Optimisation of patch distribution strategies for AMR applications

As core counts increase in the world's most powerful supercomputers, applications are becoming limited not only by computational power, but also by data availability. In the race to exascale, efficient and effective communication policies are key to achieving optimal application performance. Applications using adaptive mesh refinement (AMR) trade off communication for computational load balancing, to enable the focused computation of specific areas of interest. This class of application is particularly susceptible to the communication performance of the underlying architectures, and are inherently difficult to scale efficiently. In this paper we present a study of the effect of patch distribution strategies on the scalability of an AMR code. We demonstrate the significance of patch placement on communication overheads, and by balancing the computation and communication costs of patches, we develop a scheme to optimise performance of a specific, industry-strength, benchmark application

Visualization of bone details in a novel photon-counting dual-source CT scanner—comparison with energy-integrating CT

OBJECTIVES: Photon-counting detector CT (PCD-CT) promises a leap in spatial resolution due to smaller detector pixel sizes than implemented in energy-integrating detector CTs (EID-CT). Our objective was to compare the visualization of smallest bone details between PCD-CT and EID-CT using a mouse as a specimen. MATERIALS AND METHODS: Two euthanized mice were scanned at a 20-slice EID-CT and a dual-source PCD-CT in single-pixel mode at various CTDI(Vol) values. Image noise and signal-to-noise ratio (SNR) were evaluated using repeated ROI measurements. Edge sharpness of bones was compared by the maximal slope within CT value plots along sampling lines intersecting predefined bones of the spine. Two readers evaluated bone detail visualization at four regions of the spine on a three-point Likert scale at various CTDI(Vol)’s. Two radiologists selected the series with better detail visualization among each of 20 SNR-matched pairs of EID-CT and PCD-CT series. RESULTS: In CTDI(Vol)-matched scans, PCD-CT series showed significantly lower image noise (Noise(CTDI=5 mGy): 16.27 ± 1.39 vs. 23.46 ± 0.96 HU, p < 0.01), higher SNR (SNR(CTDI=5 mGy): 20.57 ± 1.89 vs. 14.00 ± 0.66, p < 0.01), and higher edge sharpness (Edge Slope(lumbar spine): 981 ± 160 vs. 608 ± 146 HU/mm, p < 0.01) than EID-CT series. Two radiologists considered the delineation of bone details as feasible at consistently lower CTDI(Vol) values at PCD-CT than at EID-CT. In comparison of SNR-matched reconstructions, PCD-CT series were still considered superior in almost all cases. CONCLUSIONS: In this head-to-head comparison, PCD-CT showed superior objective and subjective image quality characteristics over EID-CT for the delineation of tiniest bone details. Even in SNR-matched pairs (acquired at different CTDI(Vol)’s), PCD-CT was strongly preferred by radiologists. KEY POINTS: • In dose-matched scans, photon-counting detector CT series showed significantly less image noise, higher signal-to-noise ratio, and higher edge sharpness than energy-integrating detector CT series. • Human observers considered the delineation of tiny bone details as feasible at much lower dose levels in photon-counting detector CT than in energy-integrating detector CT. • In direct comparison of series matched for signal-to-noise ratio, photon-counting detector CT series were considered superior in almost all cases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00330-021-08441-4

Remanent Magnetic Measurements on Perpendicular Recording Materials with Compensation for Demagnetizing Fields

Existing techniques for characterization of longitudinal recording media using remanence measurements are extended to perpendicular media, in particular to Alumite, and correction for demagnetizing fields is taken into account. It is found that these techniques have limited value because of the sensitivity of the analysis to the correction factor used. Measurement of the recoil lines is investigated as an alternative method of probing the reversal processes

Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sub-lethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analyzed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analyzed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sub-lethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts

SPE-44 Implements Sperm Cell Fate

The sperm/oocyte decision in the hermaphrodite germline of Caenorhabditis elegans provides a powerful model for the characterization of stem cell fate specification and differentiation. The germline sex determination program that governs gamete fate has been well studied, but direct mediators of cell-type-specific transcription are largely unknown. We report the identification of spe-44 as a critical regulator of sperm gene expression. Deletion of spe-44 causes sperm-specific defects in cytokinesis, cell cycle progression, and organelle assembly resulting in sterility. Expression of spe-44 correlates precisely with spermatogenesis and is regulated by the germline sex determination pathway. spe-44 is required for the appropriate expression of several hundred sperm-enriched genes. The SPE-44 protein is restricted to the sperm-producing germline, where it localizes to the autosomes (which contain sperm genes) but is excluded from the transcriptionally silent X chromosome (which does not). The orthologous gene in other Caenorhabditis species is similarly expressed in a sex-biased manner, and the protein likewise exhibits autosome-specific localization in developing sperm, strongly suggestive of an evolutionarily conserved role in sperm gene expression. Our analysis represents the first identification of a transcriptional regulator whose primary function is the control of gamete-type-specific transcription in this system

Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts