Processing-in-memory (PIM) promises to alleviate the data movement bottleneck in modern computing systems. However, current real-world PIM systems have the inherent disadvantage that their hardware ...is more constrained than in conventional processors (CPU, GPU), due to the difficulty and cost of building processing elements near or inside the memory. As a result, general-purpose PIM architectures support fairly limited instruction sets and struggle to execute complex operations such as transcendental functions and other hard-to-calculate operations (e.g., square root). These operations are particularly important for some modern workloads, e.g., activation functions in machine learning applications. In order to provide support for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, we present \emph{TransPimLib}, a library that provides CORDIC-based and LUT-based methods for trigonometric functions, hyperbolic functions, exponentiation, logarithm, square root, etc. We develop an implementation of TransPimLib for the UPMEM PIM architecture and perform a thorough evaluation of TransPimLib's methods in terms of performance and accuracy, using microbenchmarks and three full workloads (Blackscholes, Sigmoid, Softmax). We open-source all our code and datasets at~\url{https://github.com/CMU-SAFARI/transpimlib}.
A simplified method is presented for determining epoxidized soy bean oil (ESBO) in food or food simulants, such as olive oil. ESBO is transesterified with methoxide/methanol directly in the ...homogenated food, i.e. without prior extraction, and analyzed on a cyanopropyl or phenyl polysiloxane stationary phase without formation of dioxolanes. For most foods, flame ionization detection (FID) was appropriate, but for samples with interfering components, GC-MS was needed. Chemical ionization (CI) with ammonia is more sensitive and more selective than electron impact ionization (EI). In CI, positive and negative ion monitoring (PCI and NCI) are similar in sensitivity, but different in selectivity, i.e. the combination of the two is well suited for confirmation. Results are shown to be in agreement with on-line LC-GC-FID.
The spectroscopic and structural properties of the His93Tyr variant of horse heart myoglobin have been studied to assess the effects of replacing the proximal His residue of this protein with a ...tyrosyl residue as occurs in catalases from various sources. The variant in the ferric form exhibits electronic spectra that are independent of pH between pH 7 and 10; and it exhibits changes in absorption maxima and intensity that are consistent with a five-coordinate heme iron center at the active site. The EPR spectrum of the variant is that of a high-spin, rhombic system similar to that reported for bovine liver catalase. The 1D 1H-NMR spectrum of the variant confirms the five-coordinate nature of the heme iron center and exhibits a broad resonance at 112.5 ppm that is attributable to the meta protons of the phenolate ligand. This result indicates that the new Tyr ligand flips at a significant rate in this protein. The thermal stability of the Fe(III) derivative is unchanged from that of the wild-type protein (pH 8) while the midpoint reduction potential -208 mV vs SHE (pH 8.0, 25 degrees C) is about 250 mV lower. The three-dimensional structure of the variant determined by X-ray diffraction analysis confirms the five-coordinate nature of the heme iron center and establishes that the introduction of a proximal Tyr ligand is accommodated by a shift of the F helix (residues 88-99) in which this residue resides away from the heme pocket. Additional effects of this change are small shifts in the positions of Leu29, a heme propionate, and a heme vinyl group that are accompanied by altered hydrogen bonding interactions with the heme prosthetic group. The position of the Tyr93 residue with respect to the heme group is also different from that of the His93 residue normally present and resembles that of the proximal Tyr residue of bovine liver catalase.
The Syd protein has been implicated in the Sec-dependent transport of
polypeptides across the bacterial inner membrane. Using Nanodiscs, we here
provide direct evidence that Syd binds the SecY ...complex, and we demonstrate
that interaction involves the two electropositive and cytosolic loops of the
SecY subunit. We solve the crystal structure of Syd and together with cysteine
cross-link analysis, we show that a conserved concave and electronegative
groove constitutes the SecY-binding site. At the membrane, Syd decreases the
activity of the translocon containing loosely associated SecY-SecE subunits,
whereas in detergent solution Syd disrupts the SecYEG heterotrimeric
associations. These results support the role of Syd in proofreading the SecY
complex biogenesis and point to the electrostatic nature of the Sec channel
interaction with its cytosolic partners.
Mating success not only depends on genetic quality, but also equally on environmental factors, most prominently food availability. We investigated the interactive effects of nutritional state and ...body size on mating success and copula duration in yellow dung fly males (Scathophaga stercoraria; Diptera: Scathophagidae) of three body size selection lines in the laboratory in both non‐competitive (single) and competitive (group) situations. Adults require protein and lipids from prey to reproduce, as well as sugars as an energy source for reproductive activity. We expected mating success to decrease with time because of sperm depletion (sugar treatment) and/or energy shortage (water treatment) relative to the control, prey plus sugar treatment. Based on physiological scaling, we also expected large‐line males to become depleted either sooner because of their higher energy and sperm demands, or later because of their more efficient energy use. Average mating success indeed declined over a period of 5–7 d (or 5–15 potential copulations per male), but equally for all food treatments and body size classes. Surprisingly, water‐fed and small‐line males had the highest mating probability in the non‐competitive setting, while in the competitive setting large‐line males had the highest success. Energy‐depleted males showed apparent terminal investment. Small males acquired females more readily but eventually lost them to larger males in the competitive situation. As shown before, copula duration was inversely related to body size and increased with copulation number, independent of food treatment. We conclude that sugar or prey shortage has little effect on mating success in the short term, and does not differentially affect males of different sizes.
Injector‐internal thermal desorption from edible oil or fat is a convenient sample preparation technique for the analysis of solutes in lipids or extracts from fatty foods. The injector temperature ...is selected to vaporize the solutes of interest while minimizing evaporation of the bulk material of the oil. This technique has been in routine use for pesticides for some time. Now its potential is explored for migrants from food contact materials, such as packaging, into simulant D (olive oil) or fatty/oily food, which means extending the range of application towards less volatile compounds. The performance for high boiling components was investigated for diisodecyl phthalate (DIDP) and diundecyl phthalate (DUP). Since the injector temperature needs to be as high as 260°C, some bulk material of the oil enters the column and must be removed after every analysis. This is achieved by a coated precolumn backflushed towards the end of each analysis. Desorption of the solutes is particularly efficient in the initial phase, when a thin sample film is spread on the liner wall, and is largely determined by the diffusion speed in the oil after the latter has contracted to droplets. An increased carrier gas flow rate during the splitless period supports the transfer into the column. It is concluded that the technique is attractive for migrant analysis, with DUP being at the upper limit of the boiling point.
Phonons have the characteristic linear dispersion relation of massless relativistic particles. They arise as low energy excitations of Bose-Einstein condensates and, in nonhomogeneous situations, are ...governed by a space- and time-dependent acoustic metric. We discuss how this metric can be experimentally designed to realize curved spacetime geometries, in particular, expanding Friedmann-Lemaître-Robertson-Walker cosmologies, with negative, vanishing, or positive spatial curvature. A nonvanishing Hubble rate can be obtained through a time-dependent scattering length of the background condensate. For relativistic quantum fields this leads to the phenomenon of particle production, which we describe in detail. We explain how particle production and other interesting features of quantum field theory in curved spacetime can be tested in terms of experimentally accessible correlation functions.
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