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Global identification of circular RNAs in chronic myeloid leukemia reveals hsa{sub c}irc{sub 0}080145 regulates cell proliferation by sponging miR-29b
Highlights: • A large number of circRNAs aberrantly expressed in chronic myeloid leukemia. • Top 20 aberrantly expressed interacted with leukemia-associated miRNAs. • hsa{sub c}irc{sub 0}080145 knockdown significantly suppressed CML cell proliferation. • hsa{sub c}irc{sub 0}080145 acts as an miR-29b sponge in CML. Circular RNAs (circRNAs) are a class of non-coding RNAs that participate in various biological processes and disease pathogenesis. However, the role of circRNAs in chronic myeloid leukemia (CML) remains largely unknown. In this study, high-throughput sequencing was performed to explore the expression profile of circRNAs in CML patients for the first time, and a large number of differentially expressed circRNAs were identified. In addition, we constructed potential circRNA-miRNA interaction networks in CML, including a detailed hsa{sub c}irc{sub 0}080145-mediated competing endogenous RNA (ceRNA) regulatory network. Furthermore, functional experiments demonstrated that hsa{sub c}irc{sub 0}080145 knockdown significantly suppressed CML cell proliferation and hsa{sub c}irc{sub 0}080145 regulated CML cell proliferation by acting as an miR-29b sponge.
RMACXX: An Efficient High-Level C++ Interface over MPI-3 RMA
Parallel scientific applications can benefit from de- coupling communication and synchronization. One-sided pro- gramming abstractions, which separate communication from syn- chronization, have in fact served as a motivation for partitioned global address space (PGAS) models. However, the use of PGAS models in application codes in a manner that fully exploits the benefit of these programming models requires significant development effort. Meanwhile, a vast majority of scientific codes already use the Message Passing Interface (MPI) and need convenient features to support application-specific one-sided communication scenarios. MPI Remote Memory Access (RMA) can be employed for this purpose. MPI is a low-level API, however, and developing applications with MPI RMA requires programmers to be well versed in its nuances. We present RMACXX, a compact set of C++ bindings to MPI-3 RMA, to ease the use of MPI RMA. Unlike other PGAS models, which may have interoperability issues with MPI, RMACXX is written on top of MPI and uses the same runtime as MPI. The basic functionality of RMACXX adds only a relatively small number of extra instructions (about 20) to the critical communication path. Moreover, RMACXX provides an intuitive API for building a wide variety of scientific applications while enjoying performance matching handwritten MPI-3 RMA codes.
Community College Energy Code Training Program
The U.S. Department of Energy (DOE) Office of Energy Efficiency and Renewable Energy (EERE) funded a series of research and training programs under the Advanced Building Construction with Energy Efficient Technologies and Practices (ABC) initiative. The aim is to develop new training programs to support the development of a skilled workforce in the building energy efficiency industry. In response, the University of Illinois Smart Energy Design Assistance Center (SEDAC), in collaboration with State Energy Offices in Illinois, Hawaii, and Nevada, developed the Community College Energy Code Training Program. The program is designed to prepare a new generation of energy-literate professionals that understand energy efficiency and its relation to energy codes for new construction and existing buildings through: a) the development of a curriculum and innovative pedagogical materials, b) dissemination through a national network of state energy offices: c) outreach targeting Community College students and instructors.
FLASSH 1.0: Thermal scattering law evaluation and cross section generation for reactor physics applications
The Full Law Analysis Scattering System Hub (FLASSH) is a modern, advanced code which evaluates the thermal scattering law (TSL) along with accompanying cross sections. FLASSH features generalized methods which accommodate any material structure. Historical approximations including the incoherent and cubic approximations have been removed. Instead, the latest release of FLASSH features advanced physics options including distinct corrections (1-phonon contributions) and non-cubic formulations. The non-cubic elastic and inelastic contributions are necessary to accurately evaluate 1-phonon contributions. Both non-cubic and 1-phonon calculations require high-density sampling of the various scattering directions. Optimization and parallelization of these routines were therefore necessary to produce results in a reasonable timeframe. With these notable improvements to the generalized TSL, FLASSH 1.0 meets benchmark requirements, demonstrating noticeable agreement with experiment for both TSLs and the resulting integrated cross sections. Additional features including a graphical user interface (GUI), plotting diagnostics, and formatted output options including ACE files allow users to complete a TSL evaluation with minimal input and maximum flexibility. The user GUI creates input files for FLASSH, reducing user error and also providing built-in error checks. Autofill options and suggested input values help make TSL evaluation accessible to novice users. The FLASSH code is compiled to run on both Windows and Linux platforms with automatic parallelization. (authors)
Validation of heat transport modeling using directly driven beryllium spheres
Recent experiments involving directly driven beryllium spheres are reported. Plasma conditions are measured using Thomson scattering with the probe beam pointed 200, 300, and 400 μ m from the surface of the sphere. Laser coupling is assessed using calorimeters that collect scattered light placed at various locations within the target chamber. Laser intensities of 1 0 14 W / c m 2 and 2.5 × 1 0 14 W / c m 2 are chosen to minimize unmodeled laser-plasma interactions (LPIs) that lead to laser-target decoupling. Two-dimensional simulations are compared to the interpreted data using the radiation-hydrodynamics code Lasnex. Heat transport is simulated using flux-limited Spitzer–Harm with both high ( f = 0.15) and low ( f = 0.03) flux limiters and the Schurtz–Nicolai-Busquet (SNB) model. At 1 0 14 W / c m 2 , all three heat transport models agree well with the measurement, demonstrating that the heat flux is local at low intensities near the measurement locations. At 2.5 × 1 0 14 W / c m 2 , the SNB and high flux model roughly match the plasma conditions but predict 2% uncoupled light compared to 10% measured. Additionally, the use of drive multipliers to match the measured coupled light does not alter the agreement between measured and simulated plasma conditions, suggesting that decoupling due to LPI is unlikely to alter this agreement. The low flux model cannot match the plasma conditions and results in 19% scattered light. The use of a resonant absorption model can be used to bring the simulated scattered light into agreement, but the simulated plasma conditions are still in disagreement with the measurement. For this reason, the low flux model is rejected.
Analysis of HolosGen Sub-Scale Simulator with Plant Dynamics Code
The Subcritical Power Module Sub-scale Simulator (SPM-SS) has been designed and constructed by HolosGen LLC under the ARPA-E MEITNER program to simulate the thermal-hydraulic and heat transfer behavior of the full-scale Holos-Quad Subcritical Power Modules (SPMs). Four coupled SPMs, each rated at 5.5MW, form the Holos-Quad gas-cooled microreactor design. The SPM-SS represents a substantially scaled-down system with a power rating less than 40 kW, equipped with an electrically heated fuel cartridge heat exchanger, an electrically heated compressor heat exchanger, and a valve actuated turbine heat exchanger, in addition to a recuperator and a cooler heat exchanger. The fuel cartridge represents a portion of the full-scale SPM core, the compressor heat exchanger mimics the temperature changes resulting from the compressor’s turbomachinery inefficiencies, the turbine heat exchanger mimics the expansion process normally occurring through the turbine, while the recuperator and cooler heat exchangers complete the subscale simulator loop. The heaters equipping the fuel cartridge and the compressor heat exchangers are electronically controlled to simulate normal and off-normal SPM operating conditions. The full-scale Holos-Quad SPM design eliminates the traditional balance of plant and executes thermal-to-electric energy conversion by means of an intercooled Brayton cycle with decoupled compressor-turbine turbomachinery. The Holos-Quad full-scale design is equipped with a multi-stage axial Low- and High-Pressure compressor, and a multistage axial turbine. The SPM-SS is designed for testing and validation of selected components which are instead coupled by a traditional balance of plant. The SPMSS is not equipped with turbo-machinery (compressor and turbine) as the development of these components were excluded from the scope of work under the ARPA-E MEITNER funding program. The SPM-SS balance of plant enables modifications, replacement and testing of individual components with different working fluids and is designed to include the turbo-machinery components that will be developed in future research . The SPM-SS can be operated with different gases, variable mass-flow-rates, pressures, and temperatures to obtain test data for selected components, whose performance can be scaled to validate the computer model of the full-scale SPM at various conditions (e.g., start-up, transients conditions). The SPM-SS can operate at the maximum Holos-Quad design pressure of 7 MPa, and a maximum temperature limited to 650 °C by the electrical heaters. Several SPM-SS tests have been conducted and analyzed with the Plant Dynamics Code (PDC) developed at the Argonne National Laboratory (ANL). These tests aimed at validating the PDC modeled predictions of the full-scale Holos-Quad design with data from selected SPM-SS components. In order to address SPM-SS specific characteristics, such as components heat losses and absence of turbomachinery components, some modifications to the PDC have been implemented to factor the design differences from the full-scale Holos-Quad SPM to the SPM-SS. As the PDC offers capabilities to analyze systems with different working fluids, air, nitrogen, and helium were utilized as the SPM-SS working fluids. Air was utilized to fine-tune the SPM-SS Systems Structures and Components (SSCs), nitrogen was utilized to pressure test the SPM-SS loop at the SPMs design maximum pressure of 7MPa. Helium was utilized as the working fluid circulating through the SPM-SS SSCs for specific tests to validate the PDC predictions of the fuel cartridge heat exchanger. SPM-SS tests data were also analyzed with both the steady-state and transient analysis capabilities offered by the PDC. This report describes the PDC analysis of the SPM-SS tests data, including the necessary code modifications and comparison of the code results with the experimental data. Based on the results, a discussion is presented on how the analysis supports design and transient calculations of the full-scale Holos-Quad microreactor. Also based on the results of this work, recommendations are made for future optimizations of the SPM-SS components and PDC model development needs.
Precise Dynamical Masses and Orbital Fits for β Pic b and β Pic c
We present a comprehensive orbital analysis to the exoplanets β Pictoris b and c that resolves previously reported tensions between the dynamical and evolutionary mass constraints on β Pic b. We use the Markov Chain Monte Carlo orbit code orvara to fit 15 years of radial velocities and relative astrometry (including recent GRAVITY measurements), absolute astrometry from Hipparcos and Gaia, and a single relative radial velocity measurement between β Pic A and b. We measure model-independent masses of 9.3{sub −2.5}{sup +2.6} M {sub Jup} for β Pic b and 8.3 ± 1.0 M {sub Jup} for β Pic c. These masses are robust to modest changes to the input data selection. We find a well-constrained eccentricity of 0.119 ± 0.008 for β Pic b, and an eccentricity of 0.21{sub −0.09}{sup +0.16} for β Pic c, with the two orbital planes aligned to within ∼05. Both planets’ masses are within ∼1σ of the predictions of hot-start evolutionary models and exclude cold starts. We validate our approach on N-body synthetic data integrated using REBOUND. We show that orvara can account for three-body effects in the β Pic system down to a level ∼5 times smaller than the GRAVITY uncertainties. Systematics in the masses and orbital parameters from orvara’s approximate treatment of multiplanet orbits are a factor of ∼5 smaller than the uncertainties we derive here. Future GRAVITY observations will improve the constraints on β Pic c’s mass and (especially) eccentricity, but improved constraints on the mass of β Pic b will likely require years of additional radial velocity monitoring and improved precision from future Gaia data releases.
Error-Correcting Codes for Code-Division Multiplexed TES Detectors
Transition edge sensors (TESs) have proven to be highly sensitive and versatile X-ray spectrometers. Upcoming missions, including Athena X-IFU, will rely on highly multiplexed focal planes where more than 32 TES pixels are read out using a single SQUID amplifier channel. We have implemented an error correction algorithm for code-division multiplexed TES signals that can compensate for potential failures of individual SQUID readout channels and that is both scalable and easily implemented in hardware. We present this algorithm for error correction and show results of laboratory tests to assess algorithm performance at recovering TES channels after a SQUID failure.
Moonshine, superconformal symmetry, and quantum error correction
Special conformal field theories can have symmetry groups which are interesting sporadic finite simple groups. Famous examples include the Monster symmetry group of a c = 24 twodimensional conformal field theory (CFT) constructed by Frenkel, Lepowsky and Meurman, and the Conway symmetry group of a c = 12 CFT explored in detail by Duncan and Mack-Crane. The Mathieu moonshine connection between the K3 elliptic genus and the Mathieu group M24 has led to the study of K3 sigma models with large symmetry groups. A particular K3 CFT with a maximal symmetry group preserving (4, 4) superconformal symmetry was studied in beautiful work by Gaberdiel, Taormina, Volpato, and Wendland [41]. The present paper shows that in both the GTVW and c = 12 theories the construction of superconformal generators can be understood via the theory of quantum error correcting codes. The automorphism groups of these codes lift to symmetry groups in the CFT preserving the superconformal generators. In the case of the N = 1 supercurrent of the GTVW model our result, combined with a result of T. Johnson-Freyd implies the symmetry group is the maximal subgroup of M24 known as the sextet group. (The sextet group is also known as the holomorph of the hexacode.) Building on [41] the Ramond-Ramond sector of the GTVW model is related to the Miracle Octad Generator which in turn leads to a role for the Golay code as a group of symmetries of RR states. Moreover, (4, 1) superconformal symmetry suffices to define and decompose the elliptic genus of a K3 sigma model into characters of the N = 4 superconformal algebra. The symmetry group preserving (4, 1) is larger than that preserving (4, 4).
Thermodynamic Model of COREX Melter Gasifier Using FactSage™ and Macro Facility
In the current study, the thermochemical model of the COREX melter gasifier has been developed using the FactSage™ thermodynamic software, and macro programming facility. The melter gasifier was conceptually divided into various equilibrium zones dealing with the reactions happening in the reactor. The coal char and the coke being used are divided among them optimally. The model has been validated with respect to the plant data for the hot-metal, slag, and reducing gas composition. The effects of the variation in the degree of metallization, on the final hot metal, slag, and reducing gas, have been predicted using this model. The variations in the process parameters for the different industrial coal grades used in the COREX plant have been determined. The effects of the volatile, ash, and the moisture contents of the coal on the hot-metal and the reducing gas compositions have been reported.
Implementation and verification of PyNE R2S with DAG-OpenMC
The mesh-based Rigorous-Two-Step (R2S) method has been widely used in the accurate estimation of the shutdown dose rate (SDR) of fusion systems. Several mesh-based R2S code has been implemented based on Monte Carlo particle transport code MCNP5 or DAG-MCNP5 and inventory calculation code such as FISPACT-II, ALARA or ACAB. Recently, the OpenMC, a community-developed Monte Carlo particle transport code, implemented the photon particle transport capability, which enables OpenMC to be used in R2S. In this paper, PyNE R2S is extended with the support of DAG-OpenMC, i.e., OpenMC with DAGMC. Modifications that allow PyNE to read the flux result in the state point file of OpenMC has been implemented to PyNE R2S workflow. A custom source routine of OpenMC that reads the photon source file from PyNE R2S and sampling photon particle in OpenMC photon transport has been implemented in OpenMC. With these modifications, PyNE R2S is now capable of performing R2S calculations with both DAG-MCNP5 and DAG-OpenMC. The ITER FNG dose rate benchmark problem has been used to validate the code. The FNG neutron source has been modified for neutron transport with DAG-OpenMC. The shutdown dose rate of 19 cooling times has been calculated and compared with the experimental data and the computational results of other R2S codes. The results of PyNE R2S with DAG-OpenMC show satisfactory agreement with the experimental data and other computational results. Therefore, we consider PyNE R2S with DAG-OpenMC is a reliable code to calculate the SDR of fusion systems.
Application of performance portability solutions for GPUs and many-core CPUs to track reconstruction kernels
Next generation High-Energy Physics (HEP) experiments are presented with significant computational challenges, both in terms of data volume and processing power. Using compute accelerators, such as GPUs, is one of the promising ways to provide the necessary computational power to meet the challenge. The current programming models for compute accelerators often involve using architecture-specific programming languages promoted by the hardware vendors and hence limit the set of platforms that the code can run on. Developing software with platform restrictions is especially unfeasible for HEP communities as it takes significant effort to convert typical HEP algorithms into ones that are efficient for compute accelerators. Multiple performance portability solutions have recently emerged and provide an alternative path for using compute accelerators, which allow the code to be executed on hardware from different vendors. We apply several portability solutions, such as Kokkos, SYCL, C++17 std::execution::par, Alpaka, and OpenMP/OpenACC, on two mini-apps extracted from the mkFit project: p2z and p2r. These apps include basic kernels for a Kalman filter track fit, such as propagation and update of track parameters, for detectors at a fixed z or fixed r position, respectively. The two mini-apps explore different memory layout formats. We report on the development experience with different portability solutions, as well as their performance on GPUs and many-core CPUs, measured as the throughput of the kernels from different GPU and CPU vendors such as NVIDIA, AMD and Intel.
X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction
Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. Here, to better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ~13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe–Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO 3 ) and K-citrate [K 3 (C 6 H 5 O 7 )·H 2 O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO 3 has both the lowest and highest lying energy features, and K 3 (C 6 H 5 O 7 )·H 2 O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.
Validation study of GENE on ASDEX Upgrade using perturbative thermal diffusivity measured with partial sawtooth heat pulses
Perturbative thermal diffusivity is measured with partial sawtooth-generated heat pulses on ASDEX Upgrade for the first time, and these measurements are used to validate the first nonlinear ion-scale gyrokinetic simulation that agrees with experimentally measured perturbative diffusivity. Recent work on Alcator C-Mod and DIII-D has shown that ion-scale gyrokinetics cannot adequately describe certain plasma conditions, and that in these instances multi-scale simulations may resolve the observed discrepancies. This work presents the first measurements of electron perturbative thermal diffusivity with partial sawteeth on ASDEX Upgrade (measuring values between 2 and 9 m 2 s -1 ), and compares these measurements to those made with more established modulated electron cyclotron heating measurements, finding good agreement within experimental uncertainty. Perturbative diffusivity is found to scale inversely with collisionality across ASDEX Upgrade and Alcator C-Mod plasmas. Finally, perturbative diffusivity is used as a validation constraint in a study with the gyrokinetic code GENE, showing the first instance where an ion-scale gyrokinetic simulation can simultaneously match the experimental ion and electron heat fluxes and the perturbative thermal diffusivity. Here these results indicate that multi-scale effects may only be important in some plasmas, and the collisionality and ratio of high to low wavenumber linear growth rates may distinguish these cases.
Signatures of Selection for Resistance/Tolerance to Perkinsus olseni in Grooved Carpet Shell Clam ( Ruditapes decussatus ) Using a Population Genomics Approach
ABSTRACT The grooved carpet shell clam ( Ruditapes decussatus ) is a bivalve of high commercial value distributed throughout the European coast. Its production has suffered a decline caused by different factors, especially by the parasite Perkinsus olsenii . Improving production of R . decussatus requires genomic resources to ascertain the genetic factors underlying resistance/tolerance to P. olseni i . In this study, the first reference genome of R . decussatus was assembled through long‐ and short‐read sequencing (1677 contigs; 1.386 Mb) and further scaffolded at chromosome level with Hi‐C (19 superscaffolds; 95.4% of assembly). Repetitive elements were identified (32%) and masked for annotation of 38,276 coding‐ and 13,056 non‐coding genes. This genome was used as a reference to develop a 2bRAD‐Seq 13,438 SNP panel for a genomic screening on six shellfish beds distributed across the Atlantic Ocean and Mediterranean Sea. Beds were selected by perkinsosis prevalence and the infection level was individually evaluated in all the samples. Genetic diversity was significantly higher in the Mediterranean than in the Atlantic region. The main genetic breakage was detected between those regions (F ST = 0.224), being the Mediterranean more heterogeneous than the Atlantic. Several loci under divergent selection (394 outliers; 261 genomic windows) were detected across shellfish beds. Samples were also inspected to detect signals of selection for resistance/tolerance to P. olseni i by using infection‐level and population‐genomics approaches, and 90 common divergent outliers for resistance/tolerance to perkinsosis were identified and used for gene mining. Candidate genes and markers identified provide invaluable information for controlling perkinsosis and for improving production of the grooved carpet shell clam.
COWALKER:EFFECTIVE TRANSPORT PROPERTIES OF COMPOSITE MATERIALS
SF-23-026 This software computes effective transport properties of composite materials involving fibers and nanoparticles using a random-walk algorithm that efficiently scales to an arbitrary number of processes and cores. Effective transport properties (thermal, electrical) are key to bridge the microstructure of complex materials with its macroscopic behavior. Traditional approaches either use effective medium approximations (closed mathematical expressions that are approximation for certain conditions) or continuum simulation models such as finite element or finite volume, which require the generation of a mesh for each configuration explored. cowalker leverages the equivalence between laplacian or heat equation-based models and random walks to compute the asymptotic transport properties from an ensemble of first sojourn times of a random walker moving through the composite material. This allows us to directly define a composite material as a collection of particles and use algorithms developed for molecular dynamics to quickly compute the intersection of the walker with the different interfaces in the material. cowalker is developed in C++, and it relies on the GNU Scientific Library for random generation. cowalker is currently delivered as source code, so the GSL library is not included in cowalker's distribution. A more userfriendly version, cowalker.jl is currently in development and will be released as part of cowalker.
Unprecedented cloud resolution in a GPU-enabled full-physics atmospheric climate simulation on OLCF’s summit supercomputer
Clouds represent a key uncertainty in future climate projection. While explicit cloud resolution remains beyond our computational grasp for global climate, we can incorporate important cloud effects through a computational middle ground called the Multi-scale Modeling Framework (MMF), also known as Super Parameterization. This algorithmic approach embeds high-resolution Cloud Resolving Models (CRMs) to represent moist convective processes within each grid column in a Global Climate Model (GCM). The MMF code requires no parallel data transfers and provides a self-contained target for acceleration. This study investigates the performance of the Energy Exascale Earth System Model-MMF (E3SM-MMF) code on the OLCF Summit supercomputer at an unprecedented scale of simulation. Hundreds of kernels in the roughly 10K lines of code in the E3SM-MMF CRM were ported to GPUs with OpenACC directives. A high-resolution benchmark using 4600 nodes on Summit demonstrates the computational capability of the GPU-enabled E3SM-MMF code in a full physics climate simulation.