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At least 73 records · Page 4

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics dataand collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretationof the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLabhave begunand will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Getachew Gebre↗

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data, and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Gebre↗

WEBINAR, May 6: New Discoveries Using GeneLab

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetry data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Sylvain V. Costes↗

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗

Relaxation time in disk galaxy simulations.

An initially stationary and stable axisymmetric disk of stars with a mass spectrum of stars is used to determine the collisional relaxation time. The relaxation time as determined from the rate of energy equipartition was found to be 560 rotation periods for stars with 10 times the mean star mass and was 1700 rotation periods for stars with 0.55 times the mean star mass. These times are in general agreement with theoretical predictions for the relaxation time of the two mass groups. The results show that the model used for the large-scale gravitational N-body calculations is indeed 'collisionless.'

Hohl, F.↗

AutoEnRichness: A hybrid empirical and analytical approach for estimating the richness of galaxy clusters

ABSTRACT We introduce AutoEnRichness, a hybrid approach that combines empirical and analytical strategies to determine the richness of galaxy clusters (in the redshift range of 0.1 ≤ z ≤ 0.35) using photometry data from the Sloan Digital Sky Survey Data Release 16, where cluster richness can be used as a proxy for cluster mass. In order to reliably estimate cluster richness, it is vital that the background subtraction is as accurate as possible when distinguishing cluster and field galaxies to mitigate severe contamination. AutoEnRichness is comprised of a multistage machine learning algorithm that performs background subtraction of interloping field galaxies along the cluster line of sight and a conventional luminosity distribution fitting approach that estimates cluster richness based only on the number of galaxies within a magnitude range and search area. In this proof-of-concept study, we obtain a balanced accuracy of 83.20 per cent when distinguishing between cluster and field galaxies as well as a median absolute percentage error of 33.50 per cent between our estimated cluster richnesses and known cluster richnesses within r200. In the future, we aim for AutoEnRichness to be applied on upcoming large-scale optical surveys, such as the Legacy Survey of Space and Time and Euclid, to estimate the richness of a large sample of galaxy groups and clusters from across the halo mass function. This would advance our overall understanding of galaxy evolution within overdense environments as well as enable cosmological parameters to be further constrained.

79 ASTRONOMY AND ASTROPHYSICS↗

The isotopic composition of iron-group cosmic rays

Measurements are reported of the relative abundances of Mn, Fe, Co, and Ni isotopes in Galactic cosmic rays with energies of about 325 MeV per nucleon. The observed limit (Mn-54)/(Mn-53) of less than 0.25 is significantly less than the value of about 0.8-0.9 expected if Mn-54 were stable, indicating that most of the Mn-54 produced during cosmic-ray propagation in the Galaxy has undergone radioactive decay. Relative source abundances of iron and nickel isotopes, and in particular the ratio (Fe-54)/(Fe-56) = 0.046 +/- 0.020, are generally consistent with solar system values. One exception is the source ratio (Ni-60)/(Ni-58) for which an enhancement by a factor of 2.8 +/- 1.0 over the solar value is found. The isotope (Co-59) is found to make up a sizable fraction of the observed Co, indicating a time delay more than about 100,000 yr between nucleosynthesis and acceleration if this nuclide is synthesized as (Cu-59) or (Ni-59).

Leske, Richard A.↗

The 2175 Å bump features in FeLoBAL quasars: One indicator of MW-like dust in the nuclear region of quasars

To investigate the properties of dust in the nuclear region of quasars, we explored the extinction curves of the iron low-ionisation broad absorption line (FeLoBAL) quasar SDSS J163004.29+311957.6 and its two analogues. The parametrised extinction curves indicated the Milky Way-like 2175 Å bump features in underlying extinction, which are similar to those seen in the Local Group and in a subset of high-redshift star-forming galaxies. Compared to the bump features in the Large Magellanic Cloud (LMC), the detections in this work are much closer to those in the Milky Way (MW). These bump features, as well as those in the high- and low-ionisation broad absorption line (BAL) quasars with 2175 Å bumps, are probably the counterpart of the 2175 Å bump features in the quasar environment. This type of dust grain is generally small, easily disrupted by high-energy photons, and has difficulty surviving in the radiation field of the active galactic nucleus. However, due to the presence of absorption-line outflows, the 2175 Å bump feature in quasars, which should be rare, is seen many times in BAL quasars. The shielding effect of outflow clouds allows the MW-like dust grains to be assembled or extends the survival period in the quasar nuclear region. The process and physical and chemical conditions deserve further observational study and investigation.

79 ASTRONOMY AND ASTROPHYSICS↗

Possibilities and Limitations of Kinematically Identifying Stars from Accreted Ultra-faint Dwarf Galaxies

Abstract The Milky Way has accreted many ultra-faint dwarf galaxies (UFDs), and stars from these galaxies can be found throughout our Galaxy today. Studying these stars provides insight into galaxy formation and early chemical enrichment, but identifying them is difficult. Clustering stellar dynamics in 4D phase space ( E , L z , J r , J z ) is one method of identifying accreted structure that is currently being utilized in the search for accreted UFDs. We produce 32 simulated stellar halos using particle tagging with the Caterpillar simulation suite and thoroughly test the abilities of different clustering algorithms to recover tidally disrupted UFD remnants. We perform over 10,000 clustering runs, testing seven clustering algorithms, roughly twenty hyperparameter choices per algorithm, and six different types of data sets each with up to 32 simulated samples. Of the seven algorithms, HDBSCAN most consistently balances UFD recovery rates and cluster realness rates. We find that, even in highly idealized cases, the vast majority of clusters found by clustering algorithms do not correspond to real accreted UFD remnants and we can generally only recover 6% of UFDs remnants at best. These results focus exclusively on groups of stars from UFDs, which have weak dynamic signatures compared to the background of other stars. The recoverable UFD remnants are those that accreted recently, z accretion ≲ 0.5. Based on these results, we make recommendations to help guide the search for dynamically linked clusters of UFD stars in observational data. We find that real clusters generally have higher median energy and J r , providing a way to help identify real versus fake clusters. We also recommend incorporating chemical tagging as a way to improve clustering results.

79 ASTRONOMY AND ASTROPHYSICS↗

The kinematics of dense clusters of galaxies. 3: Comparison with cosmological models

We compare the combined distribution of 31 group and 25 cluster velocity dispersions with the ensemble of 32 models for the formation and evolution of large-scale structure examined by Weinberg & Cole (1992). The models include Gaussian and non-Gaussian initial fluctuations, different power law spectra (n = -1, n = 0, n = -2, 'pancake'), flat (Omega = 1) and open (Omega = 0.2) cosmologies, and unbiased (b(sub 8) = 1) and biased (b(sub 8) = 2) galaxy formation. The set of initial conditions we test, although limited, samples enough parameter space to indicate which general classes of models are consistent with the data. The two Gaussian, n = -1 models which best approximate the standard and open Cold Dark Matter (CDM) models do not match the observed distribution of velocity dispersions; models with b(sub 8) = 2 and Omega = 1 ('standard') or b(sub 8) = 1 and Omega = 0.2 ('open') predict too large a ratio of low to high velocity dispersion systems. A 'COBE-normalized' CDM model with b(sub 8) = 1 and Omega = 1 produces clusters with velocity dispersions higher than those measured. All three models overestimate the total abundance of systems.

Zabludoff, Ann I.↗

Theoretical Astrophysics at Fermilab

The Theoretical Astrophysics Group works on a broad range of topics ranging from string theory to data analysis in the Sloan Digital Sky Survey. The group is motivated by the belief that a deep understanding of fundamental physics is necessary to explain a wide variety of phenomena in the universe. During the three years 2001-2003 of our previous NASA grant, over 120 papers were written; ten of our postdocs went on to faculty positions; and we hosted or organized many workshops and conferences. Kolb and collaborators focused on the early universe, in particular and models and ramifications of the theory of inflation. They also studied models with extra dimensions, new types of dark matter, and the second order effects of super-horizon perturbations. S tebbins, Frieman, Hui, and Dodelson worked on phenomenological cosmology, extracting cosmological constraints from surveys such as the Sloan Digital Sky Survey. They also worked on theoretical topics such as weak lensing, reionization, and dark energy. This work has proved important to a number of experimental groups [including those at Fermilab] planning future observations. In general, the work of the Theoretical Astrophysics Group has served as a catalyst for experimental projects at Fennilab. An example of this is the Joint Dark Energy Mission. Fennilab is now a member of SNAP, and much of the work done here is by people formerly working on the accelerator. We have created an environment where many of these people made transition from physics to astronomy. We also worked on many other topics related to NASA s focus: cosmic rays, dark matter, the Sunyaev-Zel dovich effect, the galaxy distribution in the universe, and the Lyman alpha forest. The group organized and hosted a number of conferences and workshop over the years covered by the grant. Among them were:

Source record↗

Comparison of dynamical approximation schemes for nonlinear gravitaional clustering

We have recently conducted a controlled comparison of a number of approximations for gravitational clustering against the same n-body simulations. These include ordinary linear perturbation theory (Eulerian), the lognormal approximation, the adhesion approximation, the frozen-flow approximation, the Zel'dovich approximation (describable as first-order Lagrangian perturbation theory), and its second-order generalization. In the last two cases we also created new versions of the approximation by truncation, i.e., by smoothing the initial conditions with various smoothing window shapes and varying their sizes. The primary tool for comparing simulations to approximation schemes was cross-correlation of the evolved mass density fields, testing the extent to which mass was moved to the right place. The Zel'dovich approximation, with initial convolution with a Gaussian e(exp -k(exp 2)/k(sub G(exp 2)), where k(sub G) is adjusted to be just into the nonlinear regime of the evolved model (details in text) worked extremely well. Its second-order generalization worked slightly better. We recommend either n-body simulations or our modified versions of the Zel'dovich approximation, depending upon the purpose. The theoretical implication is that pancaking is implicit in all cosmological gravitational clustering, at least from Gaussian initial conditions, even when subcondensations are present. This in turn provides a natural explanation for the presence of sheets and filaments in the observed galaxy distribution. Use of the approximation scheme can permit extremely rapid generation of large numbers of realizations of model universes with good accuracy down to galaxy group mass scales.

Melott, Adrian L.↗

Improving Neural Network Generalization Ability Using Outlier Analysis and Voronoi Tessellation

The data used in this study was obtained from the Sloan Digital Sky Survey (SDSS), which provides astronomers with what is currently the most extensive mapping of the universe, covering 25% of the sky and cataloging the spectral properties (e.g., luminosity, color, surface temperature) of over 100 million celestial objects. Images generated by the SDSS are collected through 5 filters named u, g, r, l, and z that have respective wavelengths of 3540, 4750, 6222, 7632, and 9049 A. By measuring the photometric redshifts of the aforementioned wavelengths of a galaxy, astronomers can ascertain the extent to which galaxy is receding from which the distance to the galaxy can be calculated. Data collected for a small select group of galaxies (approximately 30, 000) contains accurate measurements of the galaxies' redshifts, in addition to measurements of their spectral properties. The above dataset containing both redshift measurements as well as spectral properties of the selected galaxies served as the training set for the purposes of this study; the data set containing only the spectra properties of a separate group of galaxies served as the test set.

Ho, Michelle↗

Numerical Model for Cosmic Rays Species Production and Propagation in the Galaxy

In recent years, considerable progress has been made in studying the propagation and origin of cosmic rays, as new and more accurate data have become available. Many models have been developed to study cosmic ray interactions and propagation showed flexibility in resembling various astrophysical conditions and good agreement with observational data. However, some astrophysical problems cannot be addressed using these models, such as the stochastic nature of the cosmic rays source, small-scale structures and inhomogeneities in the interstellar gas that can affect radioactive secondary abundance in cosmic rays. We have developed a new model and a corresponding computer code that can address some of these limitations. The model depends on the expansion of the backward stochastic solution of the general diffusion transport equation (Zhang 1999) starting from an observer position to solve a group of diffusion transport equations each of which represents a particular element or isotope of cosmic ray nuclei. In this paper we are focusing on key abundance ratios such as B/C, sub-Fe/Fe, (10)Be/(9)Be, (26)Al/(27)Al, (36)Cl/(37)Cl and (54)Mn/(55)Mn, which all have well established cross sections, to evaluate our model. The effect of inhomogeneity in the interstellar medium is investigated. The contribution of certain cosmic ray nuclei to the production of other nuclei is addressed. The contribution of various galactic locations to the production of cosmic ray nuclei observed at solar system is also investigated.

Farahat, Ashraf↗

The velocity field of clusters of galaxies within 100 megaparsecs. II - Northern clusters

Distances and peculiar velocities for galaxies in eight clusters and groups have been determined by means of the near-infrared Tully-Fisher relation. With the possible exception of a group halfway between us and the Hercules Cluster, we observe peculiar velocities of the same order as the measuring errors of about 400 km/s. The present sample is drawn from the northern Galactic hemisphere and delineates a quiet region in the Hubble flow. This contrasts with the large-scale flows seen in the Hydra-Centaurus and Perseus-Pisces regions. We compare the observed peculiar velocities with predictions based upon the gravity field inferred from the IRAS redshift survey. The differences between the observed and predicted peculiar motions are generally small, except near dense structures, where the observed motions exceed the predictions by significant amounts. Kinematic models of the velocity field are also compared with the data. We cannot distinguish between parameterized models with a great attractor or models with a bulk flow.

Mould, J. R.↗

The environment of Lyman break analogues (ELBA) survey: star-forming galaxies in small groups

ABSTRACT The environment of Lyman break analogues survey is an imaging survey of 33 deg2 of the southern sky. The survey was observed in u, g, r, and i bands with the Dark Energy Camera on the Blanco telescope. The main goal of this project is to investigate the environment of Lyman break analogues (LBAs) low-redshift (z ∼0.2) galaxies that are remarkably similar to typical star-forming galaxies at z ∼ 3. We explore whether the environment has any influence on the observed properties of these galaxies, providing valuable insight on the formation and evolution of galaxies over cosmic time. Using the nearest neighbour method, we measure the local density of each object ranging from small to large scales (clusters of galaxies). Comparing the environment around LBAs with that of the general galaxy population in the field, we conclude that LBAs, on average, populate denser regions at small scales, but are located in similar environment to other star-forming galaxies at larger cluster-like scales. This offers evidence that nearby encounters such as mergers may influence the star formation activity in LBAs, before infall on to larger galaxy clusters. We interpret this as an indication of galaxy pre-processing, in agreement with theoretical expectations for galaxies at z ∼ 2–3 where the gravitational interactions are more intense in early formation processes of these objects.

79 ASTRONOMY AND ASTROPHYSICS↗

Three New Spiral Galaxies with Active Nuclei Producing Double Radio Lobes

Abstract Double radio lobes are generally believed to be produced by active nuclei of elliptical galaxies. However, several double-lobed radio sources have been solidly found to be associated with spiral galaxies. By cross-matching ∼9 × 10 5 spiral galaxies selected from the Sloan Digital Sky Survey DR8 data with the full 1.4 GHz radio source catalogs of NRAO VLA Sky Survey and Faint Images of the Radio Sky at Twenty-centimeters, we identify three new spiral galaxies: J0326−0623, J1110+0321 and J1134+3046 that produce double radio lobes, and five double-lobed spirals previously known. By combining the newly discovered and all the other known cases in literature, we confirm the relation that more massive spiral galaxies could produce more powerful radio lobes. We find that most of these spiral galaxies are located in a galaxy group or a poor cluster, in which the environment is denser than in the field, and about half of them are the central brightest galaxies in their parent system. We therefore suggest that the environment is one of the key factors for a spiral to produce double radio lobes.

Astronomy & Astrophysics↗

The co-evolution of strong AGN and central galaxies in different environments

We exploit a sample of 80 000 Sloan Digital Sky Survey central galaxies to investigate the effect of active galactic nucleus (AGN) feedback on their evolution. We trace the demographics of optically selected AGN (Seyferts) as a function of their internal properties and environment. We find that the preeminence of AGN as the dominant ionizing mechanism increases with stellar mass, overtaking star formation for galaxies with M stellar ≥ 10 10 M ⊙ . The AGN fraction changes systematically with the galaxies’ star formation activity. Within the blue cloud, this fraction increases as star formation activity declines, reaching a maximum near the green valley (⁠~17 ± 4 per cent), followed by a decrease as the galaxies transition into the red sequence. This systematic trend provides evidence that AGN feedback plays a key role in regulating and suppressing star formation. In general, Seyfert central galaxies achieve an early-type morphology while they still host residual star formation. This suggests that, in all environments, the morphology of Seyfert galaxies evolves from late- to early-type before their star formation is fully quenched. Stellar mass plays an important role in this morphological transformation: while low-mass systems tend to emerge from the green valley with an elliptical morphology (T-Type ∼ −2.5 ± 0.7), their high-mass counterparts maintain a spiral morphology deeper into the red sequence. In high-stellar mass centrals, the fraction of Seyferts increases from early- to late-type galaxies, indicating that AGN feedback may be linked with the morphology and its transformation. As a result, our analysis further suggests that AGN are fuelled by their own host halo gas reservoir, but when in group centrals can also increase their gas reservoir via interactions with satellite galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗