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At least 991 records · Page 55

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗

Hydrogen Dispersion Modeling for Development of Smart Distributed Monitoring

Studying hydrogen dispersion is crucial for ensuring the safe and effective deployment of hydrogen as an energy carrier. This study presents a comprehensive CFD modeling framework for simulating hydrogen dispersion at a real-world hydrogen production, storage, and utilization facility. Utilizing the Hydrogen Research Facility under the Advanced Research on Integrated Energy Systems (ARIES) at the National Renewable Energy Laboratory's (NREL) Flatirons campus, controlled hydrogen releases at 27 kg-H2/hr were simulated. The model incorporated site-specific atmospheric conditions, including hourly wind speeds and temperatures recorded between 8 AM and 8 PM from October to December 2023. To reduce computational demands, a statistical reduction technique was applied to condense the dataset to 100 representative scenarios, validated by statistical tests for wind speeds and power law coefficients. Simulations were conducted using the Reynolds-Averaged Navier-Stokes equations. Results demonstrated that wind speed substantially influences hydrogen dispersion, with low wind conditions forming concentrated clouds and higher wind speeds stretching the plume. Additionally, clustering analysis informed optimal sensor placement at various elevations with up to 10 sensor locations on each elevation. This framework offers a robust approach for understanding hydrogen behavior in ambient conditions and informing detection strategies.

08 HYDROGEN↗

Observations of galactic X-ray sources by OSO-7

We present the MIT data from the OSO-7 satellite for observations of the galactic plane between 1971 and 1974. A number of sources discovered in the MIT all-sky survey are described in detail: MX 0049 + 59, MX 0836 - 42, MX 1353 - 64, MX 1406 - 61, MX 1418 - 61, MX 1709 - 40, and MX 1608 - 52 (the persistent source suggested to be associated with the X-ray burst source XB 1608 - 52). Upper limits to the X-ray emission from a number of interesting objects are also derived. General results describing all of our observations of galactic sources are presented. Specifically, we display the number-intensity diagrams, luminosity functions, and color-color diagrams for all of the sources we detected. The data are divided between disk and bulge populations, and the characteristics of the two groups are contrasted. Finally, the concept of X-ray source populations and the relationship of globular cluster sources and burst sources to the disk and bulge populations are discussed.

Markert, T. H.↗

Infrared observations of the dark matter lens candidate Q2345+007

Deep K-band observations are presented of the double image quasar Q2345+007. This has the largest separation (7.1 sec) of any quasar image pair considered as gravitationally lensed, so the required lens is massive (10(exp 13) solar masses). No lens has been detected in previous deep images at visible wavelengths, and we find no lens to limiting K magnitude 20.0 in the infrared image. This constrains any lens to being much less luminous than brightest cluster galaxies, while the lens must be much more massive than such galaxies to produce the observed separation. Because spectral data indicate exceptional intrinsic similarity in the quasar image components, this pair remains as the most intriguing example of an observed configuration requiring the presence of massive, concentrated dark matter acting as a gravitational lens.

Mcleod, Brian↗

Gamma Ray Emission from Chaotic Winds of Massive Stars

The purpose of this proposal was to search for gamma-ray emission from the winds of hot, massive stars. According to our theoretical calculations, shocks in the winds of massive stars accelerate particles to high energies. The high-energy particles emit synchrotron radio emission (observed by ground-based radio telescopes) and high-energy gamma-ray emission that we predicted should be detectable by the EGRET instrument on the Compton Gamma Ray Observatory between 100 MeV and a few GeV. We obtained EGRET from phases 1, 2, and 3 of the Cygnus OB2 association, a cluster of massive, young stars, to search for this gamma-ray emission. The data products and analysis show a source consistent with the position of Cyg OB2 with approximately the predicted count rate and spectrum.

White, Richard L.↗

Analysis of the PKS0637-752 X-Ray Jet System

The X-ray jet emitted from the quasar PKS0637-752 is the largest and most luminous detected to date. It extends 10 arcsec west of the nucleus, and is coincident with GHz radio jet emission in this region. If the individual X-ray/optical/radio knots in this jet were detected as isolated objects, they might be classified as BL Lac objects or quasars. We present a detailed analysis of the Chandra observations of this system, including a search for an intra-cluster medium to confine the jet, and limits to X-ray emission from the eastern radio knot and past the bend of the radio jet to the northwest. The projection in the plane of the sky implies that the X-ray jet is an aligned extension of the pc-scale jet, for which VLBI/VSOP observations show super-luminal motion with an apparent velocity of 11c. In this case, the X-ray jet is of order 1 Mpc in length, and explaining the X-ray emission mechanism presents new challenges.

Schwartz, D. A.↗

The Anisotropy of the Microwave Background to l=3500: Mosaic Observations with the Cosmic Background Imager

Using the Cosmic Background Imager, a 13-element interferometer array operating in the 26-36 GHz frequency band, we have observed 40 deg (sup 2) of sky in three pairs of fields, each approximately 145 feet x 165 feet, using overlapping pointings: (mosaicing). We present images and power spectra of the cosmic microwave background radiation in these mosaic fields. We remove ground radiation and other low-level contaminating signals by differencing matched observations of the fields in each pair. The primary foreground contamination is due to point sources (radio galaxies and quasars). We have subtracted the strongest sources from the data using higher-resolution measurements, and we have projected out the response to other sources of known position in the power-spectrum analysis. The images show features on scales approximately 6 feet-15 feet, corresponding to masses approximately 5-80 x 10(exp 14) solar mass at the surface of last scattering, which are likely to be the seeds of clusters of galaxies. The power spectrum estimates have a resolution delta l approximately 200 and are consistent with earlier results in the multipole range l approximately less than 1000. The power spectrum is detected with high signal-to-noise ratio in the range 300 approximately less than l approximately less than 1700. For 1700 approximately less than l approximately less than 3000 the observations are consistent with the results from more sensitive CBI deep-field observations. The results agree with the extrapolation of cosmological models fitted to observations at lower l, and show the predicted drop at high l (the "damping tail").

Pearson, T. J.↗

Structure in the 3D Galaxy Distribution. III. Fourier Transforming the Universe: Phase and Power Spectra

We demonstrate the effectiveness of a relatively straightforward analysis of the complex 3D Fourier transform of galaxy coordinates derived from redshift surveys. Numerical demonstrations of this approach are carried out on a volume-limited sample of the Sloan Digital Sky Survey redshift survey. The direct unbinned transform yields a complex 3D data cube quite similar to that from the Fast Fourier Transform of finely binned galaxy positions. In both cases, deconvolution of the sampling window function yields estimates of the true transform. Simple power spectrum estimates from these transforms are roughly consistent with those using more elaborate methods. The complex Fourier transform characterizes spatial distributional properties beyond the power spectrum in a manner different from (and we argue is more easily interpreted than) the conventional multipoint hierarchy. We identify some threads of modern large-scale inference methodology that will presumably yield detections in new wider and deeper surveys.

Galaxies↗

Laboratory Measurements of X-ray Emission from Highly Charged Argon Ions

Uncertainties in atomic models will introduce noticeable additional systematics in calculating the flux of weak dielectronic recombination (DR) satellite lines, affecting the detection and flux measurements of other weak spectral lines. One important example is the Ar xvii Heβ DR, which is expected to be present in emission from the hot intracluster medium of galaxy clusters and could impact measurements of the flux of the 3.5 keV line that has been suggested as a secondary emission from a dark matter interaction. We perform a set of experiments using the Lawrence Livermore National Laboratory's electron beam ion trap (EBIT-I) and the X-ray Spectrometer quantum calorimeter (XRS/EBIT) to test the Ar xvii Heβ DR origin of the 3.5 keV line. We measured the X-ray emission following resonant DR onto helium-like and lithium-like Argon using EBIT-I's Maxwellian simulator mode at a simulated electron temperature of T(e) = 1.74 keV. The measured flux of the Ar xvii Heβ DR lined is too weak to account for the flux in the 3.5 keV line, assuming reasonable plasma parameters. We, therefore, rule out Ar xvii Heβ DR as a significant contributor to the 3.5 keV line. A comprehensive comparison between the atomic theory and the EBIT experiment results is also provided.

Esra Bulbul↗

On Dark Peaks and Missing Mass: A Weak-Lensing Mass Reconstruction of the Merging Cluster System A520

Merging clusters of galaxies are unique in their power to directly probe and place limits on the self-interaction cross-section of dark matter. Detailed observations of several merging clusters have shown the intracluster gas to be displaced from the centroids of dark matter and galaxy density by ram pressure, while the latter components are spatially coincident, consistent with collisionless dark matter. This has been used to place upper limits on the dark matter particle self-interaction cross-section of order 1 sq cm/g. The cluster A520 has been seen as a possible exception. We revisit A520 presenting new Hubble Space Telescope Advanced Camera for Surveys mosaic images and a Magellan image set. We perform a detailed weak-lensing analysis and show that the weak-lensing mass measurements and morphologies of the core galaxy-filled structures are mostly in good agreement with previous works. There is, however, one significant difference: We do not detect the previously claimed "dark core" that contains excess mass with no significant galaxy overdensity at the location of the X-ray plasma. This peak has been suggested to be indicative of a large self-interaction cross-section for dark matter (at least approx 5alpha larger than the upper limit of 0.7 sq cm/g determined by observations of the Bullet Cluster). We find no such indication and instead find that the mass distribution of A520, after subtraction of the X-ray plasma mass, is in good agreement with the luminosity distribution of the cluster galaxies.We conclude that A520 shows no evidence to contradict the collisionless dark matter scenario.

Clowe, Douglas↗

General Purpose Data-Driven Monitoring for Space Operations

As modern space propulsion and exploration systems improve in capability and efficiency, their designs are becoming increasingly sophisticated and complex. Determining the health state of these systems, using traditional parameter limit checking, model-based, or rule-based methods, is becoming more difficult as the number of sensors and component interactions grow. Data-driven monitoring techniques have been developed to address these issues by analyzing system operations data to automatically characterize normal system behavior. System health can be monitored by comparing real-time operating data with these nominal characterizations, providing detection of anomalous data signatures indicative of system faults or failures. The Inductive Monitoring System (IMS) is a data-driven system health monitoring software tool that has been successfully applied to several aerospace applications. IMS uses a data mining technique called clustering to analyze archived system data and characterize normal interactions between parameters. The scope of IMS based data-driven monitoring applications continues to expand with current development activities. Successful IMS deployment in the International Space Station (ISS) flight control room to monitor ISS attitude control systems has led to applications in other ISS flight control disciplines, such as thermal control. It has also generated interest in data-driven monitoring capability for Constellation, NASA's program to replace the Space Shuttle with new launch vehicles and spacecraft capable of returning astronauts to the moon, and then on to Mars. Several projects are currently underway to evaluate and mature the IMS technology and complementary tools for use in the Constellation program. These include an experiment on board the Air Force TacSat-3 satellite, and ground systems monitoring for NASA's Ares I-X and Ares I launch vehicles. The TacSat-3 Vehicle System Management (TVSM) project is a software experiment to integrate fault and anomaly detection algorithms and diagnosis tools with executive and adaptive planning functions contained in the flight software on-board the Air Force Research Laboratory TacSat-3 satellite. The TVSM software package will be uploaded after launch to monitor spacecraft subsystems such as power and guidance, navigation, and control (GN&C). It will analyze data in real-time to demonstrate detection of faults and unusual conditions, diagnose problems, and react to threats to spacecraft health and mission goals. The experiment will demonstrate the feasibility and effectiveness of integrated system health management (ISHM) technologies with both ground and on-board experiments.

Iverson, David L.↗

CO–induced roughening of Cu(111): formation and detection of reactive nanoclusters on metal surfaces

The formation of nanoclusters on metal surfaces in the presence of reactive environments is a phenomenon with important implications for catalysis. These nanoclusters are composed of atoms ejected from undercoordinated sites such as step edges, and their presence alters the catalytic properties of solid materials. We perform density functional theory (DFT) and kinetic Monte Carlo (KMC) simulations to investigate the formation and reactivity of copper clusters on Cu(111). Our results indicate a considerably higher reactivity of small copper nanoclusters, with up to seven atoms in size on roughened copper surfaces than on pristine Cu(111) and Cu(211). Regarding the restructuring events that give rise to nanoclusters under CO atmospheres, we determine that the ejection of Cu atoms from step edges and their migration therefrom to adjacent Cu(111) terraces are, by and large, driven by CO coverage effects. By means of KMC simulations, which account for CO–CO lateral interactions and CO–induced surface restructuring, we show that temperature programmed desorption (TPD) holds promise for the detection of highly reactive nanoclusters. Furthermore, our approach showcases how surface restructuring and surface–adsorbate bond breaking can be combined when modeling surface reactions and contributes to the development of an advanced understanding of the nature of active site under reaction conditions.

catalyst dynamic restructuring↗

Characterizing the Gamma-Ray Emission Properties of the Globular Cluster M5 with the Fermi-LAT

Abstract We analyzed the globular cluster M5 (NGC 5904) using 15 yr of gamma-ray data from the Fermi Large Area Telescope (LAT). Using rotation ephemerides generated from Arecibo and FAST radio telescope observations, we searched for gamma-ray pulsations from the seven millisecond pulsars (MSPs) identified in M5. We detected no significant pulsations from any of the individual pulsars. In addition, we searched for possible variations of the gamma-ray emission as a function of orbital phase for all six MSPs in binary systems, but we did not detect any significant modulations. The gamma-ray emission from the direction of M5 is well described by an exponentially cutoff power-law spectral model, although other models cannot be excluded. The phase-averaged emission is consistent with being steady on a timescale of a few months. We estimate the number of MSPs in M5 to be between 1 and 10, using the gamma-ray conversion efficiencies for well-characterized gamma-ray MSPs in the Third Fermi-LAT Catalog of Gamma-ray Pulsars, suggesting that the sample of known MSPs in M5 is (nearly) complete, even if it is not currently possible to rule out a diffuse component of the observed gamma rays from the cluster.

Astronomy & Astrophysics↗

Deletion analysis of the itaconic acid biosynthesis gene cluster components in Aspergillus pseudoterreus ATCC32359

The filamentous fungus Aspergillus terreus has been successfully used for industrial production of itaconic acid (IA) for many years. The IA biosynthesis pathway has recently been characterized at a molecular genetic level as an IA gene cluster (IA cluster) by a clone-based transcriptomic approach. The cluster consists of four genes, including genes for cis-aconitic acid decarboxylase (cadA), a predicted transcription factor (tf), mitochondrial organic acid transporter (mttA), and MFS (Major Facilitator Superfamily) type transporter (mfsA). In this research, we performed EST (Expressed Sequence Tag) analysis and systematic gene deletions to investigate the role of those genes in IA biosynthesis in A. pseudoterreus ATCC32359. EST analysis showed a similar expression pattern among those four genes that was distinct from neighbouring genes and further confirmed that they belong to the same biosynthesis cluster. Systematic gene deletion analysis demonstrated that tf, cadA, mttA, and mfsA genes in the cluster are essential for IA production. Deletion of any of them will either completely abolish the IA production or dramatically decrease amount of IA produced. More importantly, a significant amount of aconitic acid was detected in the cadA deletion strain but not in the other deletion strains. Therefore, the cadA deletion strain is a novel microorganism host for production of aconitic acid and other value-added chemicals from lignocellulosic biomass.

Deng, Shuang↗

Combining field and remote sensing data to estimate forest canopy damage and recovery following tropical cyclones across tropical regions

Abstract As tropical forests cycle the most water and carbon, it is crucial to understand the short- and long-term effects of intensifying cyclones on these ecosystems. Soil nutrient status has been shown to moderate forest cyclone responses using field litterfall measurements, but litterfall is one of the multiple cyclone impact metrtics, which may or may not be correlated with one another or with site nutrients. We used remotely sensed vegetation indices to quantify immediate damage and two-year recovery for 42 cases across nine tropical forests in Hawaii, Puerto Rico, Mexico, Australia, and Taiwan affected by 12 cyclones between 2004 and 2017. We tested whether changes in leaf area index (LAI) and enhanced vegetation index (EVI) correlated with changes in litterfall observations and how changes varied with total soil phosphorus (P) concentrations across regions. We compared cyclone-induced changes and recovery of LAI and EVI to litterfall observations compiled in a pantropical meta-analysis. We found large variation in changes in LAI and EVI across forests, with the greatest reductions in LAI (−77%) and EVI (−77%) in Mexico (Jalisco) and Puerto Rico, respectively. LAI ( r = −0.52) and EVI ( r = −0.60) changes correlated with those in litterfall across cases. Post-cyclone data showed recovery of LAI by four months, EVI by two months, and litterfall by ten months. We detected larger changes in LAI and EVI in forests with higher soil P, but these relationships were not significant when accounting for cyclone and site as random effects. Principal component analyses indicated a regional clustering of cases related to their contrasting cyclone regimes, with the frequency and intensity of cyclone events negatively correlated. Overall, remote sensing observations complement but do not substitute for ground observations that reveal cyclone damage and post-cyclone recovery in tropical forests, and soil phosphorus moderates some but not all metrics of stability in response to cyclones.

Bloom, Dellena E. (ORCID:0000000205981747)↗

FGC 1287 and its enigmatic 250 kpc long HI tail in the outskirts of Abell 1367

ABSTRACT We present H i and radio continuum, narrow-band Hα imaging, IFU spectroscopy, and X-ray observations of the FGC 1287 triplet projected ∼1.8 Mpc west of the galaxy cluster Abell 1367. One triplet member, FGC 1287, displays an exceptionally long, 250 kpc H i tail and an unperturbed stellar disc which are the typical signatures of ram pressure stripping (RPS). To generate detectable RPS signatures the presence of an Intracluster medium ICM or intragroup medium IGM with sufficient density to produce RPS at a realistic velocity relative to the ICM or IGM is a prerequisite. However, XMM–Newton observations were not able to detect X-ray emission from the triplet, implying that if a hot ICM/IGM is present, its density, ne, is less than 2.6 × 10−5 cm−3. Higher resolution VLA H i data presented here show FGC 1287’s H i disc is truncated and significantly warped, whereas the H i tail is clumpy. TNG Hα imaging identified three star-forming clumps projected within 20 kpc of FGC 1287’s disc, with VIMOS–IFU data confirming two of these are counterparts to H i clumps in the tail. The triplet’s H i kinematics, together with Hα and radio continuum imaging suggests an interaction may have enhanced star formation in FGC 1287’s disc, but cannot readily account for the origin of the long H i tail. We consider several scenarios which might reconcile RPS with the non-detection of ICM or IGM X-ray emission but none of these unambiguously explains the origin of the long H i tail.

Scott, T. C. (ORCID:0000000237464859)↗

Containers on Switches: A Cluster School Experience

Network switches, such as those from Arista and Mellanox, often have underutilized computational resources in the form of built-in processors and memory. By leveraging these untapped resources, we can optimize functionality and efficiency of computational cluster networks. Our research focuses on deploying containers directly onto these switches to execute various auxiliary tasks ranging from metric logging to system-wide management via post-boot configuration. By doing so, we can significantly enchance the capabilities of the cluster without the need for additional dedicated hardware. Our research involved five distinct scenarios where switch utilization could have a profound impact on HPC Clusters: run cloud-init services via link-local connection; configuring a Telegraf container to export metrics; deploying a caching proxy; creating a reconfigurable IPv6 DHCP/DNS provider for VLAN; and implementing a client detection with Magellan discovery. These scenarios were containerized with podman and docker, and tested both physically on the switch virtually on a QEMU VM both running SONiC OS. Testing and findings indicate that network switches can indeed be used for these scenarios. They offer a wide range of possibilities beyond these applications. They run as expected as containers on the switches, and although there were some minor issues, work-arounds were implemented. Overall, this is a positive result that can be further explored with more scenarios.

97 MATHEMATICS AND COMPUTING↗

Discovery of an Ultra-faint Stellar System near the Magellanic Clouds with the DECam Local Volume Exploration Survey

We report the discovery of a new ultra-faint stellar system found near the Magellanic Clouds in the DECam Local Volume Exploration Survey. This new system, DELVE J0155−6815 (DELVE 2), is located at a heliocentric distance of D ⊙ = 71 ± 4 kpc, which places it at a 3D physical separation of 12 ± 3 kpc from the center of the Small Magellanic Cloud and from the center of the Large Magellanic Cloud (LMC). DELVE 2 is identified as a resolved overdensity of old (τ > 13.3 Gyr) and metal-poor ( dex) stars with a projected half-light radius of and an absolute magnitude of . The size and luminosity of DELVE 2 are consistent with both the population of recently discovered ultra-faint globular clusters and the smallest ultra-faint dwarf galaxies. However, its photometrically derived age and metallicity would place it among the oldest and most metal-poor globular clusters in the Magellanic system. In the absence of spectroscopic measurements of the system’s metallicity dispersion and internal kinematics, we are unable to conclusively classify this system at this time. DELVE 2 is detected in Gaia DR2 with a clear proper-motion signal, with multiple blue horizontal-branch stars near the centroid of the system with proper motions consistent with the systemic mean. We measure the system proper motion to be = mas yr−1. We compare the spatial position and proper motion of DELVE 2 with simulations of the accreted satellite population of the LMC and find that it is very likely to be associated with the LMC.

79 ASTRONOMY AND ASTROPHYSICS↗