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Multi-Omics Analysis of Mouse Retina Following Low Dose Radiation and/or Hindlimb Unloading

Rodent models have been used as analogs for studying the effects of spaceflight. NASA’s GeneLab provides access to omics datasets generated from spaceflight and ground-based experiments allowing for additional retrospective analysis. We used GeneLab’s GLDS-203, a dataset generated by researchers at Loma Linda University to study the impact of prolonged unloading and/or low-dose radiation on mouse retina. The purpose of this study was to understand the effect of gamma radiation and/or hindlimb unloading on mice retinas through a multi-omics analysis. In the experiment that generated the omics data, mice were irradiated with gamma-ray and/or subjected to hindlimb unloading for 21 days and multi-omics analysis was performed at 7 days, 1 month, or 4 months post exposure. In the current study, for each of the three timepoints, we compared epigenomic profiles for retinas from exposed mice against timepoint-matched controls. We identified a total of 5,271 differentially methylated loci (DML) and 321 differentially methylated regions (DMR; using a sliding window and step size of 500 bp) with methylation difference > 10% and q-value < 0.05 (sliding linear model corrected p-value) across the nine exposure groups. Highest correlation in methylation difference was seen for significant DMLs (q-value < 0.05) across different conditions at same post exposure timepoint (Figure 1).The location of DMLs and DMRs were characterized with respect to CpG islands and shores, putative promoters, gene body, and intergenic regions (Table 1). We analyzed RNA-seq counts and performed gene set enrichment analysis using differential expression results from comparing each exposure group to its timepoint-matched control group. Significant pathways (adjusted p-value <0.05) enriched in all three microgravity-only groups were related to morphogenesis of a branching epithelium, skeletal muscle cell differentiation, and response to fibroblast growth factor. Common processes across all timepoints in the radiation-only groups were retina homeostasis, synaptic vesicle exocytosis-endocytosis, and chemotaxis. In the combination groups, regulation of trans-synaptic signaling, and Rho protein signal transduction were enriched at all three timepoints. Processes related to purine nucleotide metabolism were enriched in all nine exposure groups, with activation at 1 month, and suppression at 7 days and 4 months. A total of 14 genes contained at least one DML and were differentially expressed at adjusted p-value < 0.05, including genes implicated in cataract development (Sipa1l3, Crybb3) and those involved in cytoskeletal organization (Plec, Flnb, Eef1a1). This analysis is part of a larger effort to understand the molecular mechanisms following spaceflight exposures that can help translate effects observed in animal models to human impacts.

Prachi Kothiyal↗

Evolutionary problems of Cepheids and other giants investigated with new radiative opacities

Comparison of evolutionary tracks, pulsation constants, and linearized pulsational-stability coefficients for stellar models applicable to the problems of classical Cepheids, whose structures were calculated using the Cox-Stewart (1965) opacities and a recently computed set of opacities. The latter are based on the hot 'Thomas-Fermi' statistical model of the atom for all elements heavier than hydrogen and helium; they contain larger helium and metals contributions, but a smaller hydrogen contribution than the former ones for the same chemical composition. The difference in metals contribution affects mainly the location and shape of the evolutionary tracks on the H-R diagram, while the difference in hydrogen and helium contributions has its greatest effect on the pulsational properties of the Cepheid models. From the comparison of evolutionary tracks it is concluded that: (1) the theoretical M/L relation for evolved giants is changed very little by using the second set of opacities; (2) Q-values for the fundamental mode of radial pulsation in Cepheid envelope models increase if the second set is used, but the classical mass discrepancy remains; and (3) the second set leads to pulsational-instability.

Carson, T. R.↗

Internal friction and velocity measurements

The Q of a lunar basalt sample was measured under varying vacuum conditions, and it was found that even at pressures as low as 10 to the -7th to 10 to the -10th torr, substantial increases in Q with decreasing pressure are observed, while the resonant frequency increases only slightly. This suggests that only small amounts of volatiles are sufficient to increase the internal friction (lower the Q) dramatically. The technique of vibrating encapsulated samples in the torsional mode was used to measure Q of terrestrial rocks as a function of hydrostatic pressure under lunar vacuum conditions. Young's modulus measurements in the temperature range 25-600 C under a variety of conditions including high vacuum show no evidence of any irreversibility upon temperature cycling and no indication that the high Q-values obtained are associated with any permanent structure changes such as the formation of lossless 'welded' contacts.

Tittmann, B. R.↗

Realizable feed-element patterns and optimum aperture efficiency in multibeam antenna systems

The results of an earlier paper by Rahmat-Samii et al. (1981), regarding realizable patterns from feed elements that are part of an array that feeds a reflector antenna, are extended. The earlier paper used a cos exp q theta model for the element radiation pattern, whereas here a parametric study is performed, using a model that assumes a central beam of cos exp q theta shape, with a constant sidelobe level outside the central beam. Realizable q-values are constrained by the maximum directivity based on feed element area. The optimum aperture efficiency (excluding array feed network losses) in an array-reflector system is evaluated as a function of element spacing using this model as well as the model of the earlier paper. Experimental data for tapered slot antenna (TSA) arrays are in agreement with the conclusions based on the model.

Yngvesson, K. S.↗

Sequentially evaporated thin film YBa2Cu3O(7-x) superconducting microwave ring resonator

There is great interest in the application of thin film high temperature superconductors in high frequency electronic circuits. A ring resonator provides a good test vehicle for assessing the microwave losses in the superconductor and for comparing films made by different techniques. Ring resonators made of YBa2Cu3O(7-x) have been investigated on LaAlO3 substrates. The superconducting thin films were deposited by sequential electron beam evaporation of Cu, Y, and BaF2 with a post anneal. Patterning of the superconducting film was done using negative photolithography. A ring resonator was also fabricated from a thin gold film as a control. Both resonators had a gold ground plane on the backside of the substrate. The ring resonators' reflection coefficients were measured as a function of frequency from 33 to 37 GHz at temperatures ranging from 20 K to 68 K. The resonator exhibited two resonances which were at 34.5 and 35.7 GHz at 68 K. The resonant frequencies increased with decreasing temperature. The magnitude of the reflection coefficients was in the calculation of the unloaded Q-values. The performance of the evaporated and gold resonator are compared with the performance of a laser ablated YBa2Cu3O(7-x) resonator. The causes of the double resonance are discussed.

Rohrer, Norman J.↗

Microwave characterization of high-temperature superconducting thin films using stripline resonators

A method was derived for the extraction of the surface resistivity (Rs) of high-Tc superconducting (HTS) thin films at microwave frequencies, using a stripline resonator circuit. Surface resistivity values were calculated by measuring the difference in Q-values of a stripline resonator configuration when an HTS thin film was substituted for one of the metallic ground planes. Cryogenic tests were completed for several stripline resonator structures, yielding accurate predictions of the HTS thin-film performance at frequencies between 3 and 26 GHz (in harmonics of approximately 3 GHz). These results were then used to illustrate the dependence of HTS surface resistivity on frequency and temperature in the microwave frequency band.

Macdonald, Alan D.↗

Measurement and analysis of a microwave oscillator stabilized by a sapphire dielectric ring resonator for ultra-low noise

Phase-noise measurements are presented for a microwave oscillator whose frequency is stabilized by a whispering-gallery sapphire ring resonator with Q of 200,000. This mode involves little metallic conduction and allows nearly full use of the very low dielectric loss in sapphire. Several mode families have been identified, in good agreement with frequency calculations. For a 5-cm wheel resonator in a 7.6-cm container, Q values above 100,000 were found at room temperature for all of the modes in this sequence. Coupling Q-values for these same modes ranged from 10,000 (n = 5) to 100,000 (n = 10) for a WR112 waveguide port at the center of the cylinder wall of the containing can. Phase noise measurements for a transistor oscillator locked to the n = 10 (7.84-GHz) mode showed a 1/f cubed dependence for low offset frequencies, and a value of L(f) = -55 dB/Hz at an offset of 10 Hz from the carrier.

Dick, G. John↗

Nonaxisymmetric evolution in protostellar disks

We present a two-dimensional, multigridded hydrodynamical simulation of the collapse of an axisymmetric, rotating, 1 solar mass protostellar cloud, which forms a resolved, hydrotastic disk. The code includes the effects of physical viscosity, radiative transfer and radiative acceleration but not magnetic fields. We examine how the disk is affected by the inclusion of turbulent viscosity by comparing a viscous simulation with an inviscid model evolved from the same initial conditions, and we derive a disk evolutionary timescale on the order of 300,000 years if alpha = 0.01. Effects arising from non-axisymmetric gravitational instabilities in the protostellar disk are followed with a three-dimensional SPH code, starting from the two-dimensional structure. We find that the disk is prone to a series of spiral instabilities with primary azimulthal mode number m = 1 and m = 2. The torques induced by these nonaxisymmetric structures elicit material transport of angular momentum and mass through the disk, readjusting the surface density profile toward more stable configurations. We present a series of analyses which characterize both the development and the likely source of the instabilities. We speculate that an evolving disk which maintains a minimum Toomre Q-value approximately 1.4 will have a total evolutionary span of several times 10(exp 5) years, comparable to, but somewhat shorter than the evolutionary timescale resulting from viscous turbulence alone. We compare the evolution resulting from nonaxisymmetric instabilities with solutions of a one-dimensional viscous diffusion equation applied to the initial surface density and temperature profile. We find that an effective alpha-value of 0.03 is a good fit to the results of the simulation. However, the effective alpha will depend on the minimum Q in the disk at the time the instability is activated. We argue that the major fraction of the transport characterized by the value of alpha is due to the action of gravitational torques, and does not arise from inherent viscosity within the smoothed particle hydrodynamics method.

Laughlin, Gregory↗

High Power Intermodulation Measurements up to 30 W of High Temperature Superconducting Filters

We have demonstrated a high power intermodulation measurement set-up capable of delivering 30 W in each of two fundamental tones. For closely spaced frequencies (less than 35 MHz), the dynamic range of the measurement is limited by the nonlinear performance of the mixer in the front end of the HP71210C spectrum analyzer. A tunable TE(sub 011) mode copper cavity was fabricated in which one of the endwalls could be adjusted shifting its resonant frequency between 5.7 and 6.6 GHz. Since the Q-value of this cavity is high, greater than 10(exp 4), and its bandwidth is small, less than 1 MHz, it can be used to attenuate the two fundamental tones relative to one of the harmonic tones, which greatly enhances the dynamic range of the measurement. This set-up can be used to measure the two-tone intermodulation distortion of any passive microwave device, e.g. a HTS filter, a connector, a cable, etc., over a frequency range of 5.9 to 6.4 GHz and a power range of 0.1 to 30 W. The third order intercept (TOI) of a prototype HTS filter measured at powers up to 30 W was +81.3 dBm.

Wilker, Charles↗

Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)

The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple model of a nanocrystal with spherical shape and centro-symmetric strain at the surface shell we obtain theoretical alp-Q values which match very well the alp-Q plots determined experimentally for Sic, GaN, and diamond nanopowders. The theoretical models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the surface shell. According to our calculations, the part of the diffraction pattern measured at relatively low diffraction vectors Q (below 10/angstrom) provides information on the surface strain, whle determination of the lattice parameters in the grain core requires measurements at large Q-values (above 15 - 20/angstrom).

Palosz, B.↗

Effect of the Chemical State of the Surface on the Relaxation of the Surface Shell Atoms in SiC and GaN Nanocrystals

The effect of the chemical state of the surface of nanoparticles on the relaxation in the near-surface layer was examined using the concept of the apparent lattice parameter (alp) determined for different diffraction vectors Q. The apparent lattice parameter is a lattice parameter determined either from an individual Bragg reflection, or from a selected region of the diffraction pattern. At low diffraction vectors the Bragg peak positions are affected mainly by the structure of the near-surface layer, while at high Q-values only the interior of the nano-grain contributes to the diffraction pattern. Following the measurements on raw (as prepared) powders we investigated powders cleaned by annealing at 400C under vacuum, and the same powders wetted with water. Theoretical alp-Q plots showed that the structure of the surface layer depends on the sample treatment. Semi-quantitative analysis based on the comparison of the experimental and theoretical alp-Q plots was performed. Theoretical alp-Q relations were obtained from the diffraction patterns calculated for models of nanocrystals with a strained surface layer using the Debye functions.

Palosz, B.↗

Carbon Nanofiber-Based, High-Frequency, High-Q, Miniaturized Mechanical Resonators

High Q resonators are a critical component of stable, low-noise communication systems, radar, and precise timing applications such as atomic clocks. In electronic resonators based on Si integrated circuits, resistive losses increase as a result of the continued reduction in device dimensions, which decreases their Q values. On the other hand, due to the mechanical construct of bulk acoustic wave (BAW) and surface acoustic wave (SAW) resonators, such loss mechanisms are absent, enabling higher Q-values for both BAW and SAW resonators compared to their electronic counterparts. The other advantages of mechanical resonators are their inherently higher radiation tolerance, a factor that makes them attractive for NASA s extreme environment planetary missions, for example to the Jovian environments where the radiation doses are at hostile levels. Despite these advantages, both BAW and SAW resonators suffer from low resonant frequencies and they are also physically large, which precludes their integration into miniaturized electronic systems. Because there is a need to move the resonant frequency of oscillators to the order of gigahertz, new technologies and materials are being investigated that will make performance at those frequencies attainable. By moving to nanoscale structures, in this case vertically oriented, cantilevered carbon nanotubes (CNTs), that have larger aspect ratios (length/thickness) and extremely high elastic moduli, it is possible to overcome the two disadvantages of both bulk acoustic wave (BAW) and surface acoustic wave (SAW) resonators. Nano-electro-mechanical systems (NEMS) that utilize high aspect ratio nanomaterials exhibiting high elastic moduli (e.g., carbon-based nanomaterials) benefit from high Qs, operate at high frequency, and have small force constants that translate to high responsivity that results in improved sensitivity, lower power consumption, and im - proved tunablity. NEMS resonators have recently been demonstrated using topdown, lithographically fabricated ap - proaches to form cantilever or bridgetype structures. Top-down approaches, however, rely on complicated and expensive e-beam lithography, and often require a release mechanism. Reso - nance effects in structures synthesized using bottom-up approaches have also recently been reported based on carbon nanotubes, but such approaches have relied on a planar two-dimensional (2D) geometry. In this innovation, vertically aligned tubes synthesized using a bottom- up approach have been considered, where the vertical orientation of the tubes has the potential to increase integration density even further. The simulation of a vertically oriented, cantilevered carbon nanotube was performed using COMSOL Multi - physics, a finite element simulation package. All simulations were performed in a 2D geometry that provided consistent results and minimized computational complexity. The simulations assumed a vertically oriented, cantilevered nanotube of uniform density (1.5 g/cu cm). An elastic modulus was assumed to be 600 GPa, relative permittivity of the nanotube was assumed to be 5.0, and Poisson s ratio was assumed to be 0.2. It should be noted that the relative permittivity and Poisson s ratio for the nanotubes of interest are not known accurately. However, as in previous simulations, the relative permittivity and Poisson s ratios were treated as weak variables in the simulation, and no significant changes were recognized when these variables were varied.

Kaul, Anupama B.↗

Development of Metallic Magnetic Calorimeters for High Precision Measurements of Calorimetric Re-187 and Ho-163 Spectra

The measurement of calorimetric spectra following atomic weak decays, beta (b) and electron capture (EC), of nuclides having a very low Q-value, can provide an impressively high sensitivity to a non-vanishing neutrino mass. The achievable sensitivity in this kind of experiments is directly connected to the performance of the used detectors. In particular an energy resolution of a few eV and a pulse formation time well below 1 microsecond are required. Low temperature Metallic Magnetic Calorimeters (MMCs) for soft X-rays have already shown an energy resolution of 2.0 eV FWHM and a pulse rise-time of about 90 ns for fully micro-fabricated detectors. We present the use of MMCs for high precision measurements of calorimetric spectra following the beta-decay of Re-187 and the EC of Ho-163. We show results obtained with detectors optimized for Re-187 and for Ho-163 experiments respectively. While the detectors equipped with superconducting Re absorbers have not yet reached the aimed performance, a first detector prototype with a Au absorber having implanted Ho-163 ions already shows excellent results. An energy resolution of 12 eV FWHM and a rise time of 90 ns were measured.

Ranitzsch, P. C.-O.↗

Radiation Quality Effects on Transcriptome Profiles in 3-d Cultures After Particle Irradiation

In this work, we evaluate the differential effects of low- and high-LET radiation on 3-D organotypic cultures in order to investigate radiation quality impacts on gene expression and cellular responses. Reducing uncertainties in current risk models requires new knowledge on the fundamental differences in biological responses (the so-called radiation quality effects) triggered by heavy ion particle radiation versus low-LET radiation associated with Earth-based exposures. We are utilizing novel 3-D organotypic human tissue models that provide a format for study of human cells within a realistic tissue framework, thereby bridging the gap between 2-D monolayer culture and animal models for risk extrapolation to humans. To identify biological pathway signatures unique to heavy ion particle exposure, functional gene set enrichment analysis (GSEA) was used with whole transcriptome profiling. GSEA has been used extensively as a method to garner biological information in a variety of model systems but has not been commonly used to analyze radiation effects. It is a powerful approach for assessing the functional significance of radiation quality-dependent changes from datasets where the changes are subtle but broad, and where single gene based analysis using rankings of fold-change may not reveal important biological information. We identified 45 statistically significant gene sets at 0.05 q-value cutoff, including 14 gene sets common to gamma and titanium irradiation, 19 gene sets specific to gamma irradiation, and 12 titanium-specific gene sets. Common gene sets largely align with DNA damage, cell cycle, early immune response, and inflammatory cytokine pathway activation. The top gene set enriched for the gamma- and titanium-irradiated samples involved KRAS pathway activation and genes activated in TNF-treated cells, respectively. Another difference noted for the high-LET samples was an apparent enrichment in gene sets involved in cycle cycle/mitotic control. It is plausible that the enrichment in these particular pathways results from the complex DNA damage resulting from high-LET exposure where repair processes are not completed during the same time scale as the less complex damage resulting from low-LET radiation.

Patel, Z. S.↗

Vehicle Design Data Format and Process for a Complete TARIS and OLTARIS Radiation Analysis for Designers and Engineers

Protecting astronauts from space radiation is a complex task when it comes to modeling and simulation. This document shows what information is needed from a spacecraft designer using CAD (Computer-Assisted Design) at each phase of the design to enable the engineers to evaluate the design phase against space radiation limits to determine the suitability of the design for space flight. The current personal exposure limits are listed in NASA STD-3001. A proxy to determine the REID (Radiation Exposure Induced Death) in NASA STD-3001 is the whole body effective dose equivalent (E or effective dose). For short-term tissue effects, organ-averaged gray equivalent (G (sub T)) is used. The TARIS (Tool for the Assessment of Radiation In Space - for LaRC (Langley Research Center) engineers) and OLTARIS (On-Line TARIS) - for designers) systems are used to generate these response functions. The E can use ICRP60 or NASA Q-values. A possible space radiation design basis environment for short-term tissue effects is described and used in all analyses. A single space vehicle was designed with three astronaut configurations and two of those configurations were used in a storm shelter thickness perturbation analysis. Conversion of the data from the CAD model to input necessary for TARIS and OLTARIS is also discussed in detail with relevant examples.

Singleterry, Robert C.↗

MULTI-OMICS STUDY OF THE EFFECT OF REDOX-ACTIVE METALLOPORPHYRIN ON MURINE RETINA DURING SPACEFLIGHT

Astronauts returning from spaceflight have experienced eye problems, which may decrease retinal performance and lead to long-term effects on visual acuity. This study leverages the collected data from spaceflown murine retinas that were treated with redox-active metalloporphyrin (BuOE) to mitigate spaceflight-induced changes and respective ground controls. 10-week-old adult C57BL/6 male mice (n=5 in each of BuOE treated and saline control groups for spaceflown and ground control samples) were flown on Space-X 24 to the ISS national lab, kept in low earth orbit for 35 days and returned to Earth alive. Our multi-omics analysis of RNA-sequencing and reduced representation bisulfite sequencing (RRBS) data generated from subsequent murine retina tissues uncovered genes, pathways, and epigenetic modifications consistent with therapeutic potential of BuOE. From RNA-Seq analysis of spaceflown murine samples, the treatment group show differentially expressed genes relative to saline controls that reached significance (adjusted p-value < 0.05) and included genes Gpx3 and Crhbp, which are related to protection against cell oxidative damage and cellular response to organonitrogen compounds. Ranked fold-changes from the same contrast were used for gene set enrichment analysis, which showed biological processes reaching significance (adjusted p-value < 0.05) including glutathione metabolic processes and cellular response to xenobiotic stimulus. RRBS data of the spaceflown murine samples found 139 hyper or hypo differentially methylated sites spread across chromosomes 1-19 (20% promoters, 21% exons, 43% introns | 20 CpG islands, 7 CpG shores) with a 10% methylation difference (q-value < 0.05).The findings from this investigation have the potential to provide valuable insights into the molecular mechanisms underlying conditions like spaceflight associated neuro-ocular syndrome and assess the effectiveness of BuOE as a countermeasure for astronauts experiencing neuro-ophthalmic abnormalities, which can lead to long-term effects on visual acuity.

Biostatistics↗

Multi-Omics Study of the Effect of Redox-Active Metalloporphyrin on Murine Retina During Spaceflight

Astronauts returning from spaceflight have experienced eye problems, which may decrease retinal performance and lead to long-term effects on visual acuity. This study leverages the collected data from spaceflown murine retinas that were treated with redox-active metalloporphyrin (BuOE) to mitigate spaceflight-induced changes and respective ground controls. 10-week-old adult C57BL/6 male mice (n=5 in each of BuOE treated and saline control groups for spaceflown and ground control samples) were flown on Space-X 24 to the ISS national lab, kept in low earth orbit for 35 days and returned to Earth alive. Our multi-omics analysis of RNA-sequencing and reduced representation bisulfite sequencing (RRBS) data generated from subsequent murine retina tissues uncovered genes, pathways, and epigenetic modifications consistent with therapeutic potential of BuOE. From RNA-Seq analysis of spaceflown murine samples, the treatment group show differentially expressed genes relative to saline controls that reached significance (adjusted p-value < 0.05) and included genes Gpx3 and Crhbp, which are related to protection against cell oxidative damage and cellular response to organonitrogen compounds. Ranked fold-changes from the same contrast were used for gene set enrichment analysis, which showed biological processes reaching significance (adjusted p-value < 0.05) including glutathione metabolic processes and cellular response to xenobiotic stimulus. RRBS data of the spaceflown murine samples found 139 hyper or hypo differentially methylated sites spread across chromosomes 1-19 (20% promoters, 21% exons, 43% introns | 20 CpG islands, 7 CpG shores) with a 10% methylation difference (q-value < 0.05).The findings from this investigation have the potential to provide valuable insights into the molecular mechanisms underlying conditions like spaceflight associated neuro-ocular syndrome and assess the effectiveness of BuOE as a countermeasure for astronauts experiencing neuro-ophthalmic abnormalities, which can lead to long-term effects on visual acuity.

Biostatistics↗