.2 min scan time), L1 and LR T1 maps exhibit a loss of spatially refined details compared to CD + r. CONCLUSION: The use of an untrained neural network together with a physics-based regularization loss shows promise as a measure for determining the optimal stopping point in training without relying on fully-sampled ground truth data.

Patient Outcomes Related to In-Hospital Delays in Appendicectomy for Appendicitis: A Retrospective Study.

Background and objective In many hospitals, the availability of operating theatres and access to senior surgical and anaesthetic support diminish during night hours. Therefore, urgent surgery is sometimes postponed until the following morning rather than performed overnight, if it is judged to be safe. In this study, we aimed to determine if a delay in laparoscopic appendicectomy in cases of acute appendicitis of over 12 hours, analogous to an overnight delay, correlated with worse patient outcomes. Our primary outcome was delayed discharge from the hospital. Our secondary outcomes were appendicitis severity, conversions, and postoperative complications. Methods We undertook a retrospective review of the medical records of patients who underwent laparoscopic appendicectomy for appendicitis at a UK district general hospital between 01/01/2018 and 30/08/2019. For each patient, clinical and demographic information, and time of hospital admission, surgery, and discharge were collected. Delayed discharge was defined as "time to discharge" >24 hours after surgery. Results A total of 446 patients were included in the study. In 137 patients (30.7%), "time to surgery" was under 12 hours; in 309 patients (69.3%) "time to surgery" was over 12 hours. Of note, 319 patients (71.5%) had a delayed discharge; 303 patients (67.9%) had complicated appendicitis, and 143 patients had severe appendicitis (32.1%). No statistically significant association between "time to surgery" and delayed discharge, appendicitis severity, conversion, or 30-day re-presentations was observed. Conclusion Time from admission to the start of appendicectomy did not affect patient outcomes. Short in-hospital delays in appendicectomy, such as an overnight delay, may be safe in certain patients and should be determined based on clinical judgement.

UALCAN: An update to the integrated cancer data analysis platform.

Cancer genomic, transcriptomic, and proteomic profiling has generated extensive data that necessitate the development of tools for its analysis and dissemination. We developed UALCAN to provide a portal for easy exploring, analyzing, and visualizing these data, allowing users to integrate the data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web portal enables analyzing and delivering cancer transcriptome, proteomics, and patient survival data to the cancer research community. With data obtained from The Cancer Genome Atlas (TCGA) project, UALCAN has enabled users to evaluate protein-coding gene expression and its impact on patient survival across 33 types of cancers. The web portal has been used extensively since its release and received immense popularity, underlined by its usage from cancer researchers in more than 100 countries. The present manuscript highlights the task we have undertaken and updates that we have made to UALCAN since its release in 2017. Extensive user feedback motivated us to expand the resource by including data on a) microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and promoter DNA methylation from TCGA and b) mass spectrometry-based proteomics from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). UALCAN provides easy access to pre-computed, tumor subgroup-based gene/protein expression, promoter DNA methylation status, and Kaplan-Meier survival analyses. It also provides new visualization features to comprehend and integrate observations and aids in generating hypotheses for testing. UALCAN is accessible at http://ualcan.path.uab.edu.

Vitamin K deficiency bleeding of newborn masquerading haemophilia B.

The term infant is remarkably resistant to bleeding despite physiologically low levels of procoagulant proteins. However, because of their unique haemostatic systems, neonates are vulnerable to haemorrhagic disorders. The prevention of early vitamin K deficiency bleeding (VKDB) of newborn by oral or parenteral administration of vitamin K has been well established. However, rarely, a newborn can present with bleeding manifestations even after routine vitamin K prophylaxis at birth. A 2-day-old healthy male baby presented with catastrophic pulmonary haemorrhage with severely deranged coagulation profile even after receiving vitamin K prophylaxis at birth. His presentation, initial laboratory findings and course in the hospital were very much in favour of haemophilia B, but follow-up factor IX level and clinical exome sequencing did not confirm it. However, protein induced in vitamin K absence-II was found to be raised just before the discharge, and we concluded this case as a rare presentation of classical VKDB.

Is aggressive therapy the answer for all cases of emphysematous pyelonephritis: a report of three cases.

Emphysematous Pyelonephritis (EPN) is a severe, necrotizing, life threatening infection of the renal parenchyma and management is not standardised due to scarcity of literature. We present 3 patients with this rare entity. All 3 patients were of class III on CECT findings based on Huang's classification and had more than two risk factors. Our first patient underwent percutaneous drainage of his condition upon which he recovered. The second and third patients underwent a laparotomy and nephrectomy. The second patient recovered after a stormy post operative period and the third patient died. Management of the first patient was contrary to that recommended in literature, for the other two it was as per recommendations. On successful management of our first patient without surgery and seeing no discernable benefits of surgery for our other two patients, it is possible that percutaneous drainage alone, coupled with antibiotics may be a viable strategy for managing this condition with nephrectomy being considered as a second tier option.