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At least 91 records · Page 5

Controlling the toxicity of biomass-derived difunctional molecules as potential pharmaceutical ingredients for specific activity toward microorganisms and mammalian cells

A biomass-derived difuran compound, denoted as HAH (HMF–acetone–HMF), synthesized by aldol-condensation of 5-hydroxyfurfural (HMF) and acetone, can be partially hydrogenated to provide an electron-rich difuran compound (PHAH) for Diels–Alder reactions with maleimide derivatives. The nitrogen (N) site in the maleimide can be substituted by imidation with amine-containing compounds to control the hydrophobicity of the maleimide moiety in adducts of furans and maleimide by Diels–Alder reaction, denoted as norcantharimides (Diels–Alder adducts). The structural effects on the toxicity of various biomass-derived small molecules synthesized in this manner to regulate biological processes, defined as low molecular weight (≤1000 g mol -1 ) organic compounds, were investigated against diverse microbial and mammalian cell types. The biological toxicity increased when hydrophobic N-substitutions and C[double bond, length as m-dash]C bonds were introduced into the molecular structure. Among the synthesized norcantharamide derivatives, some compounds demonstrated pH-dependent toxicities against specific cell types. Reaction kinetics analyses of the norcantharimides in biological conditions suggest that this pH-dependent toxicity of norcantharimides could arise from retro Diels–Alder reactions in the presence of a Brønsted acid that catalyzes the release of an N-substituted maleimide, which has higher toxicity against fungal cells than the toxicity of the Diels–Alder adduct. These synthetic approaches can be used to design biologically-active small molecules that exhibit selective toxicity against various cell types (e.g., fungal, cancer cells) and provide a sustainable platform for production of prodrugs that could actively or passively affect the viability of infectious cells.

60 APPLIED LIFE SCIENCES↗

Deterministic scattering of relativistic electron beams by off-resonant circularly polarized electromagnetic waves

A mechanism is presented whereby relativistic electron beams localized in phase space are deterministically scattered by coherent circularly polarized electromagnetic waves without stochastic processes. It is shown via an exact single-particle analysis that the condition for maximal scattering is an off-resonant condition, contrary to previous kinetic analyses that predict maximal diffusion or interaction at exact resonance or its harmonics. The mechanism, verified by single-particle simulations, enables a fast, nonlinear redistribution of the beam particles. A possible application of this mechanism to runaway electron suppression is presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis

HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Here, we present X-ray crystal structures and biochemical characterization of the Bacillus megaterium HD domain phosphohydrolase OxsA, involved in the biosynthesis of the antitumor, antiviral, and antibacterial compound oxetanocin-A. Here, these studies reveal a previously uncharacterized reaction for this family; OxsA catalyzes the conversion of a triphosphorylated compound into a nucleoside, releasing one molecule of inorganic phosphate at a time. Remarkably, this functionality is a result of the OxsA active site, which based on structural and kinetic analyses has been tailored to bind the small, four-membered ring of oxetanocin-A over larger substrates. Furthermore, our OxsA structures show an active site that switches from a dinuclear to a mononuclear metal center as phosphates are eliminated from substrate.

59 BASIC BIOLOGICAL SCIENCES↗

Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling

Inositol diphosphates (PP-IPs), also known as inositol pyrophosphates, are high-energy cellular signaling codes involved in nutrient and regulatory responses. We report that the evolutionarily conserved gene product, Vip1, possesses autonomous kinase and pyrophosphatase domains capable of synthesis and destruction of D-1 PP-IPs. Our studies provide atomic-resolution structures of the PP-IP products and unequivocally define that the Vip1 gene product is a highly selective 1-kinase and 1-pyrophosphatase enzyme whose activities arise through distinct active sites. Kinetic analyses of kinase and pyrophosphatase parameters are consistent with Vip1 evolving to modulate levels of 1-IP 7 and 1,5-IP 8 . Individual perturbations in kinase and pyrophosphatase activities in cells result in differential effects on vacuolar morphology and osmotic responses. Analogous to the dual-functional key energy metabolism regulator, phosphofructokinase 2, Vip1 is a kinase and pyrophosphatase switch whose 1-PP-IP products play an important role in a cellular adaptation.

59 BASIC BIOLOGICAL SCIENCES↗

Rewinding evolution in planta: A Rubisco-null platform validates high-performance ancestral enzymes

Improving the photosynthetic enzyme Rubisco is a key target for enhancing C3 crop productivity, but progress has been hampered by the difficulty of evaluating engineered variants in planta without interference from the native enzyme. Here, we report the creation of a Rubisco-null Nicotiana tabacum platform by using CRISPR-Cas9 to knock out all 11 nuclear-encoded small subunit (rbcS) genes. Knockout was achieved in a line expressing cyanobacterial Rubisco from the plastid genome, allowing the recovery of viable plants. We then developed a chloroplast expression system for coexpressing both large and small subunits from the plastid genome. We expressed two resurrected ancestral Rubiscos from the Solanaceae family. The resulting transgenic plants were phenotypically normal and accumulated Rubisco to wild-type levels. Importantly, kinetic analyses of the purified ancestral enzymes revealed they possessed a 16 to 20% higher catalytic efficiency (k cat,air /K c,air ) under ambient conditions, driven by a significantly faster turnover rate (k cat,air ). We have demonstrated that our system allows robust in vivo assessment of novel Rubiscos and that ancestral reconstruction is a powerful strategy for identifying superior enzymes to improve photosynthesis in C3 crops.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates

Inositol pyrophosphates (PP-InsPs) are “energetic” intracellular signals that are ubiquitous in animals, plants, and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35-Å-resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae and a member of the protein tyrosine-phosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. Iin this work, we demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2-Å-deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively charged PP-InsPs. (a) The catalytic P-loop with the CX 5 R(S/T) PTP motif contains additional, positively charged residues. (b) A loop between the $α$5 and $α$6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that extend into the catalytic pocket due to displacement of the $α$5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues. (c) The general-acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.

59 BASIC BIOLOGICAL SCIENCES↗

Compatibility of Type 304H Stainless Steel in Static Molten FLiBe for Inertial Confinement Fusion Reactors: Role of Impurities and Redox Control

Molten fluoride salts, such as FLiBe (LiF-BeF2), are promising candidates for tritium breeding and heat transfer in fusion reactors, but corrosion of structural materials remains a major challenge. This study investigates the corrosion behavior of austenitic stainless steel 304H in purified and NiF2-containing FLiBe at 500°C and 600°C, focusing on the effects of impurities and redox control. Exposure to purified FLiBe resulted in the concurrent depletion of Cr, Mn, and Fe, with corrosion at 500 °C dominated by the combined oxide formation and elemental dissolution, while at 600°C elemental depletion was predominant. The addition of a controlled NiF2 impurity significantly accelerated corrosion at both temperatures, demonstrating the sensitivity of 304H to the salt redox state. Beryllium additions were effective in mitigating corrosion for both baseline and NiF2-containing FLiBe; minimal depletion of Cr, Mn, and Fe occurred with Be additions as low as 2.5 mg (147 wppm), and no NiBe intermetallics formed at 5 mg (294 wppm), indicating that small Be inventories can provide substantial protection without deleterious phase formation. Thermodynamic equilibrium and coupled thermodynamic-kinetic analyses at the salt-alloy interface suggested low corrosion rates in systems with limited hydrogen fluoride (HF) generation, highlighting the importance of salt redox control. Estimates for a Be addition rate were calculated for the HYLIFE-II fusion reactor that can mitigate corrosion-induced degradation, assuming complete conversion of tritium to tritium fluoride (TF). Overall, 304H shows reasonable compatibility with FLiBe under optimized redox conditions. These results provide quantitative guidance for material selection and salt management in fusion blanket and heat exchanger systems and motivate validation under flowing, nonisothermal, and irradiated conditions.

Pillai, Rishi [ORNL] (ORCID:0000000243688197)↗

1D modeling of plasma streamers at ammonia-air flame conditions

Abstract Self-consistent 1D modeling of streamers in ammonia-oxygen-nitrogen-water mixtures has been performed in this work. A fluid model that includes species transport, electrostatic potential, and detailed chemistry was developed and verified. This model is then used to simulate the avalanche, streamer formation and propagation phases, driven by a nanosecond voltage pulse, at different thermochemical conditions derived from a 1D laminar premixed ammonia-air flame. The applicability of the Meek’s criterion in predicting the streamer inception location was successfully confirmed. Streamer formation and propagation duration were found to vary significantly with different thermochemical conditions, due to the difference in ionization rates. The thermochemical state also affected the breakdown characteristics which was tested by maintaining the background reduced electric field constant. Detailed kinetic analyses revealed the importance of O ( 1 D ) in the production of key radicals, such as O, OH, and NH 2 . Furthermore, the contributions of the dissociative electronic excitation of NH 3 towards the production of H and NH 2 radicals have also been reported. Spatial and temporal evolution of the electron energy loss fractions for various inelastic collision processes at different thermochemical states uncovered the input plasma energy spent of fuel dissociation and the large variability in the dominant processes during the avalanche and streamer propagation phases. The methodology and analyses reported in this work are key towards developing effective strategies for controlled nanosecond-pulsed non-equilibrium plasma sources used for ammonia ignition and flame stabilization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

ABSTRACT Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosA KP ). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosA KP were also compared to those of FosA from Pseudomonas aeruginosa (FosA PA ), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosA KP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosA PA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosA KP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosA KP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosA KP and FosA3 than in FosA PA , and kinetic analyses of FosA KP and FosA PA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.

Klontz, Erik H.↗

A Rapid Compression Machine Study of 2-Phenylethanol Autoignition at Low-To-Intermediate Temperatures

To meet the increasing anti-knocking quality demand of boosted spark-ignition engines, fuel additives are considered an effective approach to tailor fuel properties for satisfying the performance requirements. Thus, screening/developing bio-derived fuel additives that are best-suited for advanced spark-ignition engines has become a significant task. 2-Phenylethanol (2-PE) is an attractive candidate that features high research octane number, high octane sensitivity, low vapor pressure, and high energy density. Recognizing that the low temperature autoignition chemistry of 2-PE is not well understood and the need for fundamental experimental data at engine-relevant conditions, rapid compression machine (RCM) experiments are therefore conducted herein to measure ignition delay times (IDTs) of 2-PE in air over a wide range of conditions to fill this fundamental void. These newly acquired IDT data at low-to-intermediated temperatures, equivalence ratios of 0.35–1.5, and compressed pressures of 10–40 bar are then used to validate the 2-PE model developed by Shankar et al. (2017). It is found that this literature model greatly overpredicts the current RCM data. The comparison of experimental and simulated results also provides insights into 2-PE autoignition behaviors at varying conditions. Further chemical kinetic analyses demonstrate that the absence of the O2-addition pathway of β-R. radical in the 2-PE model of Shankar et al. (2017) could account for the model discrepancies observed at low-to-intermediated temperatures.

Fang, Ruozhou (ORCID:0000000348315100)↗

Investigation of evolution-related aspects of bacterial rhodopsins

We have investigated evolution-related aspects of bacterial rhodopsins, the unique retinal-based energy transducing systems of halophilic archae. The approach was to describe both structural and functional aspects: the structure by sequencing genes to explore which regions are conserved, and the function by comparing proton and chloride transport in the closely related systems, bacteriorhodopsin and halorhodopsin, respectively. In the latter, we have made a good start toward the ultimate goal of separating the attributes of the general principles of retinal-based ionic pumps from those of the specific ion specificities, by determining the thermodynamics of the internal steps of the protein-mediated active transport process, as well as some of the intraprotein ion-transfer steps. Our present emphasis is on continuing to acquire the tools for studying what distinguishes proton transport from chloride transport. We consider it important, therefore, that we have been able to provide firm mathematical grounds for the kinetics analyses which underlies these studies. Our molecular biological studies have received a great boost from the expression vector for the bop gene based on a halobacterial plasmid, that we recently developed.

Source record↗

Ecophysiological Characteristics of Obligate Methanotrophic Bacteria and Methane Oxidation In Situ

Most of the obligate methane-oxidizing bacteria (MOB) described to date are neutrophilic mesophiles that grow optimally in dilute media. Kinetic analyses generally indicate that bacterial methane uptake occurs by transport systems with a K(sub m) greater than l micronM. These and other properties of MOB are inconsistent with characteristics of methane oxidation in situ. The inconsistencies indicate a need for greater attention to the ecophysiological characteristics of isolates and the design of enrichment and isolation schemes which emphasize ecologically relevant parameters (e.g., low temperature, limited and diverse substrate availability, low water potential).

King, Gary M.↗

Time-Resolved O3 Chemical Chain Reaction Kinetics Via High-Resolution IR Laser Absorption Methods

Excimer laser photolysis in combination with time-resolved IR laser absorption detection of OH radicals has been used to study O3/OH(v = 0)/HO2 chain reaction kinetics at 298 K, (i.e.,(k(sub 1) is OH + 03 yields H02 + 02 and (k(sub 2) is H02 + 03 yields OH + 202). From time-resolved detection of OH radicals with high-resolution near IR laser absorption methods, the chain induction kinetics have been measured at up to an order of magnitude higher ozone concentrations ([03] less than or equal to 10(exp 17) molecules/cu cm) than accessible in previous studies. This greater dynamic range permits the full evolution of the chain induction, propagation, and termination process to be temporally isolated and measured in real time. An exact solution for time-dependent OH evolution under pseudo- first-order chain reaction conditions is presented, which correctly predicts new kinetic signatures not included in previous OH + 03 kinetic analyses. Specifically, the solutions predict an initial exponential loss (chain "induction") of the OH radical to a steady-state level ([OH](sub ss)), with this fast initial decay determined by the sum of both chain rate constants, k(sub ind) = k(sub 1) + k(sub 2). By monitoring the chain induction feature, this sum of the rate constants is determined to be k(sub ind) = 8.4(8) x 10(exp -14) cu cm/molecule/s for room temperature reagents. This is significantly higher than the values currently recommended for use in atmospheric models, but in excellent agreement with previous results from Ravishankara et al.

Kulcke, Axel↗

Non-unity molecular heritability demonstrated by continuous evolution in vitro

INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

Non-NASA Center↗

In-situ Measurements of the Radiolytic Destruction of Glycine in Ices: Applications to the Martian Subsurface

Amino acids and other organic molecules are thought to be easily destroyed on the surface of Mars by the high flux of incident ultraviolet rays or by chemical interactions with oxidizing substances in the soil. However, organic molecules may survive in the subsurface, where chemical processes are driven by penetrating galactic cosmic rays such as MeV protons. Models of the radiation dose as a function of depth on Mars have shown that the contribution of galactic cosmic rays dominates from about one centimeter to a few meters [1 J. Theoretical models have also been published to aid in understanding molecular destruction at these depths, but these usually are based on room-temperature laboratory data, studies of single-component samples, and ex-situ methods of chemical analysis. Recent studies of amino-acid survivability include those involving UV photolysis [2, 3J and gamma radiolysis [4], but nearly all chemical and kinetic analyses from such experiments involved room-temperature measurements on samples irradiated and then removed from sealed containers. We report new laboratory studies of the radiation-induced destruction of glycine-containing ices. In-situ infrared spectroscopy was used to study decay rates as a function of temperature and initial glycine concentrations. Our results indicate that glycine's destruction rate depends on temperature, the presence of H20-ice, and the initial relative abundance of glycine. These trends are not obvious in previous work, suggesting that room-temperature measurements on pure glycine's radiation stability are not directly applicable to Mars and other environments.

Gerakines, Perry A.↗

Evaluating the De Hoffmann-Teller Cross-Shock 2 Potential at Real Collisionless Shocks

Shock waves are common in the heliosphere and beyond. The collisionless nature of most astrophysical plasmas allows for the energy processed by shocks to be partitioned amongst particle sub-populations and electromagnetic fields via physical mechanisms that are not well understood. The electrostatic potential across such shocks is frame dependent. In a frame where the incident bulk velocity is parallel to the magnetic field, the deHoffmann-Teller frame, the potential is linked directly to the ambipolar electric field established by the electron pressure gradient. Thus measuring and understanding this potential solves the electron partition problem, and gives insight into other competing shock processes. Integrating measured electric fields in space is problematic since the measurements can have offsets that change with plasma conditions. The offsets, once integrated, can be as large or larger than the shock potential. Here we exploit the high-quality field and plasma measurements from NASA’s Magnetospheric Multiscale mission to attempt this calculation. We investigate recent adaptations of the deHoffmann-Teller frame transformation to include time variability, and conclude that in practice these face difficulties inherent in the 3D time-dependent nature of real shocks by comparison to 1D simulations. Potential estimates based on electron fluid and kinetic analyses provide the most robust measures of the deHoffmann-Teller potential, but with some care direct integration of the electric fields can be made to agree. These results suggest that it will be difficult to independently assess the role of other processes, such as scattering by shock turbulence, in accounting for the electron heating.

Steven J Schwartz↗

HCV kinetic and modeling analyses indicate similar time to cure among sofosbuvir combination regimens with daclatasvir, simeprevir or ledipasvir

Recent clinical trials of direct-acting-antiviral agents (DAAs) against hepatitis C virus (HCV) achieved >90% sustained virological response (SVR) rates, suggesting that cure often took place before the end of treatment (EOT). We sought to evaluate retrospectively whether early response kinetics can provide the basis to individualize therapy to achieve optimal results while reducing duration and cost. 58 chronic HCV patients were treated with 12-week sofosbuvir + simeprevir (n = 19), sofosbuvir + daclatasvir (n = 19), or sofosbuvir + ledipasvir in three French referral centers. HCV was measured at baseline, day 2, every other week, EOT and 12 weeks post EOT. Furthermore, mathematical modeling was used to predict the time to cure, i.e., <1 virus copy in the entire extracellular body fluid. All but one patient who relapsed achieved SVR. Mean age was 60 ± 11 years, 53% were male, 86% HCV genotype-1, 9% HIV coinfected, 43% advanced fibrosis (F3), and 57% had cirrhosis. At weeks 2, 4 and 6, 48%, 88% and 100% of patients had HCV <15 IU/ml, with 27%, 74% and 91% of observations having target not detected, respectively. Modeling results predicted that 23 (43%), 16 (30%), 7 (13%), 5 (9%) and 3 (5%) subjects were predicted to reach cure within 6, 8, 10, 12 and 13 weeks of therapy, respectively. The modeling suggested that the patient who relapsed would have benefitted from an additional week of sofosbuvir + ledipasvir. Adjusting duration of treatment according to the modeling predicts reduced medication costs of 43–45% and 17–30% in subjects who had HCV <15 IU/ml at weeks 2 and 4, respectively. Finally, the use of early viral kinetic analysis has the potential to individualize duration of DAA therapy with a projected average cost saving of 16–20% per 100-treated persons.

59 BASIC BIOLOGICAL SCIENCES↗

Chemical kinetic interactions and sensitivity analyses for 2-ethylhexyl nitrate-doped PRF91 using a reduced mechanism

A numerical and experimental investigation about the chemical kinetic interactions between 2-ethylhexylnitrate (EHN) and PRF91 was performed in this study. Rapid compression machine experiments were conducted to investigate the effect of EHN on the autoignition reactivity of the fuel, and a reduced chemical kinetic mechanism was developed including an EHN sub-model. Experiments showed that the ignition delay decreases as the fuel is doped with EHN, but the effect of the doping level of EHN on the ignition is highly non-linear. Moreover, experiments showed that the EHN effectiveness is lowest during the transition between the low-temperature regime and the negative temperature coefficient (NTC) regime, and it rapidly increases as the temperature increases. Both detailed and (developed) reduced mechanisms were validated against the experimental results, allowing a more in-depth EHN-fuel chemistry study. Additionally, ignition delay sensitivity and EHN effectiveness sensitivity analyses were performed with the reduced mechanism to identify the reactions that control the interaction between EHN and the fuel. As the result, EHN thermal decomposition is only relevant for very low temperatures. The chemistry of EHN-doped fuel is more sensitive to intermediate temperature reactions than that of straight fuel, especially at lower temperatures, due to the effect of EHN on the NTC behavior of the fuel. Finally, the chemistry of EHN-doped fuel is very sensitive to NO 2 -to-NO reactions, especially at high temperatures, because these reactions transform the NO 2 generated by EHN into NO, which is a very effective fuel reactivity enhancer.

2-ethylhexyl nitrate↗