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At least 451 records · Page 25

Topological network analysis of patient similarity for precision management of acute blood pressure in spinal cord injury

Background: Predicting neurological recovery after spinal cord injury (SCI) is challenging. Using topological data analysis, we have previously shown that mean arterial pressure (MAP) during SCI surgery predicts long-term functional recovery in rodent models, motivating the present multicenter study in patients. Methods: Intra-operative monitoring records and neurological outcome data were extracted (n = 118 patients). We built a similarity network of patients from a low-dimensional space embedded using a non-linear algorithm, Isomap, and ensured topological extraction using persistent homology metrics. Confirmatory analysis was conducted through regression methods. Results: Network analysis suggested that time outside of an optimum MAP range (hypotension or hypertension) during surgery was associated with lower likelihood of neurological recovery at hospital discharge. Logistic and LASSO (least absolute shrinkage and selection operator) regression confirmed these findings, revealing an optimal MAP range of 76–[104-117] mmHg associated with neurological recovery. Conclusions: We show that deviation from this optimal MAP range during SCI surgery predicts lower probability of neurological recovery and suggest new targets for therapeutic intervention. Funding: NIH/NINDS: R01NS088475 (ARF); R01NS122888 (ARF); UH3NS106899 (ARF); Department of Veterans Affairs: 1I01RX002245 (ARF), I01RX002787 (ARF); Wings for Life Foundation (ATE, ARF); Craig H. Neilsen Foundation (ARF); and DOD: SC150198 (MSB); SC190233 (MSB); DOE: DE-AC02-05CH11231 (DM).

59 BASIC BIOLOGICAL SCIENCES↗

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

59 BASIC BIOLOGICAL SCIENCES↗

A Space and Atmospheric Visualization Science System

SAVS (a Space and Atmospheric Visualization Science system) is an integrated system with user-friendly functionality that employs a 'push-button' software environment that mimics the logical scientific processes in data acquisition, reduction, analysis, and visualization. All of this is accomplished without requiring a detailed understanding of the methods, networks, and modules that link the tools and effectively execute the functions. This report describes SAVS and its components, followed by several applications based on generic research interests in interplanetary and magnetospheric physics (IMP/ISTP), active experiments in space (CRRES), and mission planning focused on the earth's thermospheric, ionospheric, and mesospheric domains (TIMED). The final chapters provide a user-oriented description of interface functionalities, hands-on operations, and customized modules, with details of the primary modules presented in the appendices. The overall intent of the report is to reflect the accomplishments of the three-year development effort and to introduce potential users to the power and utility of the integrated data acquisition, analysis, and visualization system.

Szuszczewicz, E. P.↗

Kinetic plasma processes occurring in the outer plasmasphere

One area of data analysis work that was begun under this contract is the fitting of the perpendicular velocity distributions of equatorially trapped ions with a Kappa function. This type of characterization of the trapped ions will be very useful for comparison with velocity distributions produced by the model. A second area of data analysis is to study data from consecutive passes when DE 1's apogee was near the magnetic equator and the spacecraft was often skimming along nearly the same L shell. In 1982 three such periods occurred in May, June, and July. For these consecutive events we have Kp histories, density measurements from a number of sources (Whistler data, DE SFR, ISEE SFR) and consecutive samples of ion pitch angle distributions along field lines. It is clear from this data how the pitch angle distributions evolve during a flux tube refilling event. Our modeling of the flow of plasma along closed field lines is following two basic tracks. The first is a study of the basic refilling process without the effect of wave-particle heating near the equator or the effect of large or abrupt field-aligned electric potential drops. This model includes the effects of Coulomb self-collisions and collisions with the O+ ions in the topside ionosphere. The second track is a study of the effects of wave produced pitch-angle scattering and perpendicular heating occurring near the magnetic equator, in connection with the development of large potential drops that result from electron heating and the development of density gradients.

Wilson, Gordon R.↗

leapR: An R Package for Multiomic Pathway Analysis

A generalized goal of many high-throughput data studies is to identify functional mecha-nisms that underlie observed biological phenomena, whether disease outcomes or metabolic out-put. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, tran-scriptomic, proteomic, metabolomic) are faced with a challenge of utilizing the data in a way that maximizes utility. However, methods for integration of multiple forms of molecular data into a biolog-ically coherent frameworks are needed. Furthermore, we have developed a framework to assess biological pathway activity that relates to phenotypic outcome using multi-source data. Availability and implementation: The leapR package with user manual and example workflow is available for download from GitHub (https://github.com/biodataganache/leapR).

59 BASIC BIOLOGICAL SCIENCES↗

Joint analysis of Dark Energy Survey Year 3 data and CMB lensing from SPT and Planck . III. Combined cosmological constraints

Here we present cosmological constraints from the analysis of two-point correlation functions between galaxy positions and galaxy lensing measured in Dark Energy Survey (DES) Year 3 data and measurements of cosmic microwave background (CMB) lensing from the South Pole Telescope (SPT) and Planck. When jointly analyzing the DES-only two-point functions and the DES cross-correlations with SPT+Planck CMB lensing, we find Ω m = 0.344 ± 0.030 and S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.773 ± 0.016, assuming ΛCDM. When additionally combining with measurements of the CMB lensing autospectrum, we find Ω m = 0.306$^{+0.018}_{-0.021}$ and S 8 = 0.792 ± 0.012. The high signal-to-noise of the CMB lensing cross-correlations enables several powerful consistency tests of these results, including comparisons with constraints derived from cross-correlations only, and comparisons designed to test the robustness of the galaxy lensing and clustering measurements from DES. Applying these tests to our measurements, we find no evidence of significant biases in the baseline cosmological constraints from the DES-only analyses or from the joint analyses with CMB lensing cross-correlations. However, the CMB lensing cross-correlations suggest possible problems with the correlation function measurements using alternative lens galaxy samples, in particular the redMaGiC galaxies and high-redshift MagLim galaxies, consistent with the findings of previous studies. We use the CMB lensing cross-correlations to identify directions for further investigating these problems.

79 ASTRONOMY AND ASTROPHYSICS↗

Some Aspects of the Liquid Water Thermodynamic Behavior: From The Stable to the Deep Supercooled Regime

Liquid water is considered to be a peculiar example of glass forming materials because of the possibility of giving rise to amorphous phases with different densities and of the thermodynamic anomalies that characterize its supercooled liquid phase. In the present work, literature data on the density of bulk liquid water are analyzed in a wide temperature-pressure range, also including the glass phases. A careful data analysis, which was performed on different density isobars, made in terms of thermodynamic response functions, like the thermal expansion αP and the specific heat differences C P -C V , proves, exclusively from the experimental data, the thermodynamic consistence of the liquid-liquid transition hypothesis. The study confirms that supercooled bulk water is a mixture of two liquid “phases”, namely the high density (HDL) and the low density (LDL) liquids that characterize different regions of the water phase diagram. Furthermore, the C P -C V isobars behaviors clearly support the existence of both a liquid–liquid transition and of a liquid–liquid critical point.

59 BASIC BIOLOGICAL SCIENCES↗

DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface and command-line tool for high-dimensional mass spectrometry data analysis workflows, offering ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation: algorithm implementations utilize all dimensions simultaneously to (i) offer greater separation between features, improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS data, demonstrating the advantages of a multidimensional approach in each data processing step.

Colby, Sean M↗

Frequency-domain identification of XV-15 tilt-rotor aircraft dynamics

Frequency-domain methods are used to identify the open-loop dynamics of the XV-15 tilt-rotor aircraft from flight tests. Piloting and data analysis techniques are presented to determine frequency response plots and equivalent transfer function models. The open-loop pitch and roll dynamics for the hover flight condition exhibit unstable low-frequency oscillations, whereas the dynamics in the remaining degrees of freedom are lightly damped and generally decoupled. Comparisons of SV-13 flight-test and simulator data are more favorable for high-frequency inputs (omega greater than 1.0 rad/sec) than low-frequency inputs. The identification of symmetric and asymmetric beam-bending modes compares favorably with previous flight-test data. The results presented in this paper demonstrate the utility of the frequency-domain techniques for dynamics identification and simulator fidelity studies.

Tischler, M. B.↗

Frequency-Domain Identification of XV-15 Tilt-Rotor Aircraft Dynamics in Hovering Flight

Frequency-domain methods are used to identify the open-loop dynamics of the XV-15 tilt-rotor aircraft from flight tests. Piloting and data analysis techniques are presented to determine frequency response plots and equivalent transfer function models. The open-loop pitch and roll dynamics for the hover flight condition exhibit unstable low-frequency oscillations, whereas the dynamics in the remaining degrees of freedom are lightly damped and generally decoupled. Comparisons of XV-15 flight-test and simulator data are more favorable for high-frequency inputs (omega greater than 1.0 rad/sec) than low-frequency inputs. Time-domain comparisons of the extracted transfer functions with step response flight data are very favorable, even for large amplitude motions. The results presented in this paper demonstrate the utility of the frequency-domain techniques for dynamics identification and simulator fidelity studies.

Tischler, Mark B.↗

Required developments in structural dynamics

The finite element method, modal component synthesis, and the use of fast Fourier transformation were key developments in structural dynamics in the past 15 to 20 years. Current areas requiring additional effort include: (1) the correct calculation of modal shape and natural frequencies for complex structures; (2) the correlation of math models with test data; (3) the establishment of a criteria for "goodness" of the correlation between analysis and test; (4) the selection of the correct displacement functions when using computer programs for modal synthesis; (5) accuracy of response calculations; and (6) the inverse problem of determining the force problem from the response data. Trends identified include the use of distributed computing, greater reliance on analysis, and the possible use of artificial intelligence techniques, or some way of feeding back information, to provide solution guidance to engineers.

Wada, B. K.↗

Computational Study of Separating Flow in a Planar Subsonic Diffuser

A computational study of the separated flow through a 2-D asymmetric subsonic diffuser has been performed. The Wind Computational Fluid Dynamics code is used to predict the separation and reattachment behavior for an incompressible diffuser flow. The diffuser inlet flow is a two-dimensional, turbulent, and fully-developed channel flow with a Reynolds number of 20,000 based on the centerline velocity and the channel height. Wind solutions computed with the Menter SST, Chien k-epsilon, Spalart-Allmaras and Explicit Algebraic Reynolds Stress turbulence models are compared with experimentally measured velocity profiles and skin friction along the upper and lower walls. In addition to the turbulence model study, the effects of grid resolution and use of wall functions were investigated. The grid studies varied the number of grid points across the diffuser and varied the initial wall spacing from y(sup +) = 0.2 to 60. The wall function study assessed the applicability of wall functions for analysis of separated flow. The SST and Explicit Algebraic Stress models provide the best agreement with experimental data, and it is recommended wall functions should only be used with a high level of caution.

DalBello, Teryn↗

Detailed space–time variations of the seismic response of the shallow crust to small earthquakes from analysis of dense array data

SUMMARY We compute high-resolution space–time variations of subsurface seismic properties from autocorrelation functions (ACF’s) of noise and local earthquakes, recorded by the Sage Brush Flat dense array deployed around the Clark branch of the San Jacinto fault. The resolved temporal changes are referred to as apparent velocity changes because they reflect both nonlinear response and variations of material properties such as cracking and damage. Apparent velocity changes are estimated at four frequency bands (10–15, 10–20, 15–30 and 20–40 Hz) for two local earthquake data sets. In one analysis, ACF’s from P- and S-wave windows of 31 small events with magnitudes below 3.1 are used to compute the apparent velocity variations with respect to the mean ACF of each phase, and we also use the mean ACF of noise data as reference to estimate the changes. In a further analysis, the temporal evolution of properties is computed using moving time windows in continuous waveform over one-hour long data with noise and earthquake signals. The apparent velocity changes and recovery times are frequency dependent and present a strong spatial variability across the array. The resolved changes are larger and recovery time shorter with data associated with higher frequencies. At frequencies larger than 15 Hz, and using the mean ACF of noise data as a reference, the apparent average velocity changes across the array during the passage of the P and S waves from the small local events are 2.5 per cent and 6 per cent, respectively. The apparent velocity changes decrease by one order of magnitude when the earthquake data are used as a reference. The relatively large changes in response to very low ground motion have important implications on nonlinear processes involving degradation and healing of the subsurface material during common earthquake shaking.

Geochemistry & Geophysics↗

Parameter Estimation of Actuators for Benchmark Active Control Technology (BACT) Wind Tunnel Model with Analysis of Wear and Aerodynamic Loading Effects

This report describes the development of transfer function models for the trailing-edge and upper and lower spoiler actuators of the Benchmark Active Control Technology (BACT) wind tunnel model for application to control system analysis and design. A simple nonlinear least-squares parameter estimation approach is applied to determine transfer function parameters from frequency response data. Unconstrained quasi-Newton minimization of weighted frequency response error was employed to estimate the transfer function parameters. An analysis of the behavior of the actuators over time to assess the effects of wear and aerodynamic load by using the transfer function models is also presented. The frequency responses indicate consistent actuator behavior throughout the wind tunnel test and only slight degradation in effectiveness due to aerodynamic hinge loading. The resulting actuator models have been used in design, analysis, and simulation of controllers for the BACT to successfully suppress flutter over a wide range of conditions.

Waszak, Martin R.↗

Detection of Bi-Directionality in Strain-Gage Balance Calibration Data

An indicator variable was developed for both visualization and detection of bi-directionality in wind tunnel strain-gage balance calibration data. First, the calculation of the indicator variable is explained in detail. Then, a criterion is discussed that may be used to decide which gage outputs of a balance have bi- directional behavior. The result of this analysis could be used, for example, to justify the selection of certain absolute value or other even function terms in the regression model of gage outputs whenever the Iterative Method is chosen for the balance calibration data analysis. Calibration data of NASA s MK40 Task balance is analyzed to illustrate both the calculation of the indicator variable and the application of the proposed criterion. Finally, bi directionality characteristics of typical multi piece, hybrid, single piece, and semispan balances are determined and discussed.

Ulbrich, Norbert↗

Competing Magnetic Interactions and the Role of Unpaired 4 f Electrons in Oxygen-Deficient Perovskites Ba 3 R Fe 2 O 7.5 ( R = Y, Dy)

Oxygen-deficient perovskite compounds with the general formula Ba 3 RFe 2 O 7.5 present a good opportunity to study competing magnetic interactions between Fe 3+ 3d cations with and without the involvement of unpaired 4f electrons on R 3+ cations. From analysis of neutron powder diffraction data, complemented by ab initio density functional theory calculations, we determined the magnetic ground states when R 3+ = Y 3+ (non-magnetic) and Dy 3+ (4f 9 ). They both adopt complex long-range ordered antiferromagnetic structures below T N = 6.6 and 14.5 K, respectively, with the same magnetic space group C a 2/c (BNS #15.91). However, the dominant influence of f-electron magnetism is clear in temperature dependence and differences between the size of the ordered moments on the two crystallographically independent Fe sites, one of which is enhanced by R–O–Fe superexchange in the Dy compound, while the other is frustrated by it. We report the Dy compound also shows evidence for temperature- and field-dependent transitions with hysteresis, indicating a field-induced ferromagnetic component below TN.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling Noncollinear Ferromagnetism in van der Waals Metal–Organic Magnets

Van der Waals (vdW) magnets both allow exploration of fundamental 2D physics and offer a route toward exploiting magnetism in next generation information technology, but vdW magnets with complex, noncollinear spin textures are currently rare. We report here the syntheses, crystal structures, magnetic properties and magnetic ground states of four bulk vdW metal–organic magnets (MOMs): FeCl 2 (pym), FeCl 2 (btd), NiCl 2 (pym), and NiCl 2 (btd), pym = pyrimidine and btd = 2,1,3-benzothiadiazole. Using a combination of neutron diffraction and bulk magnetometry we show that these materials are noncollinear magnets. Although only NiCl 2 (btd) has a ferromagnetic ground state, we demonstrate that low-field hysteretic metamagnetic transitions produce states with net magnetization in zero-field and high coercivities for FeCl 2 (pym) and NiCl 2 (pym). By combining our bulk magnetic data with diffuse scattering analysis and broken-symmetry density-functional calculations, we probe the magnetic superexchange interactions, which when combined with symmetry analysis allow us to suggest design principles for future noncollinear vdW MOMs. These materials, if delaminated, would prove an interesting new family of 2D magnets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗