Exploring transient global transcriptional changes induced by ascorbic acid revealed via atKAS-seq profiling.

Transcription initiates the formation of single-stranded DNA (ssDNA) regions within the genome, delineating transcription bubbles, a highly dynamic genomic process. Kethoxal-assisted single-stranded DNA sequencing (KAS-seq) utilizing N3-kethoxal has emerged as a potent tool for mapping specific guanine positions in ssDNA on a genome-wide scale. However, the original KAS-seq method required the costly Accel-NGS Methyl-seq DNA library kit. This study introduces an optimized iteration of the KAS-seq technique, referred to as adapter-tagged KAS-seq (atKAS-seq), incorporating an adapter tagging strategy. This modification involves integrating sequencing adapters via complementary strand synthesis using random N9 tagging. Additionally, by harnessing the potential of ascorbic acid (ASC), recognized for inducing global epigenetic changes, we employed the atKAS-seq methodology to elucidate critical pathways influenced by short-term, high-dose ASC treatment. Our findings underscore that atKAS-seq enables rapid and precise analyses of transcription dynamics and enhancer activities concurrently. This method offers a streamlined, cost-efficient, and low-input approach, affirming its utility in probing intricate genomic regulatory mechanisms.

The performance of CCSD(T) for the calculation of dipole moments in diatomics.

This work analyzes the accuracy of the coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] method for predicting dipole moments. In particular, we benchmark CCSD(T) predictions for the equilibrium bond length, vibrational frequency, and dipole moment versus accurate experimental data. As a result, we find that CCSD(T) leads to accurate dipole moments. However, in some cases, it disagrees with the experimental values, and the disagreement can not be satisfactorily explained via relativistic or multi-reference effects. Therefore, our results indicate that benchmark studies for energy and geometry properties do not accurately describe other electron density magnitudes.

Molecular dynamics-driven global potential energy surfaces: Application to the AlF dimer.

In this work, we present a full-dimensional potential energy surface for AlF-AlF. We apply a general machine learning approach for full-dimensional potential energy surfaces, employing an active learning scheme trained on ab initio points, whose size grows based on the accuracy required. The training points are selected based on molecular dynamics simulations, choosing the most suitable configurations for different collision energy and mapping the most relevant part of the potential energy landscape of the system. The present approach does not require long-range information and is entirely general. As a result, it is possible to provide the full-dimensional AlF-AlF potential energy surface, requiring ≲0.01% of the configurations to be calculated ab initio. Furthermore, we analyze the general properties of the AlF-AlF system, finding critical differences with other reported results on CaF or bi-alkali dimers.

Comparison of thermal stability of Mo/Si multilayers with different crystallinities of Mo layers.

To investigate the thermal stability of Mo/Si multilayers with different initial crystallinities of Mo layers, two kinds of Mo/Si multilayers were deposited by DC magnetron sputtering and annealed at 300°C and 400°C. The period thickness compactions of multilayers with crystalized and quasi-amorphous Mo layers were 0.15 nm and 0.30 nm at 300°C, respectively, and the stronger the crystallinity, the lower the extreme ultraviolet reflectivity loss. At 400°C, the period thickness compactions of multilayers with crystalized and quasi-amorphous Mo layers were 1.25 nm and 1.04 nm, respectively. It was shown that multilayers with a crystalized Mo layer had better thermal stability at 300°C but were less stable at 400°C than multilayers with a quasi-amorphous Mo layer. These changes in stability at 300°C and 400°C were due to the significant transition of the crystalline structure. The transition of the crystal structure leads to increased surface roughness, more interdiffusion, and compound formation.

AlF-AlF Reaction Dynamics between 200 K and 1000 K: Reaction Mechanisms and Intermediate Complex Characterization.

AlF is a relevant molecule in astrochemistry as a tracer of F-bearing molecules. Additionally, AlF presents diagonal Franck-Condon factors and can be created very efficiently in the lab, which makes it a prototypical molecular for laser cooling. However, very little is known about the reaction dynamics of AlF. In this work, we report on the reaction dynamics of AlF-AlF between 200 and 1000 K using ab initio molecular dynamics and a highly efficient active learning approach for the potential energy surface, including all degrees of freedom. As a result, we identify the main reaction mechanisms and the lifetime of the intermediate complex AlF-AlF relevant to astrochemistry environments and regions in buffer gas cells.

Out-of-plane dipole-modulated photogenerated carrier separation and recombination at Janus-MoSSe/MoS2 van der Waals heterostructure interfaces: an ab initio time-domain study.

Out-of-plane mirror symmetry-breaking provides a powerful tool for engineering the electronic properties and the exciton behavior of two-dimensional materials. Here, by combining time-domain density functional theory with nonadiabatic dynamics, we investigate the underlying mechanism of how the vertical dipole moment modulates the photoexcited carrier transport and the electron-hole recombination dynamics in polar Janus MoSSe/MoS2 stacked heterostructures. It is shown that the stronger nonadiabatic coupling, interlayer-state delocalization and the built-in electric field caused by charge redistribution facilitate a more rapid photocarrier separation across the interface in the S/S stacked bilayer compared with the S/Se bilayer, explaining the experimentally observed stronger photoluminescence quenching effect in the S/S heterostructure. We also found that the photocarrier recombination of the heterostructure with the S/Se interface has a timescale up to nanoseconds, which is ∼4 times longer than that of the S/S bilayer. Such a prolonged recombination time originates from the dipole-weakened nonadiabatic coupling between occupied and unoccupied states instead of quantum coherence and the band gap effect. Overall, Janus MoSSe/MoS2 heterostructures exhibit superior photocatalytic activity, reflecting the ultrafast photocarrier separation triggered by the built-in electric field, suppressed carrier recombination, high solar-to-hydrogen conversion efficiency and the strong absorption coefficient expanding from visible-light to near-infrared-light. The above atomistic and time-domain findings reveal the intrinsic dipole as an effective freedom to regulate the nonadiabatic photocarrier dynamics in Janus-based 2D heterostructures for efficient energy harvesting and optoelectronic applications.

New theoretical insights into the photoinduced carrier transfer dynamics in WS2/WSe2 van der Waals heterostructures.

Shedding light on the dynamics of charge transfer is fundamental and important to understand the light-photocurrent power conversion in transition-metal dichalcogenide (TMD) heterostructures. Herein, based on time-dependent ab initio nonadiabatic molecular dynamics simulation, we studied the photoinduced carrier transfer dynamics in the WS2/WSe2 heterostructure and further analyzed the effects of stacking configuration and temperature. Our calculations show that the time scales of ultrafast hole transfer in the C7 and T stacking configurations are 35 fs and 30 fs, respectively, which are mainly caused by the adiabatic charge transfer mechanism. Meanwhile, the time scales of ultrafast electron transfer in the C7 and T stacking configurations are 12 fs and 40 fs, respectively, which are in good agreement with the experimental result. We also investigated in detail the photoinduced carrier transfer pathways of C7 and T stacking configurations, which appear to have some significant differences. In addition, we found that the temperature basically has no effect on the electron transfer dynamics of the WS2/WSe2 heterostructure; this is in excellent agreement with the experimental observation. In short, the reported findings can provide more in-depth insights into the photoinduced carrier transfer dynamics of TMD-based van der Waals heterostructures.

Complex Reaction Network Thermodynamic and Kinetic Autoconstruction Based on Ab Initio Statistical Mechanics: A Case Study of O2 Activation on Ag4 Clusters.

An approach based on ab initio statistical mechanics is demonstrated for autoconstructing complex reaction networks. Ab initio molecular dynamics combined with Markov state models are employed to study relevant transitions and corresponding thermodynamic and kinetic properties of a reaction. To explore the capability and flexibility of this approach, we present a study of oxygen activation on Ag4 as a model reaction. Specifically, with the same sampled trajectories, it is possible to study the structural effects and the reaction rate of the cited reaction. The results show that this approach is suitable for automatized construction of reaction networks, especially for non-well-studied reactions, which can benefit from this ab initio molecular dynamics based approach to construct comprehensive reaction networks with Markov state models without prior knowledge about the potential energy landscape.

A data-driven approach to determine dipole moments of diatomic molecules.

We present a data-driven approach for the prediction of the electric dipole moment of diatomic molecules, which is one of the most relevant molecular properties. In particular, we apply Gaussian process regression to a novel dataset to show that dipole moments of diatomic molecules can be learned, and hence predicted, with a relative error ⪅5%. The dataset contains the dipole moment of 162 diatomic molecules, the most exhaustive and unbiased dataset of dipole moments up to date. Our findings show that the dipole moment of diatomic molecules depends on atomic properties of the constituents atoms: electron affinity and ionization potential, as well as on (a feature related to) the first derivative of the electronic kinetic energy at the equilibrium distance.

Identification and Free Radical Scavenging Activity of Oligopeptides from Mixed-Distillate Fermented Baijiu Grains and Soy Sauce Residue.

This study aimed to explore the potential antioxidant activity and mechanism of oligopeptides from sauce-aroma Baijiu. The oligopeptides of Val-Leu-Pro-Phe (VLPF), Pro-Leu-Phe (PLF), Val-Gly-Phe-Cys (VGFC), Leu-Tyr-Pro (LYP), Leu-Pro-Phe (LPF), and Phe-Thr-Phe (FTF) were identified by liquid chromatography-mass spectrometry (LC-MS) from the mixed-distillate of Baijiu fermented grains and soy sauce residue (MDFS). The antioxidant mechanism of these oligopeptides on scavenging DPPH•, ABTS•+, and hydroxide radicals was investigated, respectively. Among them, VGFC had the strongest potential antioxidant activity, which was responsible for its hydrogen bonds with these radicals with high affinity. The binding energies between VGFC and these radicals were -1.26 kcal/mol, -1.33 kcal/mol, and -1.93 kcal/mol, respectively. Additionally, free radicals prefer to bind the oligopeptide composed of hydrophobic amino acid residues such as Leu, Val, Phe, and Pro, thus being scavenged for exerting antioxidant activity. It provided a new idea for the development and utilization of bioactive oligopeptides in sauce-aroma Baijiu.

Ascorbic Acid Reprograms Epigenome and Epitranscriptome by Reducing Fe(III) in the Catalytic Cycle of Dioxygenases.

Ascorbic acid (ASC) has been reported to stimulate DNA iterative oxidase ten-eleven translocation (TET) enzymes, Jumonji C-domain-containing histone demethylases, and potentially RNA m6A demethylases FTO and ALKBH5 as a cofactor. Although ascorbic acid has been widely investigated in reprogramming DNA and histone methylation status in vitro, in cultured cells and mouse models, its specific role in the catalytic cycle of dioxygenases remains enigmatic. Here, we systematically investigated the stimulation of ASC toward TET2, ALKBH3, histone demethylases, and FTO. We find that ASC reprograms epitranscriptome by erasing the hypermethylated m6A sites in mRNA. Biochemistry and electron spin resonance assays demonstrate that ASC enters the active pocket of dioxygenases and reduces Fe(III), either incorporated upon protein synthesis or generated upon rebounding the hydroxyl radical during oxidation, into Fe(II). Finally, we propose a remedied model for the catalytic cycle of dioxygenases by adding in the essential cofactor, ASC, which refreshes and regenerates inactive dioxygenase through recycling Fe(III) into Fe(II) in a dynamic "hit-and-run" manner.

Financial inclusion role on energy efficiency financing gaps in COVID-19 period: empirical outcomes of emerging nations.

The structural imposed crises of the COVID-19 have halted the system of financial intermediation at large. By this, the energy sector needs huge financing for energy efficiency maximization in the COVID-19 crises. Thus, the current research aims to inquire the role of financial inclusion in filling the energy efficiency financing gaps for the period of COVID-19 outbreak. The governments of many countries are facing fiscal deficits and trying to survive under tight substantial fiscal limitations. So providing a cheap and efficient energy in modern times, under COVID-19 crises, is merely impossible for many economies because the main source of income for energy sector is the energy users, and having inefficient energy for consumption is raising energy poverty at large. Therefore, COVID-19 crises raised a wide energy financing gap in modern times that needs a fix. However, this research is suggesting the system to make financial inclusion structure as effective, to fill the energy financing gap, for post-COVID-19 time, and to develop a viable and sustainable financing option for energy sector in long-run perspective. This study also validated the empirical role of financial inclusion on energy poverty and energy efficiency, with historical data, to justify the significance of financial inclusion for energy financing gap fulfillment. More so, this paper is also recommending new policy implications for the stakeholders to utilize. We believe if the recommended policy recommendations are considered for practice, the energy financing gap in post-COVID-19 era would be mitigated, and there is a high probability to supply the efficient energy to the end users.

Potentilla sericea stress-responsive spermine synthase PsSPMS enhances cadmium tolerance in Arabidopsis thaliana.

Potentilla sericea is resistant and tolerates rough management. It is an excellent garden groundcover for ecological restoration and soil consolidation for slope protection. Polyamines have functions such as promoting tissue growth and physiological resistance, while spermine synthase catalyzes the production of spermine. The PsSPMS gene from Potentilla sericea was cloned and transformed into Arabidopsis thaliana to study the response of transgenic Arabidopsis thaliana to cadmium stress. The results showed that the contents of spermidine, spermine as well as glutathione were higher in PsSPMS overexpressing Arabidopsis thaliana than the control, while the contents of putrescine were less than the control. Net photosynthetic rate, stomatal conductance, chlorophyll content, water use efficiency, electron transfer rate, PSII-related parameters, proline content, superoxide dismutase, and glutathione reductase activities were higher in PsSPMS overexpressing Arabidopsis thaliana than the control, while malondialdehyde, superoxide anion, and hydrogen peroxide contents were lower than the control. Correlation analysis showed significant differences between the indicators (P < 0.05 and P < 0.01). Expression of AtSPMS, AtSPD3, AtGSH2 and AtGR in transgenic Arabidopsis thaliana was higher than that of the control. Therefore, this study provides a genetic reference for the cultivation of cadmium-tolerant plants through genetic engineering and lays the foundation for further research on cadmium-tolerant Potentilla sericea.

Effects of ATP on the Physicochemical Properties and Cytocompatibility of Calcium Sulfate/Calcium Citrate Composite Cement.

Adenosine triphosphate (ATP), acting as a source of energy, has effects on cellular activities, such as adhesion, proliferation, and differentiation. In this study, ATP-loaded calcium sulfate hemihydrate/calcium citrate tetrahydrate cement (ATP/CSH/CCT) was successfully prepared for the first time. The effect of different contents of ATP on the structure and physicochemical properties of ATP/CSH/CCT was also studied in detail. The results indicated that incorporating ATP into the cement did not significantly alter their structures. However, the addition ratio of ATP directly impacted the mechanical properties and in vitro degradation properties of the composite bone cement. The compressive strength of ATP/CSH/CCT gradually decreased with an increasing ATP content. The degradation rate of ATP/CSH/CCT did not significantly change at low concentrations of ATP, but it increased with a higher ATP content. The composite cement induced the deposition of a Ca-P layer in a phosphate buffer solution (PBS, pH = 7.4). Additionally, the release of ATP from the composite cement was controlled. The ATP was controlled releasing at the 0.5% and 1% ATP in cement by the diffusion of ATP and the degradation of the cement, whereas it was controlled by the diffusion process merely at the 0.1% ATP in cement. Furthermore, ATP/CSH/CCT demonstrated good cytoactivity with the addition of ATP and is expected to be used for the repair and regeneration of bone tissue.

Polarizability characteristics of twisted bilayer graphene quantum dots in the absence of periodic moiré potential.

Recent studies have documented a rich phenomenology in twisted bilayer graphene (TBG), which is significantly relevant to interlayer electronic coupling, in particular to the cases under an applied electric field. While polarizability measures the response of electrons against applied fields, this work adopts a unique strategy of decomposing global polarizability into distributional contributions to access the interlayer polarization in TBG, as a function of varying twisting angles (θ). Through the construction of a model of twisted graphene quantum dots, we assess distributional polarizability at the first-principles level. Our findings demonstrate that the polarizability perpendicular to the graphene plates can be decomposed into intralayer dipoles and interlayer charge-transfer (CT) components, the latter of which provides an explicit measurement of the interlayer coupling strength and charge transfer potential. Our analysis further reveals that interlayer polarizability dominates the polarizability variation during twisting. Intriguingly, the largest interlayer polarizability and CT driven by an external field occur in the misaligned structures with a size-dependent small angle corresponding to the first appearance of AB stacking, rather than the well-recognized Bernal structures. A derived equation is then employed to address the size dependence on the angle corresponding to the largest values in interlayer polarizability and CT. Our investigation not only characterizes the CT features in the interlayer polarizability of TBG quantum dots, but also sheds light on the existence of the strongest interlayer coupling and charge transfer at small twist angles in the presence of an external electric field, thereby providing a comprehensive understanding of the novel properties of graphene-based nanomaterials.

Unraveling the critical role of iron-enriched sludge hydrochar in mediating the Fenton-like oxidation of triclosan.

The traditional Fenton system is subject to the low efficiency of the Fe(III)/Fe(II) conversion cycle, with significant attempts made to improve the oxidation efficiency by overcoming this hurdle. In support of this goal, iron-enriched sludge-derived hydrochar was prepared as a high-efficiency catalyst by one-step hydrothermal carbonization and its performance and mechanisms in mediating the oxidation of triclosan were explored in the present study. The hydrochar prepared at 240 °C for 4 h (HC240-4) had the highest removal of triclosan (97.0%). The removal of triclosan in the HC240-4/H2O2 system was greater than 90% in both acidic and near-neutral environments and remained as high as 83.5% after three cycles, indicating the broad pH applicability and great recycling stability of sludge-derived hydrochar in Fenton-like systems. H2O2 was activated by both persistent free radicals (PFRs; 19.7%) and iron (80.3%). The binding of Fe(III) to carboxyl decreased the electron transfer energy from H2O2 to Fe(III), making its degradation efficiency 2.6 times greater than that of the conventional Fenton reaction. The study provides a way for iron-enriched sludge utilization and reveals a role for hydrochar in promoting iron cycling and electron transfer in the Fenton reaction.

Comparative Study on Microstructure of Mo/Si Multilayers Deposited on Large Curved Mirror with and without the Shadow Mask.

The Mo/Si multilayer mirror has been widely used in EUV astronomy, lithography, microscopy and other fields because of its high reflectivity at the wavelength around 13.5 nm. During the fabrication of Mo/Si multilayers on large, curved mirrors, shadow mask was a common method to precisely control the period thickness distribution. To investigate the effect of shadow mask on the microstructure of Mo/Si multilayers, we deposited a set of Mo/Si multilayers with and without the shadow mask on a curved substrate with aperture of 200 mm by direct current (DC) magnetron sputtering in this work. Grazing incidence X-ray reflectivity (GIXR), diffuse scattering, atomic force microscope (AFM) and X-ray diffraction (XRD) were used to characterize the multilayer structure and the EUV reflectivity were measured at the National Synchrotron Radiation Laboratory (NSRL) in China. By comparing the results, we found that the layer microstructure including interface width, surface roughness, layer crystallization and the reflectivity were barely affected by the mask and a high accuracy of the layer thickness gradient can be achieved.

Revealing carbon-iron interaction characteristics in sludge-derived hydrochars under different hydrothermal conditions.

Hydrothermal conversion is seen as a potential sustainable solution for the disposal and utilization of sewage sludge. One-step hydrothermal carbonization was used to prepare iron-based sludge hydrochars, and the microstructure properties of hydrochars under different hydrothermal conditions were investigated, with emphasis on the inherent interaction mechanisms between carbon and iron. The aromaticity of hydrochars increased with increasing hydrothermal temperature and time, whereas the specific surface area and pore volume as well as magnetic characteristics of hydrochars were only contingent on temperature. Once the temperature reached 160 °C, Fe2O3 in sludge was completely transformed into Fe3O4 in hydrochars. Simulated experiments suggest that glucose is more advantageous than protein in the iron transformation and mesopore formation. The coexistence of glucose, protein, and FeCl3 improved the aromaticity as well as specific surface area and pore volume of hydrochars. This study provides a basis for designing high performance iron-based sludge hydrochars.

Eurobusones A-D, four antibacterial formyl phloroglucinol meoterpenoids from Eucalyptus robusta.

Four antibacterial formyl phloroglucinol meroterpenoids (FPMs), eurobusones A-D (1-4), as well as six known analogues (5-10), were isolated from the leaves of Eucalyptus robusta. Their structures were determined by the analysis of spectroscopic data and electron circular dichroism (ECD) calculation, along with the application of Snatzke helicity rules. Among them, compounds 2 and 8-10 showed good activity against Staphylococcus aureus, Pseudomonas aeruginosa and Bacillus subtilis with MIC50 values less than 1.00 µg/mL.

Impacts of Stressors on Riparian Health Indicators in the Upper and Lower Indus River Basins in Pakistan.

Riparian zones along rivers and streams provide ecosystem services that may change over time as disturbances increase and deteriorate these buffer zones globally. The effect of stressors on ecosystem services along the rivers in underdeveloped countries is unclear, which impacts the environment directly in the form of riparian health indicators (RHIs). This study fills this gap and measures the impact of stressors on RHIs (parameters of habitat, plant cover, regeneration, exotics, and erosion) in the Indus River basin (IRB) in Pakistan. Data on 11 stressors and 27 RHIs were collected using a field-based approach in 269 transects in the upper and lower Indus basins (UIB and LIB) in 2020 and analyzed using multivariate statistical methods. The Kruskal-Wallis tests (p < 0.05) indicated that RHIs varied significantly under the influence of stressors in the UIB and LIB. However, their highest mean values were found in the UIB. Principal component analysis revealed the key RHIs and stressors, which explained 62.50% and 77.10% of the variance, respectively. The Pearson correlation showed that stressors had greater impacts on RHIs in LIB (with r ranging from -0.42 to 0.56). Our results also showed that stressors affected RHI indices with r ranging from -0.39 to 0.50 (on habitat), -0.36 to 0.46 (on plant cover), -0.34 to 0.35 (on regeneration), -0.34 to 0.56 (on erosion), and -0.42 to 0.23 (on exotics). Furthermore, it was confirmed by the agglomerative hierarchical cluster that indices and sub-indices of RHIs and stressors differ across the UIB and LIB. These findings may serve as guidance for managers of large rivers and ecosystem service providers to minimize the environmental impact of stressors in terms of RHIs.