A modular, composite framework for the utilization of reduced-scaling Coulomb and exchange construction algorithms: Design and implementation.

Multiple algorithms exist for calculating Coulomb (J) or exchange (K) contributions to Fock-like matrices, and it is beneficial to develop a framework that allows the seamless integration and combination of different J and K construction algorithms. In Psi4, we have implemented the "CompositeJK" formalism for this purpose. CompositeJK allows for the combination of any J and K construction algorithms for any quantum chemistry method formulated in terms of J-like or K-like matrices (including, but not limited to, Hartree-Fock and density functional theory) in a highly modular and intuitive fashion, which is simple to utilize for both developers and users. Using the CompositeJK framework, Psi4 was interfaced to the sn-LinK implementation in the GauXC library, adding the first instance of noncommercial graphics processing unit (GPU) support for the construction of Fock matrix elements to Psi4. On systems with hundreds of atoms, the interface to the CPU sn-LinK implementation displays a higher performance than all the alternative JK construction methods available in Psi4, with up to x2.8 speedups compared to existing Psi4JK implementations. The GPU sn-LinK implementation, harnessing the power of GPUs, improves the observed performance gains to up to x7.0.

Effect of Diabetes on Microvascular Morphology and Permeability of Rat Skeletal Muscle: In Vivo Imaging Using Two-Photon Laser Scanning Microscopy.

This investigation evaluated the microvascular permeability and ultrastructure of skeletal muscle capillaries in skeletal muscle of diabetic (DIA) rats using two-photon laser scanning microscopy (TPLSM) and transmission electron microscopy (TEM). Microvascular permeability was assessed in the tibialis anterior muscle of control (CON) and DIA (streptozocin) male Wistar rats (n = 20, 10-14 wk) by in vivo imaging using TPLSM after fluorescent dye intravenous infusion. Fluorescent dye leakage was quantified to determine microvascular permeability. The ultrastructure was imaged by TEM ex vivo to calculate the size and number of intercellular clefts between capillary endothelial cells and also intracellular vesicles. Compared with control, the volumetrically determined interstitial fluorescent dye leakage, the endothelial cell thickness, and the number of intercellular clefts per capillary perimeter were significantly higher, and the cleft width was significantly narrower in TA of DIA (interstitial fluorescent dye leakage, 2.88 ± 1.40 vs. 10.95 ± 1.41 µm3 x min x 106; endothelial thickness 0.28 ± 0.02 vs. 0.45 ± 0.03 µm; number of intercellular clefts per capillary perimeter 6.3 ± 0.80 vs. 13.6 ± 1.7 /100 µm; cleft width 11.92 ± 0.95 vs. 8.40 ± 1.03 nm, CON vs. DIA respectively, all p <0.05). The size of intracellular vesicles in the vascular endothelium showed an increased proportion of large vesicles in the DIA group compared to the CON group (p < 0.05). Diabetes mellitus enhances the microvascular permeability of skeletal muscle microvessels, due, in part, to a higher density and narrowing of the endothelial intercellular clefts, and larger intracellular vesicles.

Accurate and efficient open-source implementation of domain-based local pair natural orbital (DLPNO) coupled-cluster theory using a t1-transformed Hamiltonian.

We present an efficient, open-source formulation for coupled-cluster theory through perturbative triples with domain-based local pair natural orbitals [DLPNO-CCSD(T)]. Similar to the implementation of the DLPNO-CCSD(T) method found in the ORCA package, the most expensive integral generation and contraction steps associated with the CCSD(T) method are linear-scaling. In this work, we show that the t1-transformed Hamiltonian allows for a less complex algorithm when evaluating the local CCSD(T) energy without compromising efficiency or accuracy. Our algorithm yields sub-kJ mol-1 deviations for relative energies when compared with canonical CCSD(T), with typical errors being on the order of 0.1 kcal mol-1, using our TightPNO parameters. We extensively tested and optimized our algorithm and parameters for non-covalent interactions, which have been the most difficult interaction to model for orbital (PNO)-based methods historically. To highlight the capabilities of our code, we tested it on large water clusters, as well as insulin (787 atoms).

Effects of aging on diaphragm hyperemia and blood flow distribution in male and female Fischer 344 rats.

Aging is associated with inspiratory muscle dysfunction, however, the impact of aging on diaphragm blood flow (BF) regulation, and whether sex-differences exist, is unknown. We tested the hypotheses in young animals, that diaphragm BF and vascular conductance (VC) would be greater in females and that aging would decrease the diaphragm's ability to increase BF with contractions. Young (4-6 months) and old (22-24 months) Fischer-344 rats were divided into four groups: Young Female (YF, n=7), Young Male (YM, n=8), Old Female (OF, n=9), and Old Male (OM, n=9). Diaphragm BF (ml/min/100g) and VC (ml/mmHg/min/100g) were determined, via fluorescent microspheres, at rest and during 1Hz contractions. In YF versus OF, aging blunted the increase in medial costal diaphragm BF (44 ± 5% vs. 16 ± 12%; P < 0.05) and VC (43 ± 7% vs. 21 ± 12%; P < 0.05). Similarly, in YM versus OM, aging blunted the increase in medial costal diaphragm BF (43 ± 6% vs. 24 ± 12%; P < 0.05) and VC (50 ± 6% vs. 34 ± 10%; P < 0.05). Compared to young, dorsal costal diaphragm BF was increased in OF while crural diaphragm BF was increased in OM (P < 0.05). Compared to age-matched females, dorsal costal diaphragm BF was lower in YM and OM (P < 0.05). Aging results in an inability to augment medial costal diaphragm BF and alters regional diaphragm BF distribution in response to muscular contractions. Further, sex differences in regional diaphragm BF are present in young and old animals.

Eccentric contraction increases hydrogen peroxide levels and alters gene expression through Nox2 in skeletal muscle of male mice.

Hydrogen peroxide (H2O2) is one of the key signaling factors regulating skeletal muscle adaptation to muscle contractions. Eccentric (ECC) and concentric (CONC) contractions drive different muscle adaptations with ECC resulting in greater changes. The present investigation tested the hypothesis that ECC produces higher cytosolic and mitochondrial H2O2 concentrations [H2O2] and alters gene expression more than CONC. Cytosolic and mitochondrial H2O2-sensitive fluorescent proteins, HyPer7 and MLS-HyPer7, were expressed in the anterior tibialis muscle of C57BL6J male mice. Before and for 60 min after either CONC or ECC (100 Hz, 50 contractions), [H2O2]cyto and [H2O2]mito were measured by in vivo fluorescence microscopy. RNA sequencing was performed in control (non-contracted), CONC and ECC muscles to identify genes impacted by the contractions. [H2O2]cyto immediately after ECC was greater than after CONC (CONC: + 6%, ECC: + 11% vs rest, p < 0.05) and remained higher for at least 60 min into recovery. In contrast, the elevation of [H2O2]mito was independent of the contraction modes (Time; p < 0.0042, contraction mode; p = 0.4965). The impact of ECC on [H2O2]cyto were abolished by NADPH oxidase 2 (Nox2) inhibition (GSK2795039). Differentially expressed genes were not present after CONC or ECC+GSK but were found after ECC and were enriched for vascular development and apoptosis-related genes, among others. In conclusion, in mouse anterior tibialis ECC, but not CONC, evoke a pronounced cytosolic H2O2 response, caused by Nox2, that is mechanistically linked to gene expression modifications.

Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors.

BACKGROUND: Direct oral factor (F)Xa inhibitors are widely used as alternatives to conventional vitamin K antagonists in managing venous thromboembolism and nonvalvular atrial fibrillation. Unfortunately, bleeding-related adverse events remain a major concern in clinical practice. In case of bleeding or emergency surgery, rapid-onset reversal agents may be required to counteract the anticoagulant activity. OBJECTIVES: The ability of FXa variants to bypass the direct oral FXa inhibitors was assessed. METHODS: Human FXa variants were generated through substitution of phenylalanine 174 (F174) for either alanine, isoleucine, or serine. FXa variants were stably expressed in HEK293 cells and purified to homogeneity using ion-exchange chromatography. RESULTS: F174-substituted human FX variants demonstrated efficacy in restoring thrombin generation in plasma containing direct FXa inhibitors (apixaban, rivaroxaban, edoxaban). Their ability to bypass the anticoagulant effects stems from a significantly reduced sensitivity for the direct FXa inhibitors due to a decrease in binding affinity determined using molecular dynamics simulations and free energy computation. Furthermore, F174 modification resulted in a partial loss of inhibition by tissue factor pathway inhibitor, enhancing the procoagulant effect of F174-substituted FX. Consequently, the F174A- and F174S-substituted FX variants effectively counteracted the effects of 2 widely used anticoagulants, apixaban and rivaroxaban, in plasma of atrial fibrillation and venous thromboembolism patients. CONCLUSION: These human FX variants have the potential to serve as a rescue reversal strategy to overcome the effect of direct FXa inhibitors in case of life-threatening bleeding events or emergency surgical interventions.

Deep Electron Redistributions Induced by Dual Junctions Facilitating Electroreduction of Dilute Nitrate to Ammonia.

The electronic states of metal catalysts can be redistributed by the rectifying contact between metal and semiconductor e.g., N-doped carbon (NC), while the interfacial regulation degree is very limited. Herein, a deep electronic state regulation is achieved by constructing a novel double-heterojunctional Co/Co3O4@NC catalyst containing Co/Co3O4 and Co3O4/NC heterojunctions. When used for dilute electrochemical NO3 - reduction reaction (NO3RR), the as-prepared Co/Co3O4@NC exhibits an outstanding Faradaic efficiency for NH3 formation (FENH3) of 97.9%, -0.4 V versus RHE and significant NH3 yield of 303.5 mmol h-1 gcat -1 at -0.6 V at extremely low nitrate concentrations (100 ppm NO3 --N). Experimental and theoretical results reveal that the dual junctions of Co/Co3O4 and Co3O4/NC drive a unidirectional electron transfer from Co to NC (Co→Co3O4→NC), resulting in electron-deficient Co atoms. The electron-deficient Co promotes NO3 - adsorption, the rate-determining step (RDS) for NO3RR, facilitating the dilute NO3RR to NH3. The design strategy provides a novel reference for unidirectional multistage regulation of metal electronic states boosting electrochemical dilute NO3RR, which opens up an avenue for deep electronic state regulation of electrocatalyst breaking the limitation of the electronic regulation degree by rectifying contact.

Pulmonary hypertension impairs vasomotor function in rat diaphragm arterioles.

Pulmonary hypertension (PH) is a chronic, progressive condition in which respiratory muscle dysfunction is a primary contributor to exercise intolerance and dyspnea in patients. Contractile function, blood flow distribution, and the hyperemic response are altered in the diaphragm with PH, and we sought to determine whether this may be attributed, in part, to impaired vasoreactivity of the resistance vasculature. We hypothesized that there would be blunted endothelium-dependent vasodilation and impaired myogenic responsiveness in arterioles from the diaphragm of PH rats. Female Sprague-Dawley rats were randomized into healthy control (HC, n = 9) and monocrotaline-induced PH rats (MCT, n = 9). Endothelium-dependent and -independent vasodilation and myogenic responses were assessed in first-order arterioles (1As) from the medial costal diaphragm in vitro. There was a significant reduction in endothelium-dependent (via acetylcholine; HC, 78 ± 15% vs. MCT, 47 ± 17%; P < 0.05) and -independent (via sodium nitroprusside; HC, 89 ± 10% vs. MCT, 66 ± 10%; P < 0.05) vasodilation in 1As from MCT rats. MCT-induced PH also diminished myogenic constriction (P < 0.05) but did not alter passive pressure responses. The diaphragmatic weakness, impaired hyperemia, and blood flow redistribution associated with PH may be due, in part, to diaphragm vascular dysfunction and thus compromised oxygen delivery which occurs through both endothelium-dependent and -independent mechanisms.

In vivo heat production dynamics during a contraction-relaxation cycle in rat single skeletal muscle fibers.

Skeletal muscle generates heat via contraction-dependent (shivering) and independent (nonshivering) mechanisms. While this thermogenic capacity of skeletal muscle undoubtedly contributes to the body temperature homeostasis of animals and impacts various cellular functions, the intracellular temperature and its dynamics in skeletal muscle in vivo remain elusive. We aimed to determine the intracellular temperature and its changes within skeletal muscle in vivo during contraction and following relaxation. In addition, we tested the hypothesis that sarcoplasmic reticulum Ca2+ ATPase (SERCA) generates heat and increases the myocyte temperature during a transitory Ca2+-induced contraction-relaxation cycle. The intact spinotrapezius muscle of anesthetized adult male Wistar rats (n = 18) was exteriorized and loaded with the fluorescent probe Cellular Thermoprobe for Fluorescence Ratio (49.3 µM) by microinjection over 1 s. The fluorescence ratio (i.e., 580 nm/515 nm) was measured in vivo during 1) temperature increases induced by means of an external heater, and 2) Ca2+ injection (3.9 nL, 2.0 mM). The fluorescence ratio increased as a linear function of muscle surface temperature from 25 °C to 40 °C (r2 = 0.97, P < 0.01). Ca2+ injection (3.9 nL, 2.0 mM) significantly increased myocyte intracellular temperature: An effect that was suppressed by SERCA inhibition with cyclopiazonic acid (CPA, Ca2+: 38.3 ± 1.4 °C vs Ca2++CPA: 28.3 ± 2.8 °C, P < 0.01 at 1 min following injection). While muscle shortening occurred immediately after the Ca2+ injection, the increased muscle temperature was maintained during the relaxation phase. In this investigation, we demonstrated a novel model for measuring the intracellular temperature of skeletal muscle in vivo and further that heat generation occurs concomitant principally with SERCA functioning and muscle relaxation.

In vivo cytosolic H2O2 changes and Ca2+ homeostasis in mouse skeletal muscle.

Hydrogen peroxide (H2O2) and calcium ions (Ca2+) are functional regulators of skeletal muscle contraction and metabolism. Although H2O2 is one of the activators of the type-1 ryanodine receptor (RyR1) in the Ca2+ release channel, the interdependence between H2O2 and Ca2+ dynamics remains unclear. This study tested the following hypotheses using an in vivo model of mouse tibialis anterior (TA) skeletal muscle. 1) Under resting conditions, elevated cytosolic H2O2 concentration ([H2O2]cyto) leads to a concentration-dependent increase in cytosolic Ca2+ concentration ([Ca2+]cyto) through its effect on RyR1; and 2) in hypoxia (cardiac arrest) and muscle contractions (electrical stimulation), increased [H2O2]cyto induces Ca2+ accumulation. Cytosolic H2O2 (HyPer7) and Ca2+ (Fura-2) dynamics were resolved by TA bioimaging in young C57BL/6J male mice under four conditions: 1) elevated exogenous H2O2; 2) cardiac arrest; 3) twitch (1 Hz, 60 s) contractions; and 4) tetanic (30 s) contractions. Exogenous H2O2 (0.1-100 mM) induced a concentration-dependent increase in [H2O2]cyto (+55% at 0.1 mM; +280% at 100 mM) and an increase in [Ca2+]cyto (+3% at 1.0 mM; +8% at 10 mM). This increase in [Ca2+]cyto was inhibited by pharmacological inhibition of RyR1 by dantrolene. Cardiac arrest-induced hypoxia increased [H2O2]cyto (+33%) and [Ca2+]cyto (+20%) 50 min postcardiac arrest. Compared with the exogenous 1.0 mM H2O2 condition, [H2O2]cyto after tetanic muscle contractions rose less than one-tenth as much, whereas [Ca2+]cyto was 4.7-fold higher. In conclusion, substantial increases in [H2O2]cyto levels evoke only modest Ca2+ accumulation via their effect on the sarcoplasmic reticulum RyR1. On the other hand, contrary to hypoxia secondary to cardiac arrest, increases in [H2O2]cyto from muscle contractions are small, indicating that H2O2 generation is unlikely to be a primary factor driving the significant Ca2+ accumulation after, especially tetanic, muscle contractions.NEW & NOTEWORTHY We developed an in vivo mouse myocyte H2O2 imaging model during exogenous H2O2 loading, ischemic hypoxia induced by cardiac arrest, and muscle contractions. In this study, the interrelationship between cytosolic H2O2 levels and Ca2+ homeostasis during muscle contraction and hypoxic conditions was revealed. These results contribute to the elucidation of the mechanisms of muscle fatigue and exercise adaptation.

Broadening the catalytic region from the cavity to windows by M6L12 nanospheres in cyclizations.

Supramolecular cages have received tremendous attention as they can contain catalysts that exhibit confinement effects in the cavity, leading to excellent performances. Herein, we report an example wherein the catalytic region is extended from the cage cavity to the windows, and investigate its confinement effect by utilizing the Pd6LAu12 cage that contains rigidly fixed and isolated gold complexes at the windows. Pd6LAu12 exhibit three features of particular interest while assessing their properties in gold-catalyzed cyclization reactions. First, the catalysts experience a cage effect as they display higher reactivity and selectivity compared to the monomeric analogue, as a result of substrate pre-organization at the windows. Second, the metal complexes are physically separated by the cage structure, preventing the formation of less active dinuclear gold complexes making it more stable under hydrous conditions. Third, the cage windows present the characteristics of enzymatic catalysis via Michaelis-Menten-type mechanism analysis. This contribution presents an alternative way to engineer supramolecular catalysts through extending the catalytic region.

Pd12MnL24 (for n = 6, 8, 12) nanospheres by post-assembly modification of Pd12L24 spheres.

In this contribution, we describe a post-assembly modification approach to selectively coordinate transition metals in Pd12L24 cuboctahedra. The herein reported approach involves the preparation of Pd12L24 nanospheres with protonated nitrogen donor ligands that are covalently linked at the interior. The so obtained Pd12(LH+)24 nanospheres are shown to be suitable for coordinative post-modification after deprotection by deprotonation. Selective formation of tetra-coordinated MB in Pd12MB6L24, tri-coordinated MB in Pd12MB8L24 nanospheres and two-coordinated MB in Pd12MB12L24 nanospheres is achieved as a result of different nitrogen donor ligands. A combination of pulsed EPR spectroscopy (DEER) to measure Cu-Cu distances in the different spheres, NMR studies and computational investigations, support the presence of the complexes at precise locations of the Pd12MB6L24 nanosphere. The general post-assembly modification methodology can be extended using other transition metal precursors or supramolecular systems and can guide precise formation and investigation of novel transition metal-complex containing nanospheres with well-defined composition.

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures.

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.