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At least 469 records · Page 26

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool.

59 BASIC BIOLOGICAL SCIENCES↗

TomocuPy – efficient GPU-based tomographic reconstruction with asynchronous data processing

Fast 3D data analysis and steering of a tomographic experiment by changing environmental conditions or acquisition parameters require fast, close to real-time, 3D reconstruction of large data volumes. Here a performance-optimized TomocuPy package is presented as a GPU alternative to the commonly used central processing unit (CPU) based TomoPy package for tomographic reconstruction. TomocuPy utilizes modern hardware capabilities to organize a 3D asynchronous reconstruction involving parallel read/write operations with storage drives, CPU–GPU data transfers, and GPU computations. In the asynchronous reconstruction, all the operations are timely overlapped to almost fully hide all data management time. Since most cameras work with less than 16-bit digital output, the memory usage and processing speed are furthermore optimized by using 16-bit floating-point arithmetic. As a result, 3D reconstruction with TomocuPy became 20–30 times faster than its multi-threaded CPU equivalent. Full reconstruction (including read/write operations and methods initialization) of a 2048 3 tomographic volume takes less than 7 s on a single Nvidia Tesla A100 and PCIe 4.0 NVMe SSD, and scales almost linearly increasing the data size. To simplify operation at synchrotron beamlines, TomocuPy provides an easy-to-use command-line interface. Efficacy of the package was demonstrated during a tomographic experiment on gas-hydrate formation in porous samples, where a steering option was implemented as a lens-changing mechanism for zooming to regions of interest.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Designing a parallel Feel-the-Way clustering algorithm on HPC systems

This paper introduces a new parallel clustering algorithm, named Feel-the-Way clustering algorithm, that provides better or equivalent convergence rate than the traditional clustering methods by optimizing the synchronization and communication costs. Our algorithm design centers on how to optimize three factors simultaneously: reduced synchronizations, improved convergence rate, and retained same or comparable optimization cost. To compare the optimization cost, we use the Sum of Square Error (SSE) cost as the metric, which is the sum of the square distance between each data point and its assigned clusters. Compared with the traditional MPI k-means algorithm, the new Feel-the-Way algorithm requires less communications among participating processes. As for the convergence rate, the new algorithm requires fewer number of iterations to converge. As for the optimization cost, it obtains the SSE costs that are close to the k-means algorithm. In the paper, we first design the full-step Feel-the-Way k-means clustering algorithm that can significantly reduce the number of iterations that are required by the original k-means clustering method. Next, we improve the performance of the full-step algorithm by adopting an optimized sampling-based approach, named reassignment-history-aware sampling. Our experimental results show that the optimized sampling-based Feel-the-Way method is significantly faster than the widely used k-means clustering method, and can provide comparable optimization costs. More extensive experiments with several synthetic datasets and real-world datasets (e.g., MNIST, CIFAR-10, ENRON, and PLACES-2) show that the new parallel algorithm can outperform the open source MPI k-means library by up to 110% on a high-performance computing system using 4,096 CPU cores. In addition, the new algorithm can take up to 51% fewer iterations to converge than the k-means clustering algorithm.

97 MATHEMATICS AND COMPUTING↗

Reliability Estimation for One-Shot Devices (Rev. 1)

We present an engineering-oriented summary of statistical methods for estimation of the reliability (or equivalently, failure probability) of one-shot devices such as explosive detonators and other weapon components. Estimates may be given as single points or intervals, based on pass/fail tests, margin analysis, computational models, expert judgment, or a combination of these. We focus on highly reliable devices for which few or no failures are expected to occur in testing.

42 ENGINEERING↗

Self-Assembling Cell-Free Systems for Scalable Bioconversion

This project focused on developing cell-free systems to directly express multi-enzyme catalysts and perform CO2 bioconversions for industrial chemical production. The use of cell-free expression (CFE) systems derived from bacterial lysates is emerging as a promising approach for biomanufacturing. CFEs are genetically programmable, permit the expression of toxic enzymes, and allow for rapid prototyping of metabolic pathways. Research Contributions: 1. Understanding the Area Investigated: This research advances the understanding of cell-free systems by demonstrating their capability to perform complex multi-enzyme reactions. By directly expressing multi-gene systems, CFEs avoid the high costs and inefficiencies associated with producing and purifying enzymes for multi-step pathways. 2. Technical Effectiveness and Economic Feasibility: The project successfully engineered a CFE-based multienzyme biocatalyst for the de novo synthesis of serine and glycine from CO2 equivalents (formate and bicarbonate) and ammonia. This method achieved a 30% conversion rate of formate into these industrially important amino acids. Additionally, an 8-gene CFE biocatalyst was developed to produce malate, conserving 43% of carbon that would otherwise be lost as CO2. This approach has the potential to reach higher carbon efficiency than microbial production. 3. Public Benefit: The cell-free production of chemicals like serine, glycine, and malate using electrochemically generated formate could significantly reduce CO2 emissions. For example, satisfying the global malate market with this method could avoid approximately 400,000 tons of CO2 emissions annually. This work demonstrates the potential of CFE systems to produce platform chemicals, contributing to environmental sustainability and reducing reliance on petrochemicals. Future Prospects: The CFE-based biocatalyst process could be extended to produce a variety of chemicals, including other industrial di-acids, aromatics, terpenes, alcohols, and polymers. This project showcases the capabilities of cell-free expression systems for prototyping carbon-conserving pathways and sustainably bioproducing platform chemicals, marking a significant step towards economically-viable industrial processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic testing of a single-degree-of-freedom strapdown gyroscope

Test methods and results are presented for the equivalent average input rate of a single-degree-of-freedom gyroscope operated both open loop and with a ternary-logic pulse-torque-to-balance loop during multiaxis angular oscillation. For the open-loop tests, good agreement was obtained with theoretical results. Two-axis testing was performed for oscillations about the Input-Output axes, the Input-Spin axes, and the Spin-Output axes. These tests run in the torque-to-balance mode revealed significant departures from open-loop results in the induced drift rate. An analysis is developed explaining much of the closed-loop data presented. Test data for the gryoscope in a ternary torque-to-balance loop with constant input rates is presented. The tests demonstrate that the instrument rate linearity does not change with interrogation frequency from 3,600 to 14,400 Hz if the torque coil is tuned to offer a resistive load to the current switch. Analysis cited shows that gyroscope lag compensation eliminates multiple pulsing and other equivalent forms of degraded resolution in a wide variety of quantizing loops. This result is test verified for the ternary delta-modulator loop.

Lory, C. B.↗

Estimates of nitric oxide production for lifting spacecraft reentry

An approximate analysis to estimate the quantity of nitric oxide that could be formed in the wake of a reentering lifting spacecraft is reported. Three different approaches are undertaken: two simplified analytical models utilizing the sudden-freezing concept named the 'trailing-edge-freezing' and 'wake-freezing' approximations, and a computer calculation involving numerical integration of chemical rate equations. The three methods predict a maximum nitric oxide production equivalent to 6, 9.5 and 8% of the mass of the spacecraft, respectively. Thus, the amount of nitric oxide expected to be produced by future space activities is negligibly small compared with that produced by the natural processes.

Park, C.↗

Comparison of aerodynamic data measured in air and Freon-12 wind-tunnel test mediums

An experimental investigation was carried out to measure two dimensional static aerodynamic characteristics of a 65 sub l-213 airfoil in air and Freon-12 (dichlorodifluoromethane) test mediums at corresponding test conditions. The purpose of the tests was to compare measurements in the two test mediums and to evaluate reported methods of converting Freon-12 data to equivalent air values. The test article was a two dimensional wing instrumented to measure chordwise surface pressure distributions. The parameters considered were Mach numbers from 0.6 to 1.0, angles of attack of zero deg and 1 deg, and Reynolds numbers based on model chord from 2,000,000 to 21,000,000. The agreement between data measured in the two test mediums is further improved by application of the transonic or area ratio similarity laws. Where flow conditions are characterized by surface shocks or stall, the effects of flow separation may not be identically reflected in the Freon-12 data, even when converted in accordance with existing similarity laws.

Weller, W. H.↗

Measurement of the oscillator strengths and autoionization widths of the neutral-aluminum multiplet 3s2 3p2 P0 - 3s 3p2 2P

The hook method is used in conjunction with absorption equivalent width measurements to determine the oscillator strengths and line widths of the Al I multiplet 3s2 3p2 P0 - 3s 3p2 2P at 176 nm. Autoionization is found to be the dominant decay channel for the two levels of the 3p2 2P term, with autoionizing widths of 4.0 and 0.87 x 10 to the 10th/sec for J of 3/2 and 1/2, respectively. The van der Waals scattering cross section for the Al I transition at 176.91 nm by He is determined to be (1.3 + or - 0.3) x 10 to the -14th sq cm at 2400 K, and a solar spectrum calculation centered at 176 nm shows that the Al I features are possible diagnostic probes of (1) solar non-LTE processes, and (2) the temperature minimum and structure of the lower chromosphere.

Lombardi, G. G.↗

Analytical and experimental study of high phase order induction motors

Induction motors having more than three phases were investigated to determine their suitability for electric vehicle applications. The objective was to have a motor with a current rating lower than that of a three-phase motor. The name chosen for these is high phase order (HPO) motors. Motors having six phases and nine phases were given the most attention. It was found that HPO motors are quite suitable for electric vehicles, and for many other applications as well. They have characteristics which are as good as or better than three-phase motors for practically all applications where polyphase induction motors are appropriate. Some of the analysis methods are presented, and several of the equivalent circuits which facilitate the determination of harmonic currents and losses, or currents with unbalanced sources, are included. The sometimes large stator currents due to harmonics in the source voltages are pointed out. Filters which can limit these currents were developed. An analysis and description of these filters is included. Experimental results which confirm and illustrate much of the theory are also included. These include locked rotor test results and full-load performance with an open phase. Also shown are oscillograms which display the reduction in harmonic currents when a filter is used with the experimental motor supplied by a non-sinusoidal source.

Klingshirn, Eugene A.↗

Spectral-Content Readout Of Birefringent Sensor

Stresses and strains measured optically at temperatures up to 2,000 degrees F. Spectrum of light processed through polarizer, sensor, analyzer, and associated optical components measured and processed to extract amount of retardation and, equivalently, stress-induced birefringence in sensor. Method offers same advantages as electrical strain sensors, including acquisition of data from multiple locations and under dynamic conditions. Additional advantage: immunity of fiber-optic transmission to interference by electromagnetic interference at radio and lower frequencies.

Redner, Alex S.↗

Estimation of Cirrus and Stratus Cloud Heights Using Landsat Imagery

A new method based upon high-spatial-resolution imagery is presented that matches cloud and shadow regions to estimate cirrus and stratus cloud heights. The distance between the cloud and the matching shadow pattern is accomplished using the 2D cross-correlation function from which the cloud height is derived. The distance between the matching cloud-shadow patterns is verified manually. The derived heights also are validated through comparison with a temperature-based retrieval of cloud height. It is also demonstrated that an estimate of cloud thickness can be retrieved if both the sunside and anti-sunside of the cloud-shadow pair are apparent. The technique requires some intepretation to determine the cloud height level retrieved (i.e., the top, base, or mid-level). It is concluded that the method is accurate to within several pixels, equivalent to cloud height variations of about +/- 250 m. The results show that precise placement of the templates is unnecessary, so that the development of a semi-automated procedure is possible. Cloud templates of about 64 pixels on a side or larger produce consistent results. The procedure was repeated for imagery degraded to simulate lower spatial resolutions. The results suggest that spatial resolution of 150-200 m or better is necessary in order to obtain stable cloud height retrievals.

Inomata, Yasushi↗

Analytic Sensitivity and Approximation of Skin Buckling Constraints in Wing-Shape Synthesis

Explicit expressions for terms of the stiffness and geometric stiffness matrices are derived for the buckling analysis of trapezoidal fiber composite wing skin panels. The formulation is based on Ritz analysis using simple polynomials, and leads to explicit expressions for the analytic sensitivities of the stiffness and geometric stiffness matrices with respect to layer thickness, fiber directions, and panel shape. Integration with wing box analysis using either the equivalent plate approach or the finite element method, makes it possible to obtain sensitivities of panel buckling constraints with respect to wing planform shape or locations of internal ribs and spars. The analytic sensitivities are used to construct approximations of panel buckling constraints for integrated wing/panel design synthesis.

Livne, Eli↗

Multi-Scale Modeling of a Graphite-Epoxy-Nanotube System

A multi-scale method is utilized to determine some of the constitutive properties of a three component graphite-epoxy-nanotube system. This system is of interest because carbon nanotubes have been proposed as stiffening and toughening agents in the interlaminar regions of carbon fiber/epoxy laminates. The multi-scale method uses molecular dynamics simulation and equivalent-continuum modeling to compute three of the elastic constants of the graphite-epoxy-nanotube system: C11, C22, and C33. The 1-direction is along the nanotube axis, and the graphene sheets lie in the 1-2 plane. It was found that the C11 is only 4% larger than the C22. The nanotube therefore does have a small, but positive effect on the constitutive properties in the interlaminar region.

Frankland, S. J. V.↗

Concrete Model Checking with Abstract Matching and Refinement

We propose an abstraction-based model checking method which relies on refinement of an under-approximation of the feasible behaviors of the system under analysis. The method preserves errors to safety properties, since all analyzed behaviors are feasible by definition. The method does not require an abstract transition relation to he generated, but instead executes the concrete transitions while storing abstract versions of the concrete states, as specified by a set of abstraction predicates. For each explored transition. the method checks, with the help of a theorem prover, whether there is any loss of precision introduced by abstraction. The results of these checks are used to decide termination or to refine the abstraction, by generating new abstraction predicates. If the (possibly infinite) concrete system under analysis has a finite bisimulation quotient, then the method is guaranteed to eventually explore an equivalent finite bisimilar structure. We illustrate the application of the approach for checking concurrent programs. We also show how a lightweight variant can be used for efficient software testing.

Pasareanu Corina S.↗

M-MRAC for Nonlinear Systems with Bounded Disturbances

This paper presents design and performance analysis of a modified reference model MRAC (M-MRAC) architecture for a class of multi-input multi-output uncertain nonlinear systems in the presence of bounded disturbances. M-MRAC incorporates an error feedback in the reference model definition, which allows for fast adaptation without generating high frequency oscillations in the control signal, which closely follows the certainty equivalent control signal. The benefits of the method are demonstrated via a simulation example of an aircraft's wing rock motion.

Stepanyan, Vahram↗

Output Feedback M-MRAC Backstepping With Aerospace Applications

The paper presents a certainty equivalence output feedback backstepping adaptive control design method for the systems of any relative degree with unmatched uncertainties without over-parametrization. It uses a fast prediction model to estimate the unknown parameters, which is independent of the control design. It is shown that the system's input and output tracking errors can be systematically decreased by the proper choice of the design parameters. The approach is applied to aerospace control problems and tested in numerical simulations.

Output feedback adaptive control↗