Tuning and optimization for a variety of many-core architectures without changing a single line of implementation code using the Alpaka library

We present an analysis on optimizing performance of a single C++11 source code using the Alpaka hardware abstraction library. For this we use the general matrix multiplication (GEMM) algorithm in order to show that compilers can optimize Alpaka code effectively when tuning key parameters of the algorithm. We do not intend to rival existing, highly optimized DGEMM versions, but merely choose this example to prove that Alpaka allows for platform-specific tuning with a single source code. In addition we analyze the optimization potential available with vendor-specific compilers when confronted with the heavily templated abstractions of Alpaka. We specifically test the code for bleeding edge architectures such as Nvidia's Tesla P100, Intel's Knights Landing (KNL) and Haswell architecture as well as IBM's Power8 system. On some of these we are able to reach almost 50\% of the peak floating point operation performance using the aforementioned means. When adding compiler-specific #pragmas we are able to reach 5 TFLOPS/s on a P100 and over 1 TFLOPS/s on a KNL system.Comment: Accepted paper for the P\^{}3MA workshop at the ISC 2017 in Frankfur

Bayliss Starling Prize Lecture 2023: Neuropeptide‐Y being ‘unsympathetic’ to the broken hearted

William Bayliss and Ernest Starling are not only famous as pioneers in cardiovascular physiology, but also responsible for the discovery of the first hormone (from the Greek ‘excite or arouse’), the intestinal signalling molecule and neuropeptide secretin in 1902. Our research group focuses on neuropeptides and neuromodulators that influence cardiovascular autonomic control as potential biomarkers in disease and tractable targets for therapeutic intervention. Acute myocardial infarction (AMI) and chronic heart failure (CHF) result in high levels of cardiac sympathetic stimulation, which is a poor prognostic indicator. Although beta‐blockers improve mortality in these conditions by preventing the action of the neurotransmitter noradrenaline, a substantial residual risk remains. Recently, we have identified the sympathetic co‐transmitter neuropeptide‐Y (NPY) as being released during AMI, leading to larger infarcts and life‐threatening arrhythmia in both animal models and patients. Here, we discuss recently published data demonstrating that peripheral venous NPY levels are associated with heart failure hospitalisation and mortality after AMI, and all cause cardiovascular mortality in CHF, even when adjusting for known risk factors (including brain natriuretic peptide). We have investigated the mechanistic basis for these observations in human and rat stellate ganglia and cardiac tissue, manipulating NPY neurochemistry at the same time as using state‐of‐the‐art imaging techniques, to establish the receptor pathways responsible for NPY signalling. We propose NPY as a new mechanistic biomarker in AMI and CHF patients and aim to determine whether specific NPY receptor blockers can prevent arrhythmia and attenuate the development of heart failure. imag

Transparent EuTiO3 films : a possible two-dimensional magneto-optical device

The magneto-optical activity of high quality transparent thin films of insulating EuTiO3 (ETO) deposited on a thin SrTiO3 (STO) substrate, both being non-magnetic materials, are demonstrated to be a versatile tool for light modulation. The operating temperature is close to room temperature and allows for multiple device engineering. By using small magnetic fields birefringence of the samples can be switched off and on. Similarly, rotation of the sample in the field can modify its birefringence Δn. In addition, Δn can be increased by a factor of 4 in very modest fields with simultaneously enhancing the operating temperature by almost 100 K

Evidence for a wide range of UV obscuration in z ~ 2 dusty galaxies from the GOODS-Herschel survey

Dusty galaxies at z ~ 2 span a wide range of relative brightness between rest-frame mid-infrared (8um) and ultraviolet wavelengths. We attempt to determine the physical mechanism responsible for this diversity. Dust-obscured galaxies (DOGs), which have rest-frame mid-IR to UV flux density ratios > 1000, might be abnormally bright in the mid-IR, perhaps due to prominent AGN and/or PAH emission, or abnormally faint in the UV. We use far-infrared data from the GOODS-Herschel survey to show that most DOGs with 10^12 L_Sun < L_IR < 10^13 L_Sun are not abnormally bright in the mid-IR when compared to other dusty galaxies with similar IR (8--1000um) luminosities. We observe a relation between the median IR to UV luminosity ratios and the median UV continuum power-law indices for these galaxies, and we find that only 24% have specific star formation rates which indicate the dominance of compact star-forming regions. This circumstantial evidence supports the idea that the UV- and IR-emitting regions in these galaxies are spatially coincident, which implies a connection between the abnormal UV faintness of DOGs and dust obscuration. We conclude that the range in rest-frame mid-IR to UV flux density ratios spanned by dusty galaxies at z ~ 2 is due to differing amounts of UV obscuration. Of galaxies with these IR luminosities, DOGs are the most obscured. We attribute differences in UV obscuration to either: 1) differences in the degree of alignment between the spatial distributions of dust and massive stars, or 2) differences in the total dust content.Comment: 9 pages, 9 figures. Accepted by Ap

Observation of the hyperfine transition in lithium-like Bismuth 209Bi80+^{209}\text{Bi}^{80+}: Towards a test of QED in strong magnetic fields

We performed a laser spectroscopic determination of the $2s$ hyperfine splitting (HFS) of Li-like $^{209}\text{Bi}^{80+}$ and repeated the measurement of the $1s$ HFS of H-like $^{209}\text{Bi}^{82+}$. Both ion species were subsequently stored in the Experimental Storage Ring at the GSI Helmholtzzentrum f\"ur Schwerionenforschung Darmstadt and cooled with an electron cooler at a velocity of $\approx 0.71\,c$. Pulsed laser excitation of the $M1$ hyperfine-transition was performed in anticollinear and collinear geometry for $\text{Bi}^{82+}$ and $\text{Bi}^{80+}$, respectively, and observed by fluorescence detection. We obtain $\Delta E^{(1s)}= 5086.3(11)\,\textrm{meV}$ for $\text{Bi}^{82+}$, different from the literature value, and $\Delta E^{(2s)}= 797.50(18)\,\textrm{meV}$ for $\text{Bi}^{80+}$. These values provide experimental evidence that a specific difference between the two splitting energies can be used to test QED calculations in the strongest static magnetic fields available in the laboratory independent of nuclear structure effects. The experimental result is in excellent agreement with the theoretical prediction and confirms the sum of the Dirac term and the relativistic interelectronic-interaction correction at a level of 0.5% confirming the importance of accounting for the Breit interaction.Comment: 5 pages, 2 figure

Post-drainage vegetation, microtopography and organic matter in Arctic drained lake basins

Wetlands in Arctic drained lake basins (DLBs) have a high potential for carbon storage in vegetation and peat as well as for elevated greenhouse gas emissions. However, the evolution of vegetation and organic matter is rarely studied in DLBs, making these abundant wetlands especially uncertain elements of the permafrost carbon budget. We surveyed multiple DLB generations in northern Alaska with the goal to assess vegetation, microtopography, and organic matter in surface sediment and pond water in DLBs and to provide the first high-resolution land cover classification for a DLB system focussing on moisture-related vegetation classes for the Teshekpuk Lake region. We associated sediment properties and methane concentrations along a post-drainage succession gradient with remote sensing-derived land cover classes. Our study distinguished five eco-hydrological classes using statistical clustering of vegetation data, which corresponded to the land cover classes. We identified surface wetness and time since drainage as predictors of vegetation composition. Microtopographic complexity increased after drainage. Organic carbon and nitrogen contents in sediment, and dissolved organic carbon (DOC) and dissolved nitrogen (DN) in ponds were high throughout, indicating high organic matter availability and decomposition. We confirmed wetness as a predictor of sediment methane concentrations. Our findings suggest moderate to high methane concentrations independent of drainage age, with particularly high concentrations beneath submerged patches (up to 200 μmol l−1) and in pond water (up to 22 μmol l−1). In our DLB system, wet and shallow submerged patches with high methane concentrations occupied 54% of the area, and ponds with high DOC, DN and methane occupied another 11%. In conclusion, we demonstrate that DLB wetlands are highly productive regarding organic matter decomposition and methane production. Machine learning-aided land cover classification using high-resolution multispectral satellite imagery provides a useful tool for future upscaling of sediment properties and methane emission potentials from Arctic DLBs

The Physical Properties of High-Mass Star-Forming Clumps: A Systematic Comparison of Molecular Tracers

We present observations of HCO+ and H^13CO+, N2H+, HCS+, HCN and HN^13C, SO and ^34SO, CCH, SO_2, and CH_3OH-E towards a sample of 27 high-mass clumps coincident with water maser emission. All transitions are observed with or convolved to nearly identical resolution (30"), allowing for inter-comparison of the clump properties derived from the mapped transitions. We find N2H+ emission is spatially differentiated compared to the dust and the other molecules towards a few very luminous cores (10 of 27) and the N2H+ integrated intensity does not correlate well with dust continuum flux. We calculate the effective excitation density, n_eff, the density required to excite a 1 K line in T_kin=20 K gas for each molecular tracer. The intensity of molecular tracers with larger effective excitation densities (n_eff > 10^5 cm^-3) appear to correlate more strongly with the submillimeter dust continuum intensity. The median sizes of the clumps are anti-correlated with the n_eff of the tracers (which span more than three orders of magnitude). Virial mass is not correlated with n_eff, especially where the lines are optically thick as the linewidths may be broadened significantly by non-virial motions. The median mass surface density and median volume density of the clumps is correlated with n_eff indicating the importance of understanding the excitation conditions of the molecular tracer when deriving the average properties of an ensemble of cores.Comment: 75 pages, 38 figure

Degeneration of Lumbar Intervertebral Discs: Characterization of Anulus Fibrosus Tissue and Cells of Different Degeneration Grades

Intervertebral disc (IVD) herniation and degeneration is a major source of back pain. In order to regenerate a herniated and degenerated disc, closure of the anulus fibrosus (AF) is of crucial importance. For molecular characterization of AF, genome-wide Affymetrix HG-U133plus2.0 microarrays of native AF and cultured cells were investigated. To evaluate if cells derived from degenerated AF are able to initiate gene expression of a regenerative pattern of extracellular matrix (ECM) molecules, cultivated cells were stimulated with bone morphogenetic protein 2 (BMP2), transforming growth factor β1 (TGFβ1) or tumor necrosis factor-α (TNFα) for 24 h. Comparative microarray analysis of native AF tissues showed 788 genes with a significantly different gene expression with 213 genes more highly expressed in mild and 575 genes in severe degenerated AF tissue. Mild degenerated native AF tissues showed a higher gene expression of common cartilage ECM genes, whereas severe degenerated AF tissues expressed genes known from degenerative processes, including matrix metalloproteinases (MMP) and bone associated genes. During monolayer cultivation, only 164 differentially expressed genes were found. The cells dedifferentiated and altered their gene expression profile. RTD-PCR analyses of BMP2- and TGFβ1-stimulated cells from mild and severe degenerated AF tissue after 24 h showed an increased expression of cartilage associated genes. TNFα stimulation increased MMP1, 3, and 13 expression. Cells derived from mild and severe degenerated tissues could be stimulated to a comparable extent. These results give hope that regeneration of mildly but also strongly degenerated disc tissue is possible

Submillimeter Follow-up of WISE-Selected Hyperluminous Galaxies

We have used the Caltech Submillimeter Observatory (CSO) to follow-up a sample of WISE-selected, hyperluminous galaxies, so called W1W2-dropout galaxies. This is a rare (~ 1000 all-sky) population of galaxies at high redshift (peaks at z=2-3), that are faint or undetected by WISE at 3.4 and 4.6 um, yet are clearly detected at 12 and 22 um. The optical spectra of most of these galaxies show significant AGN activity. We observed 14 high-redshift (z > 1.7) W1W2-dropout galaxies with SHARC-II at 350 to 850 um, with 9 detections; and observed 18 with Bolocam at 1.1 mm, with five detections. Warm Spitzer follow-up of 25 targets at 3.6 and 4.5 um, as well as optical spectra of 12 targets are also presented in the paper. Combining WISE data with observations from warm Spitzer and CSO, we constructed their mid-IR to millimeter spectral energy distributions (SEDs). These SEDs have a consistent shape, showing significantly higher mid-IR to submm ratios than other galaxy templates, suggesting a hotter dust temperature. We estimate their dust temperatures to be 60-120 K using a single-temperature model. Their infrared luminosities are well over 10^{13} Lsun. These SEDs are not well fitted with existing galaxy templates, suggesting they are a new population with very high luminosity and hot dust. They are likely among the most luminous galaxies in the Universe. We argue that they are extreme cases of luminous, hot dust-obscured galaxies (DOGs), possibly representing a short evolutionary phase during galaxy merging and evolution. A better understanding of their long-wavelength properties needs ALMA as well as Herschel data.Comment: Will be Published on Sep 1, 2012 by Ap

Ephemerality of discrete methane vents in lake sediments

Methane is a potent greenhouse gas whose emission from sediments in inland waters and shallow oceans may both contribute to global warming and be exacerbated by it. The fraction of methane emitted by sediments that bypasses dissolution in the water column and reaches the atmosphere as bubbles depends on the mode and spatiotemporal characteristics of venting from the sediments. Earlier studies have concluded that hot spots—persistent, high-flux vents—dominate the regional ebullitive flux from submerged sediments. Here the spatial structure, persistence, and variability in the intensity of methane venting are analyzed using a high-resolution multibeam sonar record acquired at the bottom of a lake during multiple deployments over a 9 month period. We confirm that ebullition is strongly episodic, with distinct regimes of high flux and low flux largely controlled by changes in hydrostatic pressure. Our analysis shows that the spatial pattern of ebullition becomes homogeneous at the sonar's resolution over time scales of hours (for high-flux periods) or days (for low-flux periods), demonstrating that vents are ephemeral rather than persistent, and suggesting that long-term, lake-wide ebullition dynamics may be modeled without resolving the fine-scale spatial structure of venting.National Science Foundation (U.S.) (1045193)United States. Department of Energy (DE-FE001399