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  1. Charlotte Liu (Ed.)
    Titanium dioxide nanoparticles (TiO2 NPs) have traditionally been utilized as industrial catalysts, finding widespread application in various chemical processes due to their exceptional stability and minimal toxicity. However, quantitatively assessing the reactive sites on TiO2 NPs remains a challenge. In this study, we employed a fluorogenic reaction to probe the apparent reactivity of TiO2 NPs. By manipulating the number of defect sites through control of hydrolysis speed and annealing temperature, we determined that the Ti(Ⅲ) content is positively correlated with the reactivity of TiO2 NPs. Additionally, these Ti(Ⅲ) sites could be introduced by reducing commercial TiO2 NPs using NaBH4. Our findings suggest that fluorogenic oxidation of Amplex Red is an effective method for probing defect site densities on TiO2 NPs. Utilizing single-molecule fluorescence imaging, we demonstrated the ability to map defect site density within TiO2 nanowires. Achieving sub-nanoparticle spatial resolution, we observed significant intraparticle and interparticle variations in the defect site distribution, leading to substantial reactivity heterogeneity. 
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    Free, publicly-accessible full text available May 1, 2025
  2. Abstract

    Atmospheric instability affects the formation of convective storms, but how it has changed during recent decades is unknown. Here we analyze the occurrence frequency of stable and unstable atmospheric conditions over land using homogenized radiosonde data from 1979 to 2020. We show that atmospheric stable (unstable) conditions have decreased (increased) significantly by ∼8%–32% (of time) from 1979 to 2020 over most land areas. In boreal summer, the mean positive buoyancy (i.e., convective available potential energy [CAPE]) also increases over East Asia while mean negative buoyancy (i.e., convective inhibition [CIN]) strengthens over Europe and North America from midnight‐dawn for unstable cases. The increased unstable cases and mean CAPE result from increased low‐level specific humidity and air temperature, which increase the buoyancy of a lifted parcel. The stronger CIN results from decreased near‐surface relatively humidity and decreased lapse rate in the lower troposphere. Our results suggest that the atmosphere has become increasingly unstable, which could lead to more convective storms.

     
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    Free, publicly-accessible full text available October 28, 2024
  3. null (Ed.)
    Abstract Light–moderate precipitation is projected to decrease whereas heavy precipitation may increase under greenhouse gas (GHG)-induced global warming, while atmospheric convective available potential energy (CAPE) over most of the globe and convective inhibition (CIN) over land are projected to increase. The underlying processes for these precipitation changes are not fully understood. Here, projected precipitation changes are analyzed using 3-hourly data from simulations by a fully coupled climate model, and their link to the CAPE and CIN changes is examined. The model approximately captures the spatial patterns in the mean precipitation frequencies and the significant correlation between the precipitation frequencies or intensity and CAPE over most of the globe or CIN over tropical oceans seen in reanalysis, and it projects decreased light–moderate precipitation (0.01 < P ≤ 1 mm h −1 ) but increased heavy precipitation ( P > 1 mm h −1 ) in a warmer climate. Results show that most of the light–moderate precipitation events occur under low-CAPE and/or low-CIN conditions, which are projected to decrease greatly in a warmer climate as increased temperature and humidity shift many of such cases into moderate–high CAPE or CIN cases. This results in large decreases in the light–moderate precipitation events. In contrast, increases in heavy precipitation result primarily from its increased probability under given CAPE and CIN, with a secondary contribution from the CAPE/CIN frequency changes. The increased probability for heavy precipitation partly results from a shift of the precipitation histogram toward higher intensity that could result from a uniform percentage increase in precipitation intensity due to increased water vapor in a warmer climate. 
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  4. Abstract Motivation

    RNA virus populations contain different but genetically related strains, all infecting an individual host. Reconstruction of the viral haplotypes is a fundamental step to characterize the virus population, predict their viral phenotypes and finally provide important information for clinical treatment and prevention. Advances of the next-generation sequencing technologies open up new opportunities to assemble full-length haplotypes. However, error-prone short reads, high similarities between related strains, an unknown number of haplotypes pose computational challenges for reference-free haplotype reconstruction. There is still much room to improve the performance of existing haplotype assembly tools.

    Results

    In this work, we developed a de novo haplotype reconstruction tool named PEHaplo, which employs paired-end reads to distinguish highly similar strains for viral quasispecies data. It was applied on both simulated and real quasispecies data, and the results were benchmarked against several recently published de novo haplotype reconstruction tools. The comparison shows that PEHaplo outperforms the benchmarked tools in a comprehensive set of metrics.

    Availability and implementation

    The source code and the documentation of PEHaplo are available at https://github.com/chjiao/PEHaplo.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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  5. The successful fabrication of black phosphorene (Black-P) in 2014 and subsequent synthesis of layered black As 1−x P x alloys have inspired research into two-dimensional (2D) binary As–P compounds. The very recent success in growing blue phosphorene (Blue-P) further motivated exploration of 2D Blue-AsP materials. Here, using ab initio swarm-intelligence global minimum structure-searching methods, we have obtained a series of novel and energetically favored 2D Blue-AsP (denoted x-AsP, x = I, II, III, IV, V) compounds with As : P = 1 : 1 stoichiometry. They display similar honeycomb structures to Blue-P. Remarkably, the lowest-energy AsP monolayer, namely I-AsP, not only possesses a quasi-direct band gap (2.41 eV), which can be tuned to a direct and optimal gap for photovoltaic applications by in-plane strain, but also has an ultrahigh electronic mobility up to ∼7.4 × 10 4 cm 2 V −1 s −1 , far surpassing that of Blue-P, and also exhibits high absorption coefficients (×10 5 cm −1 ). Our simulations also show that 30 nm-thick I-AsP sheet-based cells have photovoltaic efficiency as high as ∼12%, and the I-AsP/CdSe heterostructure solar cells possess a power conversion efficiency as high as ∼13%. All these outstanding characteristics suggest the I-AsP sheet as a promising material for high-efficiency solar cells. 
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  6. Abstract

    Increases in atmospheric greenhouse gases will not only raise Earth’s temperature but may also change its variability and seasonal cycle. Here CMIP5 model data are analyzed to quantify these changes in surface air temperature (Tas) and investigate the underlying processes. The models capture well the mean Tas seasonal cycle and variability and their changes in reanalysis, which shows decreasing Tas seasonal amplitudes and variability over the Arctic and Southern Ocean from 1979 to 2017. Daily Tas variability and seasonal amplitude are projected to decrease in the twenty-first century at high latitudes (except for boreal summer when Tas variability increases) but increase at low latitudes. The day of the maximum or minimum Tas shows large delays over high-latitude oceans, while it changes little at low latitudes. These Tas changes at high latitudes are linked to the polar amplification of warming and sea ice loss, which cause larger warming in winter than summer due to extra heating from the ocean during the cold season. Reduced sea ice cover also decreases its ability to cause Tas variations, contributing to the decreased Tas variability at high latitudes. Over low–midlatitude oceans, larger increases in surface evaporation in winter than summer (due to strong winter winds, strengthened winter winds in the Southern Hemisphere, and increased winter surface humidity gradients over the Northern Hemisphere low latitudes), coupled with strong ocean mixing in winter, lead to smaller surface warming in winter than summer and thus increased seasonal amplitudes there. These changes result in narrower (wider) Tas distributions over the high (low) latitudes, which may have important implications for other related fields.

     
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  7. Atmospheric convective available potential energy (CAPE) is expected to increase under greenhouse gas–induced global warming, but a recent regional study also suggests enhanced convective inhibition (CIN) over land although its cause is not well understood. In this study, a global climate model is first evaluated by comparing its CAPE and CIN with reanalysis data, and then their future changes and the underlying causes are examined. The climate model reasonably captures the present-day CAPE and CIN patterns seen in the reanalysis, and projects increased CAPE almost everywhere and stronger CIN over most land under global warming. Over land, the cases or times with medium to strong CAPE or CIN would increase while cases with weak CAPE or CIN would decrease, leading to an overall strengthening in their mean values. These projected changes are confirmed by convection-permitting 4-km model simulations over the United States. The CAPE increase results mainly from increased low-level specific humidity, which leads to more latent heating and buoyancy for a lifted parcel above the level of free convection (LFC) and also a higher level of neutral buoyancy. The enhanced CIN over most land results mainly from reduced low-level relative humidity (RH), which leads to a higher lifting condensation level and a higher LFC and thus more negative buoyancy. Over tropical oceans, the near-surface RH increases slightly, leading to slight weakening of CIN. Over the subtropical eastern Pacific and Atlantic Ocean, the impact of reduced low-level atmospheric lapse rates overshadows the effect of increased specific humidity, leading to decreased CAPE.

     
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