Simulation of 3D centimeter-scale continuum tumor growth at sub-millimeter resolution via distributed computing.
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ABSTRACT:
SUBMITTER: Goodin DA
PROVIDER: S-EPMC8277490 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundTo enable free-breathing whole-heart sub-millimeter resolution coronary magnetic resonance angiography (CMRA) in a clinically feasible scan time by combining low-rank patch-based undersampled reconstruction (3D-PROST) with a highly accelerated non-rigid motion correction framework.MethodsNon-rigid motion corrected CMRA combined with 2D image-based navigators has been previously proposed to enable 100% respiratory scan efficiency in modestly undersampled acquisitions. Achieving sub-millimeter isotropic resolution with such techniques still requires prohibitively long acquisition times. We propose to combine 3D-PROST reconstruction with a highly accelerated non-rigid motion correction framework to achieve sub-millimeter resolution CMRA in less than 10 min. Ten healthy subjects and eight patients with suspected coronary artery disease underwent 4-5-fold accelerated free-breathing whole-heart CMRA with 0.9 mm3 isotropic resolution. Vessel sharpness, vessel length and image quality obtained with the proposed non-rigid (NR) PROST approach were compared against translational correction only (TC-PROST) and a previously proposed NR motion-compensated technique (non-rigid SENSE) in healthy subjects. For the patient study, image quality scoring and visual comparison with coronary computed tomography angiography (CCTA) were performed.ResultsAverage scan times [min:s] were 6:01 ± 0:59 (healthy subjects) and 8:29 ± 1:41 (patients). In healthy subjects, vessel sharpness of the left anterior descending (LAD) and right (RCA) coronary arteries were improved with the proposed non-rigid PROST (LAD: 51.2 ± 8.8%, RCA: 61.2 ± 9.1%) in comparison to TC-PROST (LAD: 43.8 ± 5.1%, P = 0.051, RCA: 54.3 ± 8.3%, P = 0.218) and non-rigid SENSE (LAD: 46.1 ± 5.8%, P = 0.223, RCA: 56.7 ± 9.6%, P = 0.50), although differences were not statistically significant. The average visual image quality score was significantly higher for NR-PROST (LAD: 3.2 ± 0.6, RCA: 3.3 ± 0.7) compared with TC-PROST (LAD: 2.1 ± 0.6, P = 0.018, RCA: 2.0 ± 0.7, P = 0.014) and non-rigid SENSE (LAD: 2.3 ± 0.5, P = 0.008, RCA: 2.5 ± 0.7, P = 0.016). In patients, the proposed approach showed good delineation of the coronaries, in agreement with CCTA, with image quality scores and vessel sharpness similar to that of healthy subjects.ConclusionsWe demonstrate the feasibility of combining high undersampling factors with non-rigid motion-compensated reconstruction to obtain high-quality sub-millimeter isotropic CMRA images in ~ 8 min. Validation in a larger cohort of patients with coronary artery disease is now warranted.
| S-EPMC7161114 | biostudies-literature
Project description:PurposeTo achieve 3D T2 w imaging of the prostate with 1-mm isotropic resolution in less than 3 min.MethodsWe devised and implemented a 3D T2 -prepared multishot balanced steady state free precession (T2 prep-bSSFP) acquisition sequence with a variable density undersampled trajectory combined with a total variation regularized iterative SENSE (TV-SENSE) reconstruction. Prospectively undersampled images of the prostate (acceleration factor R = 3) were acquired in 11 healthy subjects in an institutional review board-approved study. Image quality metrics (subjective signal-to-noise ratio, contrast, sharpness, and overall prostate image quality) were evaluated by 2 radiologists. Scores of the proposed accelerated sequence were compared using the Wilcoxon signed-rank and Kruskal-Wallis non-parametric tests to prostate images acquired using a fully sampled 3D T2 prep-bSSFP acquisition, and with clinical standard 2D and 3D turbo spin echo (TSE) T2 w acquisitions. A P-value < 0.05 was considered significant.ResultsThe 3× accelerated 3D T2 prep-bSSFP images required a scan time (min:s) of 2:45, while the fully sampled 3D T2 prep-bSSFP and clinical standard 3D TSE images were acquired in 8:23 and 7:29, respectively. Image quality scores (contrast, sharpness, and overall prostate image quality) of the accelerated 3D T2 prep-bSSFP, fully sampled T2 prep-bSSFP, and clinical standard 3D TSE acquisitions along all 3 spatial dimensions were not significantly different (P > 0.05).Conclusion3D T2 w images of the prostate with 1-mm isotropic resolution can be acquired in less than 3 min, with image quality that is comparable to a clinical standard 3D TSE sequence but only takes a third of the acquisition time.
| S-EPMC6563534 | biostudies-literature
Project description:PurposeTo enable whole-heart 3D coronary magnetic resonance angiography (CMRA) with isotropic sub-millimeter resolution in a clinically feasible scan time by combining respiratory motion correction with highly accelerated variable density sampling in concert with a novel 3D patch-based undersampled reconstruction (3D-PROST).MethodsAn undersampled variable density spiral-like Cartesian trajectory was combined with 2D image-based navigators to achieve 100% respiratory efficiency and predictable scan time. 3D-PROST reconstruction integrates structural information from 3D patch neighborhoods through sparse representation, thereby exploiting the redundancy of the 3D anatomy of the coronary arteries in an efficient low-rank formulation. The proposed framework was evaluated in a static resolution phantom and in 10 healthy subjects with isotropic resolutions of 1.2 mm3 and 0.9 mm3 and undersampling factors of ×5 and ×9. 3D-PROST was compared against fully sampled (1.2 mm3 only), conventional parallel imaging, and compressed sensing reconstructions.ResultsPhantom and in vivo (1.2 mm3 ) reconstructions were in excellent agreement with the reference fully sampled image. In vivo average acquisition times (min:s) were 7:57 ± 1:18 (×5) and 4:35 ± 0:44 (×9) for 0.9 mm3 resolution. Sub-millimeter 3D-PROST resulted in excellent depiction of the left and right coronary arteries including small branch vessels, leading to further improvements in vessel sharpness and visible vessel length in comparison with conventional reconstruction techniques. Image quality rated by 2 experts demonstrated that 3D-PROST provides good image quality and is robust even at high acceleration factors.ConclusionThe proposed approach enables free-breathing whole-heart 3D CMRA with isotropic sub-millimeter resolution in <5 min and achieves improved coronary artery visualization in a short and predictable scan time.
| S-EPMC6617822 | biostudies-literature
Project description:Developing small-scale soft continuum robots with large-angle steering capacity and high-precision manipulation offers broad opportunities in various biomedical settings. However, existing continuum robots reach the bottleneck in actuation on account of the contradiction among small size, compliance actuation, large tender range, high precision, and small dynamic error. Herein, a 3D-printed millimeter-scale soft continuum robot with an ultrathin hollow skeleton wall (300 μm) and a large inner-to-outer ratio (0.8) is reported. After coating a thin ferromagnetic elastomer layer (≈100-150 μm), the proposed soft continuum robot equipped with hybrid actuation (tendon- and magnetic-driven mode) achieves large-angle (up to 100°) steering and high-precision (low to 2 μm for static positioning) micromanipulation simultaneously. Specifically, the robot implements an ultralow dynamic tracking error of ≈10 μm, which is ≈30-fold improved than the state of art. Combined with a microneedle/knife or nasopharyngeal swab, the robot reveals the potential for versatile biomedical applications, such as drug injection on the target tissue, diseased tissue ablation, and COVID-19 nasopharyngeal sampling. The proposed millimeter-scale soft continuum robot presents remarkable advances in large-range and high-precise actuation, which provides a new method for miniature continuum robot design and finds broad applications in biomedical engineering.
| S-EPMC7744893 | biostudies-literature
Project description:We demonstrate broadband non-resonant squeezing of terahertz (THz) waves through an isolated 2-nm-wide, 2-cm-long slit (aspect ratio of 10(7)), representing a maximum intensity enhancement factor of one million. Unlike resonant nanogap structures, a single, effectively infinitely-long slit passes incident electromagnetic waves with no cutoff, enhances the electric field within the gap with a broad 1/f spectral response, and eliminates interference effects due to finite sample boundaries and adjacent elements. To construct such a uniform, isolated slit that is much longer than the millimeter-scale spot of a THz beam, we use atomic layer lithography to pattern vertical nanogaps in a metal film over an entire 4-inch wafer. We observe an increasing field enhancement as the slit width decreases from 20 nm to 2 nm, in agreement with numerical calculations.
| S-EPMC4208056 | biostudies-other
Project description:Automatic cerebral cortical surface reconstruction is a useful tool for cortical anatomy quantification, analysis and visualization. Recently, the Human Connectome Project and several studies have shown the advantages of using T1-weighted magnetic resonance (MR) images with sub-millimeter isotropic spatial resolution instead of the standard 1-mm isotropic resolution for improved accuracy of cortical surface positioning and thickness estimation. Nonetheless, sub-millimeter resolution images are noisy by nature and require averaging multiple repetitions to increase the signal-to-noise ratio for precisely delineating the cortical boundary. The prolonged acquisition time and potential motion artifacts pose significant barriers to the wide adoption of cortical surface reconstruction at sub-millimeter resolution for a broad range of neuroscientific and clinical applications. We address this challenge by evaluating the cortical surface reconstruction resulting from denoised single-repetition sub-millimeter T1-weighted images. We systematically characterized the effects of image denoising on empirical data acquired at 0.6 mm isotropic resolution using three classical denoising methods, including denoising convolutional neural network (DnCNN), block-matching and 4-dimensional filtering (BM4D) and adaptive optimized non-local means (AONLM). The denoised single-repetition images were found to be highly similar to 6-repetition averaged images, with a low whole-brain averaged mean absolute difference of ~0.016, high whole-brain averaged peak signal-to-noise ratio of ~33.5 dB and structural similarity index of ~0.92, and minimal gray matter-white matter contrast loss (2% to 9%). The whole-brain mean absolute discrepancies in gray matter-white matter surface placement, gray matter-cerebrospinal fluid surface placement and cortical thickness estimation were lower than 165 μm, 155 μm and 145 μm-sufficiently accurate for most applications. These discrepancies were approximately one third to half of those from 1-mm isotropic resolution data. The denoising performance was equivalent to averaging ~2.5 repetitions of the data in terms of image similarity, and 1.6-2.2 repetitions in terms of the cortical surface placement accuracy. The scan-rescan variability of the cortical surface positioning and thickness estimation was lower than 170 μm. Our unique dataset and systematic characterization support the use of denoising methods for improved cortical surface reconstruction at sub-millimeter resolution.
| S-EPMC8421085 | biostudies-literature
Project description: Not available
| EMPIAR-11380 | biostudies-other
Project description:The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.
| S-EPMC8322767 | biostudies-literature
Project description:Tissue-on-chip systems represent promising platforms for monitoring and controlling tissue functions in vitro for various purposes in biomedical research. The two-dimensional (2D) layouts of these constructs constrain the types of interactions that can be studied and limit their relevance to three-dimensional (3D) tissues. The development of 3D electronic scaffolds and microphysiological devices with geometries and functions tailored to realistic 3D tissues has the potential to create important possibilities in advanced sensing and control. This study presents classes of compliant 3D frameworks that incorporate microscale strain sensors for high-sensitivity measurements of contractile forces of engineered optogenetic muscle tissue rings, supported by quantitative simulations. Compared with traditional approaches based on optical microscopy, these 3D mechanical frameworks and sensing systems can measure not only motions but also contractile forces with high accuracy and high temporal resolution. Results of active tension force measurements of engineered muscle rings under different stimulation conditions in long-term monitoring settings for over 5 wk and in response to various chemical and drug doses demonstrate the utility of such platforms in sensing and modulation of muscle and other tissues. Possibilities for applications range from drug screening and disease modeling to biohybrid robotic engineering.
| S-EPMC8126769 | biostudies-literature
Project description:A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
| S-EPMC7387671 | biostudies-literature