Performance Analysis Tools Allinea MAP: Use & Functionality
This presentation discusses some aspects of performance analysis and applicable tools.
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This presentation discusses some aspects of performance analysis and applicable tools.
Airborne remote sensing data collected using a DJI Phantom 4 RTK unoccupied aerial system (UAS) ? operated by the University of Maine Wheatland Geospatial Lab (https://wheatlandlab.org/). This package includes data from 17 flights flown over the NGEE-Arctic Council, Kougarok, Kougarok Mile80, Teller, and Teller Mile32 sites in July 2019. The Phantom 4 RTK is a drone platform that collects very high spatial resolution optical red/green/blue (RGB) imagery. Derived image products include point cloud, ortho-mosaiced RGB, a digital surface model (DSM) using the structure from motion (SfM) technique, and a canopy height model (CHM). Unprocessed and processed data products (1,000+ files) are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *hdr,), ENVI image file (*.dat), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence–function relationships in many phage–bacterial systems.
Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within speci fi c functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, re fl ecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial commu
Open, discrete Q-mappings in R{sup n}, n{>=}2, Q element of L{sup 1}{sub loc}, are proved to be absolutely continuous on lines, to belong to the Sobolev class W{sub loc}{sup 1,1}, to be differentiable almost everywhere and to have the N{sup -1}-property (converse to the Luzin N-property). It is shown that a family of open, discrete shell-based Q-mappings leaving out a subset of positive capacity is normal, provided that either Q has finite mean oscillation at each point or Q has only logarithmic singularities of order at most n-1. Under the same assumptions on Q it is proved that an isolated singularity x{sub 0} element of D of an open discrete shell-based Q-map f:D/{l_brace}x{sub 0{r_brace}{yields}}R-bar{sup n} is removable; moreover, the extended map is open and discrete. On the basis of these results analogues of the well-known Liouville, Sokhotskii-Weierstrass and Picard theorems are obtained. Bibliography: 34 titles.
Purpose: Pulmonary functional MRI using inhaled gas contrast agents was previously investigated as a way to identify well-functioning lung in patients with NSCLC who are clinical candidates for radiotherapy. Hyperpolarized noble-gas ({sup 3}He and {sup 129}Xe) MRI has also been optimized to measure functional lung information, but for a number of reasons, the clinical translation of this approach to guide radiotherapy planning has been limited. As an alternative, free-breathing pulmonary 1H MRI using clinically available MRI systems and pulse sequences provides a non-contrast-enhanced method to generate both ventilation and perfusion maps. Free-breathing {sup 1}H MRI exploits non-rigid registration and Fourier decomposition of MRI signal intensity differences (Bauman et al., MRM, 2009) that may be generated during normal tidal breathing. Here, our objective was to generate free-breathing {sup 1}H MRI ventilation and lung function avoidance maps in patients with NSCLC as a way to guide radiation therapy planning. Methods: Stage IIIA/IIIB NSCLC patients (n=8, 68±9yr) provided written informed consent to a randomized controlled clinical trial ( https://clinicaltrials.gov/ct2/show/NCT02002052 ) that aimed to compare outcomes related to image-guided versus conventional radiation therapy planning. Hyperpolarized {sup 3}He/{sup 129}Xe and dynamic free tidal-breathing {sup 1}H MRI were acquired as previously described (Capaldi et al., Acad Radiol, 2015). Non-rigid registration was performed using the modality-independent-neighbourhood-descriptor (MIND) deformable approach (Heinrich et al., Med Image Anal, 2012). Ventilation-defect-percent ({sup 3}He:VDP{sub He}, {sup 129}Xe:VDP{sub Xe}, Free-breathing-{sup 1}H:VDP{sub FB}) and the corresponding ventilation maps were compared using Pearson correlation coefficients (r) and the Dice similarity coefficient (DSC). Results: VDP{sub FB} was significantly related to VDP{sub He} (r=.71; p=.04) and VDP{sub Xe} (r=.80; p=.01) and there were also strong spatial relationships (DSC{sub He}/DSC{sub Xe}=89±3%/77±11%). Conclusion: In this proof of concept study in NSCLC patients, free-breathing {sup 1}H MRI ventilation defects were quantitatively and spatially related to inhaled-noble-gas MRI ventilation defects. Free-breathing {sup 1}H MRI measures lung function/ventilation that can be used to optimize radiotherapy planning in NSCLC patients.
Functional variables are often used as predictors in regression problems. A commonly used parametric approach, called scalar-on-function regression, uses the $\mathbb L^2$ inner product to map functional predictors into scalar responses. This method can perform poorly when predictor functions contain undesired phase variability, causing phases to have disproportionately large influence on the response variable. One past solution has been to perform phase–amplitude separation (as a pre-processing step) and then use only the amplitudes in the regression model. In this paper, we propose a more integrated approach, termed elastic functional regression model (EFRM), where phase-separation is performed inside the regression model, rather than as a pre-processing step. This approach generalizes the notion of phase in functional data, and is based on the norm-preserving time warping of predictors. Due to its invariance properties, this representation provides robustness to predictor phase variability and results in improved predictions of the response variable over traditional models. We demonstrate this framework using a number of datasets involving gait signals, NMR data, and stock market prices.
This study proposes an automated calibration procedure for bond parameters in bonded discrete element modelling. By exploring the underlying physical correlations between microscopic parameters of bonds and macroscopic strength parameters of the continuum to be modelled, the microscopic shear strength and tensile strength are identified as independent variables for calibration purpose. Then a physics-informed iterative scheme is proposed to automatically approximate the bond parameters by viewing the micro-macro relation as an implicitly defined mathematical mapping function. As a result of highly non-convex features of this implicit mapping, the adaptive moment estimation (Adam), which is especially suitable for problems with noisy gradients, is adopted as the basic iterative scheme, in conjunction with other numerical techniques to approximately evaluate the partial derivatives involved. The whole procedure offers a simple and effective framework for bond parameter calibration. Finally, a numerical example of SiC ceramic is provided for validation. By compared with some existing calibration methods, the proposed method shows significant advantages in terms of calibration efficiency and accuracy.
In this paper, we propose the extended virtual element method (X-VEM) to treat singularities and crack discontinuities that arise in the Laplace problem. The virtual element method (VEM) is a stabilized Galerkin formulation on arbitrary polytopal meshes, wherein the basis functions are implicit (virtual)—they are not known explicitly nor do they need to be computed within the problem domain. In this work, suitable projection operators are used to decompose the bilinear form on each element into two parts: a consistent term that reproduces the first-order polynomial space and a correction term that ensures stability. A similar approach is pursued in the X-VEM with a few notable extensions. To capture singularities and discontinuities in the discrete space, we augment the standard virtual element space with an additional contribution that consists of the product of virtual nodal basis (partition-of-unity) functions with enrichment functions. For discontinuities, basis functions are discontinuous across the crack and for singularities a weakly singular enrichment function that satisfies the Laplace equation is chosen. For the Laplace problem with a singularity, we devise an extended projector that maps functions that lie in the extended virtual element space onto linear polynomials and the enrichment function, whereas for the discontinuous problem, the consistent element stiffness matrix has a block-structure that is readily computed. An adaptive homogeneous numerical integration method is used to accurately and efficiently (no element-partitioning is required) compute integrals with integrands that are weakly singular. Once the element projection matrix is computed, the same steps as in the standard VEM are followed to compute the element stabilization matrix. Numerical experiments are performed on quadrilateral and polygonal (convex and nonconvex elements) meshes for the problem of an $\textit{L}$-shaped domain with a corner singularity and the problem of a cracked membrane under mode III loading, and results are presented that affirm the sound accuracy and demonstrate the optimal rates of convergence in the $\textit{L}^2$ norm and energy of the proposed method.
Purpose: Image-guided radiotherapy is an advanced 4D radiotherapy technique that has been developed in recent years. However, respiratory motion causes significant uncertainties in image-guided radiotherapy procedures. To address these issues, an innovative lung motion estimation model based on a robust point matching is proposed in this paper. Methods: An innovative robust point matching algorithm using dynamic point shifting is proposed to estimate patient-specific lung motion during free breathing from 4D computed tomography data. The correspondence of the landmark points is determined from the Euclidean distance between the landmark points and the similarity between the local images that are centered at points at the same time. To ensure that the points in the source image correspond to the points in the target image during other phases, the virtual target points are first created and shifted based on the similarity between the local image centered at the source point and the local image centered at the virtual target point. Second, the target points are shifted by the constrained inverse function mapping the target points to the virtual target points. The source point set and shifted target point set are used to estimate the transformation function between the source image and target image. Results: The performances of the authors’ method are evaluated on two publicly available DIR-lab and POPI-model lung datasets. For computing target registration errors on 750 landmark points in six phases of the DIR-lab dataset and 37 landmark points in ten phases of the POPI-model dataset, the mean and standard deviation by the authors’ method are 1.11 and 1.11 mm, but they are 2.33 and 2.32 mm without considering image intensity, and 1.17 and 1.19 mm with sliding conditions. For the two phases of maximum inhalation and maximum exhalation in the DIR-lab dataset with 300 landmark points of each case, the mean and standard deviation of target registration errors on the 3000 landmark points of ten cases by the authors’ method are 1.21 and 1.04 mm. In the EMPIRE10 lung registration challenge, the authors’ method ranks 24 of 39. According to the index of the maximum shear stretch, the authors’ method is also efficient to describe the discontinuous motion at the lung boundaries. Conclusions: By establishing the correspondence of the landmark points in the source phase and the other target phases combining shape matching and image intensity matching together, the mismatching issue in the robust point matching algorithm is adequately addressed. The target registration errors are statistically reduced by shifting the virtual target points and target points. The authors’ method with consideration of sliding conditions can effectively estimate the discontinuous motion, and the estimated motion is natural. The primary limitation of the proposed method is that the temporal constraints of the trajectories of voxels are not introduced into the motion model. However, the proposed method provides satisfactory motion information, which results in precise tumor coverage by the radiation dose during radiotherapy.
Highlights: Black-Right-Pointing-Pointer ct340 CRM was identified to be the posterior spiracle enhancer of gene cut. Black-Right-Pointing-Pointer ct340 is under the direct transcriptional control of Hox protein Abd-B. Black-Right-Pointing-Pointer An efficient cloning system was developed to assay protein-DNA interaction. Black-Right-Pointing-Pointer New features of Abd-B dependent target gene regulation were detected. -- Abstract: Hox transcription factors regulate the morphogenesis along the anterior-posterior (A/P) body axis through the interaction with small cis-regulatory modules (CRMs) of their target gene, however so far very few Hox CRMs are known and have been analyzed in detail. In this study we have identified a new Hox CRM, ct340, which guides the expression of the cell type specification gene cut (ct) in the posterior spiracle under the direct control of the Hox protein Abdominal-B (Abd-B). Using the ct340 enhancer activity as readout, an efficient cloning system to generate VP16 activation domain fusion protein was developed to unambiguously test protein-DNA interaction in Drosophila cell culture. By functionally dissecting the Abd-B protein, new features of Abd-B dependent target gene regulation were detected. Due to its easy adaptability, this system can be generally used to map functional domains within sequence-specific transcriptional factors in Drosophila cell culture, and thus provide preliminary knowledge of the protein functional domain structure for further in vivo analysis.
We present an Extended Vector Space Model (EVSM) for information retrieval, endowed with a new set of similarity functions. Our model considers records as multisets of tokens. A token weight function maps records into a real vectors. Using this vector representation we define a p -norm of a record and pairwise conjunction and disjunction operations on records. These oper ations prompt consistent extensions of published set-based similarity functions and yield new $\ell$ p distance-based similarities. We demonstrate that some well-known similarities form a subset of the new functions resulting from particular choices of token weights and p -values.
Remote sensing maps of plant functional type (PFT), PFT fractional cover (fCover), and fCover uncertainty maps derived from NASA’s Airborne Visible / Infrared Imaging Spectrometer – Next Generation (AVIRIS-NG). The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA’s Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE’s Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for flights over Teller, Kougarok, and Council watersheds created using eight AVIRIS-NG imagery collected in July, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as GIS *.kml files. Detailed description of the methods for each map are provided in Yang et al., (2023). These datasets are provided in support of Yang et al., (In revision) “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
Carbon capture and storage is being pursued globally as a geoengineering measure for reducing the emission of anthropogenic CO 2 the atmosphere. Comprehensive monitoring, verification, and accounting programs must be established for demonstrating the safe storage of injected CO 2 . One of the most commonly deployed monitoring techniques is time-lapse seismic reservoir monitoring (also known as 4-D seismic), which involves comparing 3-D seismic survey data taken at the same study site but over different times. Analyses of 4-D seismic data volumes can help improve the quality of storage reservoir characterization, track the movement of injected CO 2 plume, and identify potential CO 2 spillover/leakage from the storage reservoirblue. However, the derivation of high-resolution CO 2 saturation maps from 4-D seismic data is a highly nonlinear and ill-posed inverse problem, often requiring significant computational effort. In this research, we apply a physics-based deep learning method to facilitate the solution of both the forward and inverse problems in seismic inversion while honoring physical constraints. A cycle generative adversarial neural network (CycleGAN) model is trained to learn the bidirectional functional mappings between the reservoir dynamic property changes and seismic attribute changes, such that both forward and inverse solutions can be obtained efficiently from the trained model. We show that our CycleGAN-based approach not only improves the reliability of 4-D seismic inversion but also expedites the quantitative interpretation. Our deep learning-based workflow is generic and can be readily used for reservoir characterization and reservoir model updates involving the use of 4-D seismic data.
Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.
A general design of metalenses for N-beam emissions is proposed based on transformation optics. A linear mapping function is adopted to achieve the homogeneous characterization of the transforming medium, which is therefore easy to be achieved compared with previous designs limited by inhomogeneity based on transformation optics. To verify the theoretical design, a four-beam antenna constructed with ultrathin, homogenous, and uniaxial anisotropic metalens is designed, fabricated, and measured. It is shown that the realized gain of the four-beam antenna is increased by 6 dB compared with the single dipole source, while working frequency and relative bandwidth are kept unchanged. The measured far-field pattern verifies theoretical design procedure.
This research tries to make advancement in GPS signal processing to estimate the interseismic vertical deformation field at western part of Sumatra Island. The data derived by Continuous Global Positioning System (CGPS) from Badan Informasi Geospasial (BIG) between 2010 and 2012. GPS Analyze at Massachusetts Institute of Technology (GAMIT) software and Global Kalman Filter (GLOBK) software are used to process the GPS signal to estimate the vertical velocities of the CGPS station. In order to minimize noise due to atmospheric delay, Vienna Mapping Function 1 (VMF1) is used as atmospheric parameter model and include daily IONEX file provided by the Center for Orbit Determination in Europe (CODE) as well. It improves GAMIT daily position accuracy up to 0.8 mm. In a second step of processing, the GLOBK is used in order to estimate site positions and velocities in the ITRF08 reference frame. The result shows that the uncertainties of estimated displacement velocity at all CGPS stations are smaller than 1.5 mm/yr. The subsided deformation patterns are seen at the northern and southern part of west Sumatra. The vertical deformation at northern part of west Sumatra indicates postseismic phase associated with the 2010 and 2012 Northern Sumatra earthquakes and also the long-term postseismic associated with the 2004 and 2005 Northern Sumatra earthquakes. The uplifted deformation patterns are seen from Bukit Tinggi to Seblat which indicate a long-term interseismic phase after the 2007 Bengkulu earthquake and 2010 Mentawai earthquake. GANO station shows a subsidence at rate 12.25 mm/yr, indicating the overriding Indo-Australia Plate which is dragged down by the subducting Southeast Asian Plate.
Path reversibility and radial symmetry are often assumed in push-pull tracer test analysis. In reality, heterogeneous flow fields mean that both assumptions are idealizations. In this paper, to understand their impact, we perform a parametric study which quantifies the scattering effects of ambient flow, local-scale dispersion, and velocity field heterogeneity on push-pull breakthrough curves and compares them to the effects of mobile-immobile mass transfer (MIMT) processes including sorption and diffusion into secondary porosity. We identify specific circumstances in which MIMT overwhelmingly determines the breakthrough curve, which may then be considered uninformative about drift and local-scale dispersion. Assuming path reversibility, we develop a continuous-time-random-walk-based interpretation framework which is flow-field-agnostic and well suited to quantifying MIMT. Adopting this perspective, we show that the radial flow assumption is often harmless: to the extent that solute paths are reversible, the breakthrough curve is uninformative about velocity field heterogeneity. Our interpretation method determines a mapping function (i.e., subordinator) from travel time in the absence of MIMT to travel time in its presence. A mathematical theory allowing this function to be directly “plugged into” an existing Laplace-domain transport model to incorporate MIMT is presented and demonstrated. Algorithms implementing the calibration are presented and applied to interpretation of data from a push-pull test performed in a heterogeneous environment. A successful four-parameter fit is obtained, of comparable fidelity to one obtained using a million-node 3-D numerical model. In conclusion, we demonstrate analytically and numerically how push-pull tests quantifying MIMT are sensitive to remobilization, but not immobilization, kinetics.