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At least 37 records · Page 2

Evolution and folding of repeat proteins

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. These proteins constitute excellent model systems to investigate how evolution relates to structure, folding, and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat proteins. We model the energetics by a combination of an inverse Potts-model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at the single-residue level. These parameters are used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence, and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transitions are obtained for arrays with enough sequence-similar elements and strong interactions between them, while noncooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. Additionally, we characterized nucleation-propagation and multidomain folding mechanisms. We show that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.

Ezequiel A. Galpern↗

Per- and Polyfluoroalkyl Substances Confirmatory Sampling Report, South Repeater Building (SWMU 121), Kennedy Space Center, Florida

This Per- and Polyfluoroalkyl Substances (PFAS) Confirmatory Sampling (CS) Report was prepared by AECOM Technical Services, Inc. (AECOM) for the National Aeronautics and Space Administration (NASA) under Contract 80KSC019D0010, Task Order 80KSC021F0096. The purpose of this report is to document CS activities at the South Repeater Building, Solid Waste Management Unit (SWMU) 121, formerly known as the Area 3 Repeater Building (A3RB). A Phase I SWMU Assessment and Confirmatory Sampling Report (NASA 2019) and a Phase II and III SWMU Assessment and Confirmatory Sampling Report (NASA 2022b) were previously submitted detailing Center-Wide assessment activities performed at the John F. Kennedy Space Center (KSC) in Florida that identified 33 locations of concern and 19 areas of potential concern at KSC associated with the storage, use, or release of materials containing PFAS. A review of the analytical results from investigation derived waste samples collected in 2020 from the South Repeater Building area indicated concentrations of perfluorooctanesulfonic acid (PFOS) were above Florida Department of Environmental Protection (FDEP) provisional Groundwater Cleanup Target Levels of 70 nanograms per liter (ng/L) at a concentration of 1,750 ng/L. Following this review, the KSC Fire Chief was contacted; the Chief recalled fighting a brush fire in 1998 in the area, during which an unknown volume of aqueous film-forming foam was used to extinguish the fire. The Phase II and Phase III SWMU Assessment Report recommended this area proceed to CS. Historical results in this area are provided in Appendix A . PFAS CS activities were contracted at the South Repeater Building. Initial CS activities were conducted in accordance with the PFAS Assessment and Mitigation Work Plan (AECOM 2022), which was submitted to the NASA Remediation Project Management team and accepted by the team on November 1 and 8, 2021. The objectives of the PFAS CS were to: - - Confirm and begin to assess the extent of PFAS affected media in the South Repeater Building area. - - Identify locations for groundwater, soil, surface water, and soil core sampling. - - Qualitatively characterize the migration potential of released PFAS to environmental media (soil, groundwater, and surface water). The following activities were completed to meet the PFAS CS objectives: - - Installation of monitoring wells via direct push technology (DPT) and rotosonic techniques - - Groundwater, soil, and surface water sampling - - Collection of soil cores to evaluate site lithology - - Development of initial PFAS plume characterization

PFAS↗

A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium

C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. Here, the C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca 2+ showed that Tv-C2-1 bound two Ca 2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with K d s of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ c , in the apo (11.1 ns) and Ca 2+ -bound (9.2 ns) state suggests the protein becomes more compact upon Ca 2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15 N heteronuclear steady-state { 1 H}- 15 N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

NMR spectroscopy↗

De novo design of knotted tandem repeat proteins

De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (3 1 ) and pentafoil (5 1 ) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Statistical Association between the Candidate Repeating FRB 20200320A and a Galaxy Group

Abstract We present results from angular cross correlations between select samples of CHIME/FRB repeaters and galaxies in three photometric galaxy surveys, which have shown correlations with the first CHIME/FRB catalog containing repeating and nonrepeating sources: Wide-field Infrared Survey Explorer (WISE) × SCOS, DESI-BGS, and DESI-LRG. We find a statistically significant correlation (p-value <0.001, after accounting for look-elsewhere factors) between a sample of repeaters with an extragalactic dispersion measure (DM) > 395 pc cm −3 and WISE × SCOS galaxies with redshiftz> 0.275. We demonstrate that the correlation arises surprisingly because of a statistical association between FRB 20200320A (extragalactic DM ≈ 550 pc cm −3 ) and a galaxy group in the same dark matter halo at redshiftz≈ 0.32. We estimate that the host halo, along with an intervening halo at redshiftz≈ 0.12, accounts for at least ∼30% of the extragalactic DM. Our results strongly motivate incorporating galaxy group and cluster catalogs into direct host association pipelines for FRBs with ≲ 1 ′ localization precision, effectively utilizing the two-point information to constrain FRB properties such as their redshift and DM distributions. In addition, we find marginal evidence for a negative correlation at 99.4% confidence limit between a sample of repeating FRBs with baseband data (median extragalactic DM = 354 pc cm −3 ) and DESI-LRG galaxies with redshift 0.3 ≤z< 0.45, suggesting that the repeaters might be more prone than apparent nonrepeaters to propagation effects in FRB–galaxy correlations due to intervening free electrons over angular scales ∼0.°5.

Astronomy & Astrophysics↗

Study of repeater technology for advanced multifunctional communications satellites

Investigations are presented concerning design concepts and implementation approaches for the satellite communication repeater subsystems of advanced multifunctional satellites. In such systems the important concepts are the use of multiple antenna beams, repeater switching (routing), and efficient spectrum utilization through frequency reuse. An information base on these techniques was developed and tradeoff analyses were made of repeater design concepts, with the work design taken in a broad sense to include modulation beam coverage patterns. There were five major areas of study: requirements analysis and processing; study of interbeam interference in multibeam systems; characterization of multiple-beam switching repeaters; estimation of repeater weight and power for a number of alternatives; and tradeoff analyses based on these weight and power data.

Source record↗

Repeated buckling of composite shear panels

Failures in service of aerospace structures and research at the Technion Aircraft Structures Laboratory have revealed that repeatedly buckled stiffened shear panels might be susceptible to premature fatigue failures. Extensive experimental and analytical studies have been performed at Technion on repeated buckling, far in excess of initial buckling, for both metal and composite shear panels with focus on the influence of the surrounding structure. The core of the experimental investigation consisted of repeated buckling and postbuckling tests on Wagner beams in a three-point loading system under realistic test conditions. The effects of varying sizes of stiffeners, of the magnitude of initial buckling loads, of the panel aspect ratio and of the cyclic shearing force, V sub cyc, were studied. The cyclic to critical shear buckling ratios, (V sub cyc/V sub cr) were on the high side, as needed for efficient panel design, yet all within possible flight envelopes. The experiments were supplemented by analytical and numerical analyses. For the metal shear panels the test and numerical results were synthesized into prediction formulas, which relate the life of the metal shear panels to two cyclic load parameters. The composite shear panels studied were hybrid beams with graphite/epoxy webs bonded to aluminum alloy frames. The test results demonstrated that composite panels were less fatigue sensitive than comparable metal ones, and that repeated buckling, even when causing extensive damage, did not reduce the residual strength by more than 20 percent. All the composite panels sustained the specified fatigue life of 250,000 cycles. The effect of local unstiffened holes on the durability of repeatedly buckled shear panels was studied for one series of the metal panels. Tests on 2024 T3 aluminum panels with relatively small unstiffened holes in the center of the panels demonstrated premature fatigue failure, compared to panels without holes. Preliminary tests on two graphite epoxy shear panels with small holes in the center showed no similar fatigue life degradation and no shift in failure mode. Further tests on the effect of holes are in progress.

Singer, Josef↗

The effect of repeating gamma-ray bursts on V/V(sub max)

I consider the effect of repeating burst sources on the the mean value of V/V(sub max) statistic. I find that if the burst sources are distributed homogeneously in a d-dimensional space, the mean value of V/V(sub max) converges to d/(d+3) as long as the luminosity function is dependent of position. Choosing the brightest event from a cluster of k events shifts the luminosity function to higher luminosities, but if the original luminosity function is position independent, it remains so. Therefore the treatment of repeating events, if applied consistently, will not affect the effectiveness the mean value of V/V(sub max) as a test of burst homogeneity. The calculation of the mean value of V/V(sub max) for apparent repeating and non-repeating source populations will be raised by the incorrect classification of faint bursts. In conclusion, the current practice of calculating the mean value of V/V(sub max) using all bursts, even apparent repeaters, and treating multispike bursts as single bursts, is valid and consistent.

Band, David L.↗

Computation of LFT Uncertainty Bounds with Repeated Parametric Uncertainties

A new methodology in which linear fractional transformation uncertainty bounds are directly constructed for use in robust control design and analysis is proposed. Existence conditions for model validating solutions with or without repeated scalar uncertainty are given. The approach is based on minimax formulation to deal with multiple non-repeated structured uncertainty components subject to fixed levels of repeated scalar uncertainties. Input directional dependence and variations with different experiments are addressed by maximizing uncertainty levels over multiple experimental data sets. Preliminary results show that reasonable uncertainty bounds on structured non-repeated uncertainties can be identified directly from measurement data by assuming reasonable levels of repeated scalar uncertainties.

Lim, K. B.↗

Repeatability Modeling for Wind-Tunnel Measurements: Results for Three Langley Facilities

Data from extensive check standard tests of seven measurement processes in three NASA Langley Research Center wind tunnels are statistically analyzed to test a simple model previously presented in 2000 for characterizing short-term, within-test and across-test repeatability. The analysis is intended to support process improvement and development of uncertainty models for the measurements. The analysis suggests that the repeatability can be estimated adequately as a function of only the test section dynamic pressure over a two-orders- of-magnitude dynamic pressure range. As expected for low instrument loading, short-term coefficient repeatability is determined by the resolution of the instrument alone (air off). However, as previously pointed out, for the highest dynamic pressure range the coefficient repeatability appears to be independent of dynamic pressure, thus presenting a lower floor for the standard deviation for all three time frames. The simple repeatability model is shown to be adequate for all of the cases presented and for all three time frames.

Hemsch, Michael J.↗

Triboelectric Nanogenerator Repeatability and Reproducibility Study

The development of triboelectric nanogenerators (TENGs) has largely focused on optimizing output performance, often at the expense of other critical research considerations such as the development of reliable technical procedures. In particular, the reliability of reported results—specifically repeatability and reproducibility—remains underexplored and is frequently limited to brief discussion within available literature. Without rigorous validation through repeatability and reproducibility studies, the credibility and broader applicability of reported findings remain uncertain. This study addresses this gap by systematically evaluating the repeatability and reproducibility of TENG performance data. Five polymer materials—Kapton, polyethylene (PE), polyethylene terephthalate (PET), polytetrafluoroethylene (PTFE), and polyvinylidene fluoride (PVDF)—were investigated across all pairwise combinations of 25 total combinations for the reproducibility study and three selected pairs of the 25 samples were selected for the repeatability study. For each TENG pairing, we analyzed the methodology, experimental procedures, and resulting performance data to quantify consistency and reliability. The objective of this work is to assess the validity of the collected dataset and determine whether the observed performance trends are consistent for use in future TENG design and optimization studies. Establishing reliable and reproducible data is essential for advancing the development of high-output TENG systems and ensuring their dependable implementation in practical applications.

36 MATERIALS SCIENCE↗

Repeatability of ice shapes in the NASA Lewis icing research tunnel

Tests were conducted in the Icing Research Tunnel (IRT) at the NASA Lewis Research Center to document the current capability of the IRT, focused mainly on the repeatability of the ice shape over a range of icing conditions. Measurements of drag increase due to the ice accretion were also made to document the repeatability of drag. The repeatability of the ice shape was very good at low temperatures, but only fair at near freezing temperatures. In general, drag data shows good repeatability.

SHAPE REPEATABILITY↗

A preliminary estimate of geoid-induced variations in repeat orbit satellite altimeter observations

Altimeter satellites are often maintained in a repeating orbit to facilitate the separation of sea-height variations from the geoid. However, atmospheric drag and solar radiation pressure cause a satellite orbit to drift. For Geosat this drift causes the ground track to vary by + or - 1 km about the nominal repeat path. This misalignment leads to an error in the estimates of sea surface height variations because of the local slope in the geoid. This error has been estimated globally for the Geosat Exact Repeat Mission using a mean sea surface constructed from Geos 3 and Seasat altimeter data. Over most of the ocean the geoid gradient is small, and the repeat-track misalignment leads to errors of only 1 to 2 cm. However, in the vicinity of trenches, continental shelves, islands, and seamounts, errors can exceed 20 cm. The estimated error is compared with direct estimates from Geosat altimetry, and a strong correlation is found in the vicinity of the Tonga and Aleutian trenches. This correlation increases as the orbit error is reduced because of the increased signal-to-noise ratio.

Brenner, Anita C.↗

Are repeaters responsible for gamma-ray burst average V/V(max) less than 0.5?

We show that gamma-ray bursts, observed by the Konus experiment on Venera 11 and Venera 12, from the three identified sources of short-term repeating bursts have a very low average V/V(max) of only 0.17 +/- 0.10 and are very important contributors to the low average V/V(max) of 0.43 +/- 0.03 found from the entire Konus burst sample. We further point out that the expected number of additional, as yet unidentified, repeating sources is quite sufficient to account for the low Konus average V/V(max), assuming that the average V/V(max) for bursts from all other sources is 0.5. Thus we suggest that the class of short-term repeating gamma-ray burst sources, as yet only partially identified, are a high-luminosity population that could be responsible for the values of average V/V(max) less than 0.5 also found by the BATSE, SMM, and other gamma-ray burst experiments. We note, however, that repeating bursts cannot as yet be identified solely by their spectral and temporal properties.

Lingenfelter, R. E.↗

Approximate analysis for repeated eigenvalue problems with applications to controls-structure integrated design

A method for eigenvalue and eigenvector approximate analysis for the case of repeated eigenvalues with distinct first derivatives is presented. The approximate analysis method developed involves a reparameterization of the multivariable structural eigenvalue problem in terms of a single positive-valued parameter. The resulting equations yield first-order approximations to changes in the eigenvalues and the eigenvectors associated with the repeated eigenvalue problem. This work also presents a numerical technique that facilitates the definition of an eigenvector derivative for the case of repeated eigenvalues with repeated eigenvalue derivatives (of all orders). Examples are given which demonstrate the application of such equations for sensitivity and approximate analysis. Emphasis is placed on the application of sensitivity analysis to large-scale structural and controls-structures optimization problems.

Kenny, Sean P.↗

Network synthesis localization of two soft gamma repeaters

We introduce the method of 'network synthesis,' which allows the detection of very weak gamma-ray transient signals in the data of the Ulysses gamma-ray burst (GRB) experiment from repeating sources. It consists of defining a grid of alpha, delta values, and for each BATSE detection of a burst from a soft gamma repeater, predicting the arrival time of the burst at Ulysses and co-adding the Ulysses data rephased so that the burst signals are aligned in time and produce a detectable pulse. We demonstrate that this method identifies the position of the soft repeater SGR 1806-20, and apply it to the repeater B1900+14. We show that the counterpart to this burst source is probably in or in the vicinity of the Galactic supernova remnant G42.8+0.6.

Hurley, Kevin↗

The application of network synthesis to repeating classical gamma-ray bursts

It has been suggested that the Burst and Transient Source Experiment (BATSE) gamma-ray burst catalog contains several groups of bursts clustered in space or in space and time, which provide evidence that a substantial fraction of the classical gamma-ray burst sources repeat. Because many of the bursts in these groups are weak, they are not directly detected by the Ulysses GRB experiment. We apply the network synthesis method to these events to test the repeating burst hypothesis. Although we find no evidence for repeating sources, the method must be applied under more general conditions before reaching any definite conclusions about the existence of classical gamma-ray burst repeating sources.

Hurley, K.↗

A longitudinal aerodynamic data repeatability study for a commercial transport model test in the National Transonic Facility

A high Reynolds number investigation of a commercial transport model was conducted in the National Transonic Facility (NTF) at Langley Research Center. This investigation was part of a cooperative effort to test a 0.03-scale model of a Boeing 767 airplane in the NTF over a Mach number range of 0.70 to 0.86 and a Reynolds number range of 2.38 to 40.0 x 10(exp 6) based on the mean aerodynamic chord. One of several specific objectives of the current investigation was to evaluate the level of data repeatability attainable in the NTF. Data repeatability studies were performed at a Mach number of 0.80 with Reynolds numbers of 2.38, 4.45, and 40.0 x 10(exp 6) and also at a Mach number of 0.70 with a Reynolds number of 40.0 x 10(exp 6). Many test procedures and data corrections are addressed in this report, but the data presented do not include corrections for wall interference, model support interference, or model aeroelastic effects. Application of corrections for these three effects would not affect the results of this study because the corrections are systematic in nature and are more appropriately classified as sources of bias error. The repeatability of the longitudinal stability-axis force and moment data has been accessed. Coefficients of lift, drag, and pitching moment are shown to repeat well within the pretest goals of plus or minus 0.005, plus or minus 0.0001, and plus or minus 0.001, respectively, at a 95-percent confidence level over both short- and near-term periods.

Wahls, R. A.↗