OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration ...algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.
The preharvest drainage of rice paddy fields during the grain filling stage can result in a substantial mobilization of Cd in soil and, consequently, elevated grain Cd concentration. However, the ...processes controlling the mobilization of Cd remains poorly understood. Using 12 field-contaminated paddy soils, we investigated the factors controlling the temporal changes in Cd solubility in paddy soils that were incubated anaerobically for 40 d followed by a 20 d oxidation period. Soluble and extractable Cd concentrations decreased rapidly upon flooding but increased during the oxidation phase, with Cd solubility (aqueous Cd/soil Cd) largely depending upon porewater pH. Furthermore, inhibiting sulfate reduction or inhibiting oxidation dissolution of Cd-sulfides had little or no effect on the mobilization of Cd in the subsequent oxidation phase. Both sequential extraction and X-ray absorption spectroscopy (XAS) analyses revealed that changes in Cd solubility were largely dependent upon the transformation of Cd between the Fe–Mn (oxyhydro)oxide fraction and exchangeable fraction. Mobilization of Cd upon soil drainage was caused by a decrease in soil pH resulting in the release of Cd from Fe–Mn (oxyhydro)oxides. Taken together, Fe–Mn (oxyhydro)oxides play a critical (and prevalent) role in controlling the mobilization of Cd upon soil drainage in paddy systems.
Radio frequency (RF) energy transfer and harvesting techniques have recently become alternative methods to power the next-generation wireless networks. As this emerging technology enables proactive ...energy replenishment of wireless devices, it is advantageous in supporting applications with quality-of-service requirements. In this paper, we present a comprehensive literature review on the research progresses in wireless networks with RF energy harvesting capability, which is referred to as RF energy harvesting networks (RF-EHNs). First, we present an overview of the RF-EHNs including system architecture, RF energy harvesting techniques, and existing applications. Then, we present the background in circuit design as well as the state-of-the-art circuitry implementations and review the communication protocols specially designed for RF-EHNs. We also explore various key design issues in the development of RF-EHNs according to the network types, i.e., single-hop networks, multiantenna networks, relay networks, and cognitive radio networks. Finally, we envision some open research directions.
Non-nutritive sweeteners (NNSs) are widely used in various food products and soft drinks. There is growing evidence that NNSs contribute to metabolic dysfunction and can affect body weight, glucose ...tolerance, appetite, and taste sensitivity. Several NNSs have also been shown to have major impacts on bacterial growth both in vitro and in vivo. Here we studied the effects of various NNSs on the growth of the intestinal bacterium, E. coli, as well as the gut bacterial phyla Bacteroidetes and Firmicutes, the balance between which is associated with gut health. We found that the synthetic sweeteners acesulfame potassium, saccharin and sucralose all exerted strong bacteriostatic effects. We found that rebaudioside A, the active ingredient in the natural NNS stevia, also had similar bacteriostatic properties, and the bacteriostatic effects of NNSs varied among different Escherichia coli strains. In mice fed a chow diet, sucralose increased Firmicutes, and we observed a synergistic effect on Firmicutes when sucralose was provided in the context of a high-fat diet. In summary, our data show that NNSs have direct bacteriostatic effects and can change the intestinal microbiota in vivo.
Release mechanisms of major DAMPs Murao, Atsushi; Aziz, Monowar; Wang, Haichao ...
Apoptosis,
04/2021, Letnik:
26, Številka:
3-4
Journal Article
Recenzirano
Odprti dostop
Damage-associated molecular patterns (DAMPs) are endogenous molecules which foment inflammation and are associated with disorders in sepsis and cancer. Thus, therapeutically targeting DAMPs has ...potential to provide novel and effective treatments. When establishing anti-DAMP strategies, it is important not only to focus on the DAMPs as inflammatory mediators but also to take into account the underlying mechanisms of their release from cells and tissues. DAMPs can be released passively by membrane rupture due to necrosis/necroptosis, although the mechanisms of release appear to differ between the DAMPs. Other types of cell death, such as apoptosis, pyroptosis, ferroptosis and NETosis, can also contribute to DAMP release. In addition, some DAMPs can be exported actively from live cells by exocytosis of secretory lysosomes or exosomes, ectosomes, and activation of cell membrane channel pores. Here we review the shared and DAMP-specific mechanisms reported in the literature for high mobility group box 1, ATP, extracellular cold-inducible RNA-binding protein, histones, heat shock proteins, extracellular RNAs and cell-free DNA.
The homeostatic link between oxidative stress and autophagy plays an important role in cellular responses to a wide variety of physiological and pathological conditions. However, the regulatory ...pathway and outcomes remain incompletely understood. Here, we show that reactive oxygen species (ROS) function as signaling molecules that regulate autophagy through ataxia‐telangiectasia mutated (ATM) and cell cycle checkpoint kinase 2 (CHK2), a DNA damage response (DDR) pathway activated during metabolic and hypoxic stress. We report that CHK2 binds to and phosphorylates Beclin 1 at Ser90/Ser93, thereby impairing Beclin 1‐Bcl‐2 autophagy‐regulatory complex formation in a ROS‐dependent fashion. We further demonstrate that CHK2‐mediated autophagy has an unexpected role in reducing ROS levels via the removal of damaged mitochondria, which is required for cell survival under stress conditions. Finally, CHK2−/− mice display aggravated infarct phenotypes and reduced Beclin 1 p‐Ser90/Ser93 in a cerebral stroke model, suggesting an in vivo role of CHK2‐induced autophagy in cell survival. Taken together, these results indicate that the ROS‐ATM‐CHK2‐Beclin 1‐autophagy axis serves as a physiological adaptation pathway that protects cells exposed to pathological conditions from stress‐induced tissue damage.
Synopsis
Whether hypoxia and nutrient starvation are coupled to cellular autophagy remains unclear. Here, DNA damage response kinases ATM and CHK2 are shown to trigger autophagy in response to reactive oxygen species (ROS) accumulation, suggesting a novel physiological adaptation pathway toward metabolic stress.
Depletion of CHK2 or ATM impairs oxidative stress‐induced autophagy in MEFs.
CHK2 binds and phosphorylates Beclin1 at Ser90/Ser93, suppressing Beclin1‐Bcl‐2 autophagy regulatory complex formation.
CHK2‐induced autophagy limits intracellular ROS levels by clearing damaged mitochondria.
CHK2‐induced autophagy protects against cell death and tissue damage following cerebral ischemia.
ROS accumulation activates protective autophagy to prevent stress‐induced tissue damage.
Sensitivity and pressure range are two significant parameters of pressure sensors. Existing pressure sensors have difficulty achieving both high sensitivity and a wide pressure range. Therefore, we ...propose a new pressure sensor with a ternary nanocomposite Fe
O
/C@SnO
. The sea urchin-like Fe
O
structure promotes signal transduction and protects Fe
O
needles from mechanical breaking, while the acetylene carbon black improves the conductivity of Fe
O
. Moreover, one part of the SnO
nanoparticles adheres to the surfaces of Fe
O
needles and forms Fe
O
/SnO
heterostructures, while its other part disperses into the carbon layer to form SnO
@C structure. Collectively, the synergistic effects of the three structures (Fe
O
/C, Fe
O
/SnO
and SnO
@C) improves on the limited pressure response range of a single structure. The experimental results demonstrate that the Fe
O
/C@SnO
pressure sensor exhibits high sensitivity (680 kPa
), fast response (10 ms), broad range (up to 150 kPa), and good reproducibility (over 3500 cycles under a pressure of 110 kPa), implying that the new pressure sensor has wide application prospects especially in wearable electronic devices and health monitoring.
A
bstract
The anomalous magnetic moments of the electron and the muon are interesting observables, since they can be measured with great precision and their values can be computed with excellent ...accuracy within the Standard Model (SM). The current experimental measurement of this quantities show a deviation of a few standard deviations with respect to the SM prediction, which may be a hint of new physics. The fact that the electron and the muon masses differ by two orders of magnitude and the deviations have opposite signs makes it difficult to find a common origin of these anomalies. In this work we introduce a complex singlet scalar charged under a Peccei-Quinn-like (PQ) global symmetry together with the electron transforming chirally under the same symmetry. In this realization, the CP-odd scalar couples to electron only, while the CP-even part can couple to muons and electrons simultaneously. In addition, the CP-odd scalar can naturally be much lighter than the CP-even scalar, as a pseudo-Goldstone boson of the PQ-like symmetry, leading to an explanation of the suppression of the electron anomalous magnetic moment with respect to the SM prediction due to the CP-odd Higgs effect dominance, as well as an enhancement of the muon one induced by the CP-even component.
Nitrogen (N) deposition is impacting the services that ecosystems provide to humanity. However, the mechanisms determining impacts on the N cycle are not fully understood. To explore the mechanistic ...underpinnings of N impacts on N cycle processes, we reviewed and synthesised recent progress in ecosystem N research through empirical studies, conceptual analysis and model simulations. Experimental and observational studies have revealed that the stimulation of plant N uptake and soil retention generally diminishes as N loading increases, while dissolved and gaseous losses of N occur at low N availability but increase exponentially and become the dominant fate of N at high loading rates. The original N saturation hypothesis emphasises sequential N saturation from plant uptake to soil retention before N losses occur. However, biogeochemical models that simulate simultaneous competition for soil N substrates by multiple processes match the observed patterns of N losses better than models based on sequential competition. To enable better prediction of terrestrial N cycle responses to N loading, we recommend that future research identifies the response functions of different N processes to substrate availability using manipulative experiments, and incorporates the measured N saturation response functions into conceptual, theoretical and quantitative analyses.
Virtual reality is nowadays used to facilitate motor recovery in stroke patients. Most virtual reality studies have involved chronic stroke patients; however, brain plasticity remains good in acute ...and subacute patients. Most virtual reality systems are only applicable to the proximal upper limbs （arms） because of the limitations of their capture systems. Nevertheless, the functional recovery of an affected hand is most difficult in the case of hemiparesis rehabilitation after a stroke. The recently developed Leap Motion controller can track the fine movements of both hands and fingers. Therefore, the present study explored the effects of a Leap Motion-based virtual reality system on subacute stroke. Twenty-six subacute stroke patients were assigned to an experimental group that received virtual reality training along with conventional occupational rehabilitation, and a control group that only received conventional rehabilitation. The Wolf motor func- tion test （WMFT） was used to assess the motor function of the affected upper limb; functional magnetic resonance imaging was used to measure the cortical activation. After four weeks of treatment, the motor functions of the affected upper limbs were significantly improved in all the patients, with the improvement in the experimental group being significantly better than in the control group. The action perfor- mance time in the WMFT significantly decreased in the experimental group. Furthermore, the activation intensity and the laterality index of the contralateral primary sensorimotor cortex increased in both the experimental and control groups. These results confirmed that Leap Motion-based virtual reality training was a promising and feasible supplementary rehabilitation intervention, could facilitate the recovery of motor functions in subacute stroke patients. The study has been registered in the Chinese Clinical Trial Registry （registration number： ChiCTR-OCH- 12002238）.
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