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The purpose of this study was to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for the diagnosis of severe respiratory diseases based on interpretation of sequencing results. BALF samples were harvested and used for mNGS as well as microbiological detection. Infectious bacteria or fungi were defined according to relative abundance and number of unique reads. We performed mNGS on 35 BALF samples from 32 patients. The positive rate reached 100% in the mNGS analysis of nine immunocompromised patients. Compared with the culture method, mNGS had a diagnostic sensitivity of 88.89% and a specificity of 74.07% with an agreement rate of 77.78% between these two methods. Compared with the smear method and PCR, mNGS had a diagnostic sensitivity of 77.78% and a specificity of 70.00%. In 13 cases, detection results were positive by mNGS but negative by culture/smear and PCR. The mNGS findings in 11/32 (34.4%) cases led to changes in treatment strategies. Linear regression analysis showed that diversity was significantly correlated with interval between disease onset and sampling. Dynamic changes in reads could indirectly reflect therapeutic effectiveness. BALF mNGS improves sensitivity of pathogen detection and provides guidance in clinical practice. Potential pathogens can be identified based on relative abundance and number of unique reads.

In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing of certain heterochromatin-associated TEs is disrupted by heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or heat conditions obtained through Hi-C analysis, we show here that heat stress causes global rearrangement of the 3D genome in Arabidopsis thaliana . Contacts between pericentromeric regions and distal chromosome arms, as well as proximal intra-chromosomal interactions along the chromosomes, are enhanced. However, interactions within pericentromeres and those between distal intra-chromosomal regions are decreased. Many inter-chromosomal interactions, including those within the KNOT , are also reduced. Furthermore, heat activation of TEs exhibits a high correlation with the reduction of chromosomal interactions involving pericentromeres, the KNOT , the knob, and the upstream and downstream flanking regions of the activated TEs. Together, our results provide insights into the relationship between TE activation and 3D genome reorganization. Heat stress can activate heterochromatin-associated transposon elements (TEs). Here, the authors show that heat stress leads to global rearrangement of 3D genome and TEs activation closely correlates with 3D chromatin organization rearrangement in Arabidopsis .

To accommodate China’s electricity market reforms integrating medium and long-term (MLT) transactions and spot transactions, and to boost renewable energy consumption through the spot market, this paper proposes an optimized cross-provincial electricity trading strategy model based on a two-layer game framework. The proposed model incorporates an MLT green certificate contract decomposition method, enabling nested optimization of green certificate contracts and scheduling plans for cross-provincial power transactions. To encourage broader participation, a bilateral green certificate trading framework is established, which globally optimizes green certificate allocation to increase benefits for market participants. A Nash-Stackelberg game model is introduced to address complex game interactions among multiple participants under the green certificate mechanism and the limitation of assuming complete rationality. The game model combines supply and demand sides with an embedded demand-side evolutionary game. Additionally, an improved Aquila optimization algorithm (IAOA) is developed to accurately calculate electricity supply and demand. The algorithm integrates a Circle chaotic map, Sobol sequence, random walk strategy, and filtering technology to enhance optimization capabilities and manage complex constraints. The algorithm is then embedded with a distributed iterative approach to achieve equilibrium strategies. A real-world case study was conducted to validate the feasibility and effectiveness of the proposed model. The results demonstrate that the proposed approach effectively achieves equilibrium, optimizes trading strategies, and fosters win-win, coordinated development among participants in the cross-provincial electricity market.

Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5. Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.

In order to improve the early age strength of ordinary Portland cement-based materials, many early strength agents were applied in different conditions. Different from previous research, the nano calcium silicate hydrate (C-S-H) particles used in this study were synthesized through the chemical reaction of CaO, SiO2, and H2O under 120 °C using the hydrothermal method, and the prepared nano C-S-H particles were highly crystalized. The influences of different amounts of nano C-S-H particles (0%, 0.5%, 1%, 2% and 3% by weight of cement) on the setting time, compressive strength, and hydration heat of cement paste were studied. The hydration products and microstructure of the cement paste with different additions of nano C-S-H particles were investigated through thermogravimetry-differential thermal analysis (TG-DTA), X-ray powder diffraction (XRD), and scanning electron microscope (SEM) tests. The results show that the nano C-S-H particles could be used as an early strength agent, and the early strength of cement paste can be increased by up to 43% through accelerating the hydration of tricalcium silicate (C3S). However, the addition of more than 2% nano C-S-H particles was unfavorable to the later strength development due to more space being left during the initial accelerated hydration process. It is suggested that the suitable content of the nano C-S-H particles is 0.5%−1% by weight of cement.

Background Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete. Results Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes. Conclusions We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.

Light elicits different growth responses in different organs of plants. These organ-specific responses are prominently displayed during de-etiolation. While major light-responsive components and early signaling pathways in this process have been identified, this information has yet to explain how organ-specific light responses are achieved. Here, we report that members of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) transcription factor family participate in photomorphogenesis and facilitate light-induced cotyledon opening in Arabidopsis (Arabidopsis thaliana). Chromatin immunoprecipitation sequencing and RNA sequencing analyses indicated that TCP4 targets a number of SMALL AUXIN UPREGULATED RNA (SAUR) genes that have previously been shown to exhibit organ-specific, light-responsive expression. We demonstrate that TCP4-like transcription factors, which are predominantly expressed in the cotyledons of both light- and dark-grown seedlings, activate SAUR16 and SAUR50 expression in response to light. Light regulates the binding of TCP4 to the promoters of SAUR14, SAUR16, and SAUR50 through PHYTOCHROME-INTERACTING FACTORs (PIFs). PIF3, which accumulates in etiolated seedlings and its levels rapidly decline upon light exposure, also binds to the SAUR16 and SAUR50 promoters, while suppressing the binding of TCP4 to these promoters in the dark. Our study reveals that the interplay between light-responsive factors PIFs and the developmental regulator TCP4 determines the cotyledon-specific light regulation of SAUR16 and SAUR50, which contributes to cotyledon closure and opening before and after de-etiolation.

As a burgeoning branch of quantum cryptography, quantum key agreement is a kind of key establishing processes where the security and fairness of the established common key should be guaranteed simultaneously. However, the difficulty on designing a qualified quantum key agreement protocol increases significantly with the increase of the number of the involved participants. Thus far, only few of the existing multiparty quantum key agreement (MQKA) protocols can really achieve security and fairness. Nevertheless, these qualified MQKA protocols are either too inefficient or too impractical. In this paper, an MQKA protocol is proposed with single photons in travelling mode. Since only one eavesdropping detection is needed in the proposed protocol, the qubit efficiency and measurement efficiency of it are higher than those of the existing ones in theory. Compared with the protocols which make use of the entangled states or multi-particle measurements, the proposed protocol is more feasible with the current technologies. Security and fairness analysis shows that the proposed protocol is not only immune to the attacks from external eavesdroppers, but also free from the attacks from internal betrayers.

Most chromophores exhibit an aggregation-caused quenching (ACQ) effect, resulting in minimal or weak emission when incorporated into covalent organic frameworks (COFs). Consequently, the development of luminescent COFs, particularly those utilizing ACQ chromophores, presents both a compelling and formidable challenge. Herein, we report the construction of highly emissive ACQ chromophore-based COFs by an energy level matching strategy. This approach effectively modulates the electronic structures within the COFs, thereby suppressing intralayer charge transfer to ACQ chromophores, such as the imine linkage and dibenzo[g,p]chrysene unit, while simultaneously inhibiting interlayer charge transfer and non-radiative decay pathways. As a result, the undesired ACQ effect is mitigated, enabling the realization of highly emissive COFs. Notably, COF-BT-PhDBC demonstrates high brightness with a solid-state photoluminescence quantum yield of 14.7%, standing among the best ACQ chromophore-based COFs. Furthermore, COF-BT-PhDBC has been successfully utilized for in vivo three-photon fluorescence imaging of murine brain vasculature, achieving an impressive imaging depth of approximately 800 µm. As a result of aggregation-caused quenching (ACQ), many fluorophores show only weak emission when incorporated into covalent organic frameworks. Here, the authors report the development of emissive COFs from ACQ chromophores by an energy level matching strategy.

Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis . Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants. The authors employ Micro-C-XL to investigate chromatin structures in plants, specifically focusing on nucleosome-resolution chromatin organizations and enhancer-promoter chromatin loops in Arabidopsis , rice, and soybean.