Low-loss and broadband wafer-scale optical interposers for large-scale heterogeneous integration.

We design, fabricate, and demonstrate a low-loss and broadband optical interposer with high misalignment tolerance for large-scale integration of many chips using thermal compression flip-chip bonding. The optical interposer achieves flip-chip integration with photonic integrated circuit die containing evanescent couplers with inter-chip coupling loss of 0.54dB and ±3.53µm 3-dB misalignment tolerance. The loss measurement spectrum indicated wavelength-insensitive loss across O-band and C-band with negligible spectral dependence. Further, we demonstrate 1 to 100 wafer-scale equal power splitting using equal power splitters (EPS) and a path length matching design fabricated using a wafer-scale fabrication technique.

Effects of exosomes derived from platelet-rich plasma on osteogenic differentiation of dental pulp stem cells.

Platelet-rich plasma (PRP) can cause osteogenic differentiation of dental pulp stem cells (DPSCs). However, the effect of exosomes derived from PRP (PRP-Exos) on osteogenic differentiation of DPSCs remains unclear. Herein, we evaluated the impact of PRP-Exos on osteogenic differentiation of DPSCs. PRP-Exos were isolated and identified by transmission electron microscopy (TEM) and western blotting (WB). Immunofluorescence staining was performed to evaluate endocytosis of PRP-Exos by DPSCs. Alkaline phosphatase staining, alizarin red staining, western blot and qRT-PCR were carried out to evaluate the DPSCs osteogenic differentiation. The sequencing microRNA (miRNA) was conducted to determine the microRNA profile of PRP-Exos treated and untreated DPSCs. The results showed that endocytosis of PRP-Exos stimulated DPSCs odontogenic differentiation by elevated expression of ALP, DMP-1, OCN, and RUNX2. ALP activity and calcified nodules formation of PRP-Exos treated DPSCs were considerably elevated relative to that of the control group. MicroRNA sequencing revealed that 112 microRNAs considerably varied in PRP-Exos treated DPSCs, of which 84 were elevated and 28 were reduced. Pathway analysis suggested that genes targeted by differentially expressed (DE) miRNAs were contributed to many signaling cascades, such as the Wnt cascade. 65 genes targeted by 30 DE miRNA were contributed to Wnt signaling. Thus, it can be infered that PRP-Exos could enhance osteogenic differentiation and alter the miRNA expression profile of DPSCs.

Imperfect guide-RNA (igRNA) enables CRISPR single-base editing with ABE and CBE.

CRISPR base editing techniques tend to edit multiple bases in the targeted region, which is a limitation for precisely reverting disease-associated single-nucleotide polymorphisms (SNPs). We designed an imperfect gRNA (igRNA) editing methodology, which utilized a gRNA with one or more bases that were not complementary to the target locus to direct base editing toward the generation of a single-base edited product. Base editing experiments illustrated that igRNA editing with CBEs greatly increased the single-base editing fraction relative to normal gRNA editing with increased editing efficiencies. Similar results were obtained with an adenine base editor (ABE). At loci such as DNMT3B, NSD1, PSMB2, VIATA hs267 and ANO5, near-perfect single-base editing was achieved. Normally an igRNA with good single-base editing efficiency could be selected from a set of a few igRNAs, with a simple protocol. As a proof-of-concept, igRNAs were used in the research to construct cell lines of disease-associated SNP causing primary hyperoxaluria construction research. This work provides a simple strategy to achieve single-base base editing with both ABEs and CBEs and overcomes a key obstacle that limits the use of base editors in treating SNP-associated diseases or creating disease-associated SNP-harboring cell lines and animal models.

China's "coal-to-gas" policy had large impact on PM1.0 distribution during 2016-2019.

Particulate matter with an aerodynamic diameter of less than 1 µm (PM1.0) can be extremely hazardous to human health, so it is imperative to accurately estimate the spatial and temporal distribution of PM1.0 and analyze the impact of related policies on it. In this study, a stacking generalization model was trained based on aerosol optical depth (AOD) data from satellite observations, combined with related data affecting aerosol concentration such as meteorological data and geographic data. Using this model, the PM1.0 concentration distribution in China during 2016-2019 was estimated, and verified by comparison with ground-based stations. The coefficient of determination (R2) of the model is 0.94, and the root-mean-square error (RMSE) is 8.49 µg/m3, mean absolute error (MAE) is 4.10 µg/m3, proving that the model has a very high performance. Based on the model, this study analyzed the PM1.0 concentration changes during the heating period (November and December) in the regions where the "coal-to-gas" policy was implemented in China, and found that the proposed "coal-to-gas" policy did reduce the PM1.0 concentration in the implemented regions. However, the lack of natural gas due to the unreasonable deployment of the policy in the early stage caused the increase of PM1.0 concentration. This study can provide a reference for the next step of urban air pollution policy development.

Peripheral Polyfunctional PD1+ CD8+ T cells demonstrated strong immune protection in non-small cell lung cancer.

Higher frequencies of polyfunctional PD1+ CD8+ T cells exhibited a stronger capacity to kill tumor cells in vitro and in vivo experiments. These results suggested that peripheral polyfunctional PD1+ CD8+ T cells demonstrated strong immune protection. This study also provided a potential combined treatment strategy with anti-PD1 and CAR-T therapy.

Chromosome constitution and genetic relationships of Morus spp. revealed by genomic in situ hybridization.

BACKGROUND: Mulberry (Morus spp.) is an economically important woody plant, which has been used for sericulture (silk farming) for thousands of years. The genetic background of mulberry is complex due to polyploidy and frequent hybridization events. RESULTS: Comparative genomic in situ hybridization (cGISH) and self-GISH were performed to illustrate the chromosome constitution and genetic relationships of 40 mulberry accessions belonging to 12 species and three varietas in the Morus genus and containing eight different ploidy levels. We identified six homozygous cGISH signal patterns and one heterozygous cGISH signal pattern using four genomic DNA probes. Using cGISH and self-GISH data, we defined five mulberry sections (Notabilis, Nigra, Wittiorum, and Cathayana, all contained only one species; and Alba, which contained seven closely related species and three varietas, was further divided into two subsections) and proposed the genetic relationships among them. Differential cGISH signal patterns detected in section Alba allowed us to refine the genetic relationships among the closely related members of this section. CONCLUSIONS: We propose that GISH is an efficient tool to investigate the chromosome constitution and genetic relationships in mulberry. The results obtained here can be used to guide outbreeding of heterozygous perennial crops like mulberry.

Targeted C-to-T and A-to-G dual mutagenesis system for RhtA transporter in vivo evolution.

T7 RNA polymerase (T7RNAP) has been fused with cytosine or adenine deaminase individually, enabling in vivo C-to-T or A-to-G transitions on DNA sequence downstream of T7 promoter, and greatly accelerated directed protein evolution. However, its base conversion type is limited. In this study, we created a dual-functional system for simultaneous C-to-T and A-to-G in vivo mutagenesis, called T7-DualMuta, by fusing T7RNAP with both cytidine deaminase (PmCDA1) and a highly active adenine deaminase (TadA-8e). The C-to-T and A-to-G mutagenesis frequencies of T7-DualMuta were 4.02 × 10-3 and 1.20 × 10-2, respectively, with 24 h culturing and distributed mutations evenly across the target gene. The T7-DualMuta system was used to in vivo directed evolution of L-homoserine transporter RhtA, resulting in efficient variants that carried the four types of base conversions by T7-DualMuta. The evolved variants greatly increased the host growth rates at L-homoserine concentrations of 8 g/L, which was not previously achieved, and demonstrated the great in vivo evolution capacity. The novel molecular device T7-DualMuta efficiently provides both C/G-to-T/A and A/T-to-G/C mutagenesis on target regions, making it useful for various applications and research in Enzymology and Synthetic Biology studies. It also represents an important expansion of the base editing toolbox.ImportanceA T7-DualMuta system for simultaneous C-to-T and A-to-G in vivo mutagenesis was created. The mutagenesis frequency was 4.02 × 107 fold higher than the spontaneous mutation, which was reported to be approximately 10-10 bases per nucleotide per generation. This mutant system can be utilized for various applications and research in Enzymology and Synthetic Biology studies.

Reconstructed glycosylase base editors GBE2.0 with enhanced C-to-G base editing efficiency and purity.

Base editing techniques were developed for precise base conversion on cellular genomic DNA, which has great potential for the treatment of human genetic diseases. The glycosylase base editor (GBE) recently developed in our lab was used to perform C-to-G transversions in mammalian cells. To improve the application prospects of GBE, it is necessary to further increase its performance. With this aim, we replaced the human Ung in GBE with Ung1 from Saccharomyces cerevisiae. The resulting editor APOBEC-nCas9-Ung1 was tested at 17 chromosomal loci and was found to have an increased C-to-G editing efficiency ranging from 2.63% to 52.3%, with an average of 23.48%, which was a significant improvement over GBE, with an average efficiency of 15.54%, but with a decreased purity. For further improvement, we constructed APOBEC(R33A)-nCas9-Rad51-Ung1 with two beneficial modifications adapted from previous reports. This base editor was able to achieve even higher editing efficiency ranging from 8.70% to 72.1%, averaging 30.88%, while also exhibiting high C-to-G purity ranging from 35.57% to 92.92%, and was designated GBE2.0. GBE2.0 provides high C-to-G editing efficiency and purity in mammalian cells, making it a powerful genetic tool for scientific research or potential genetic therapies for disease-causing G/C mutations.

The quest for improved air quality may push China to continue its CO2 reduction beyond the Paris Commitment.

China is challenged with the simultaneous goals of improving air quality and mitigating climate change. The "Beautiful China" strategy, launched by the Chinese government in 2020, requires that all cities in China attain 35 µg/m3 or below for annual mean concentration of PM2.5 (particulate matter with aerodynamic diameter less than 2.5 µm) by 2035. Meanwhile, China adopts a portfolio of low-carbon policies to meet its Nationally Determined Contribution (NDC) pledged in the Paris Agreement. Previous studies demonstrated the cobenefits to air pollution reduction from implementing low-carbon energy policies. Pathways for China to achieve dual targets of both air quality and CO2 mitigation, however, have not been comprehensively explored. Here, we couple an integrated assessment model and an air quality model to evaluate air quality in China through 2035 under the NDC scenario and an alternative scenario (Co-Benefit Energy [CBE]) with enhanced low-carbon policies. Results indicate that some Chinese cities cannot meet the PM2.5 target under the NDC scenario by 2035, even with the strictest end-of-pipe controls. Achieving the air quality target would require further reduction in emissions of multiple air pollutants by 6 to 32%, driving additional 22% reduction in CO2 emissions relative to the NDC scenario. Results show that the incremental health benefit from improved air quality of CBE exceeds 8 times the additional costs of CO2 mitigation, attributed particularly to the cost-effective reduction in household PM2.5 exposure. The additional low-carbon energy polices required for China's air quality targets would lay an important foundation for its deep decarbonization aligned with the 2 °C global temperature target.

Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review.

OBJECTIVES: Patients with hematological malignancies have dynamic changes in oral microbial communities before and after treatment. This narrative review describes the changes in oral microbial composition and diversity, and discusses an oral microbe-oriented strategy for oral disease management. MATERIALS AND METHODS: A literature search was performed in PubMed/Medline, Web of Science, and Embase for articles published between 1980 and 2022. Any articles on the changes in oral microbial communities in patients with hematological malignancies and their effects on disease progression and prognosis were included. RESULTS: Oral sample detection and oral microbial sequencing analysis of patients with hematological malignancies showed a correlation between changes in oral microbial composition and diversity and disease progression and prognosis. The possible pathogenic mechanism of oral microbial disorders is the impairment of mucosal barrier function and microbial translocation. Probiotic strategies, antibiotic strategies, and professional oral care strategies targeting the oral microbiota can effectively reduce the risk of oral complications and the grade of severity in patients with hematological malignancies. CLINICAL RELEVANCE: This review provides dentists and hematologists with a comprehensive understanding of the host-microbe associated with hematologic malignancies and oral disease management advice.

Current Trends in MOF (Metal-Organic Framework) and Metal X-ides.

Metal-organic frameworks (MOFs) are a class of porous two- or three-dimensional infinite structure materials consisting of metal ions or clusters and organic linkers, which are connected via coordination bonds [...].

Integrative proteomics and phosphoproteomics profiling on osteogenic differentiation of periodontal ligament stem cell.

This study aims to elucidate the phosphorylated profile of periodontal ligament stem cells (PDLSCs) osteogenic differentiation, which contributes to the promotion of periodontium regeneration. PDLSCs cultured in the osteogenic induction medium for 14 days were analyzed by proteomics and phosphoproteomics. Potential functions of phosphorylated differentially expressed proteins (DEPs) were annotated and enriched based on Gene Ontology (GO). Furtherly, overlapped DEPs were identified and conducted protein-protein interaction (PPI) network united with the top 20 up/downregulated phosphorylated DEPs. Hub phosphorylated DEPs were analyzed by Cytoscape, and the protein kinase phosphorylation network was predicted by iGPS. Proteomics identified 87 upregulated and 227 downregulated DEPs. Phosphoproteomics identified 460 upregulated and 393 downregulated phosphorylated DEPs, and they were primarily enriched in mitochondrial function and ion-channel related terms. Furthermore, 63 overlapped DEPs were recognized for more accurate predictions. Among the top 10 hub phosphorylated DEPs, only Integrin alpha-5 (ITGA5) expressed upregulated phosphorylation, and half of them belonged to extracellular matrix (ECM) proteins. In addition, numerous kinases corresponding to four interactive hub phosphorylated DEPs were predicted, including Collagen alpha-2(I) (COL1A2), Syndecan-1 (SDC1), Fibrillin-1 (FBN1), and ITGA5. Our findings established a basis for further elucidation of the phosphorylation of PDLSCs osteogenic differentiation, and COL1A2/SDC1/ITGA5/FBN1 phosphorylated network may dominate this process.

Crystalline-Amorphous Ni2 P4 O12 /NiMoOx Nanoarrays for Alkaline Water Electrolysis: Enhanced Catalytic Activity via In Situ Surface Reconstruction.

Water electrolysis affords a promising approach to large-scale hydrogen yield, but its efficiency is restrained by the sluggish water dissociation kinetics. Here, an efficient bifunctional electrocatalyst of in situ formed crystalline nickel metaphosphate on amorphous NiMoOx nanoarrays supported on nickel foam (c-Ni2 P4 O12 /a-NiMoOx /NF) for both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) in alkaline solution is reported. The c-Ni2 P4 O12 /a-NiMoOx /NF can deliver a current density of 10 mA cm-2 at a low potential of 78 mV for HER, and a current density of 20 mA cm-2 at an overpotential of 250 mV for OER. Moreover, it only requires a small cell voltage of 1.55 V at 10 mA cm-2 for robust water splitting with outstanding long-term durability over 84 h. Various spectroscopic studies reveal that in situ surface reconstruction is crucial for the enhanced catalytic activity, where c-Ni2 P4 O12 /a-NiMoOx is transformed into c-Ni2 P4 O12 /a-NiMoO4 during the HER process, and into c-Ni2 P4 O12 /a-NiOOH in the OER process. This work may provide a new strategy for uncovering the catalytic mechanism of crystalline-amorphous catalysts.

A CRISPR-based chromosomal-separation technique for Escherichia coli.

BACKGROUND: Natural life systems can be significantly modified at the genomic scale by human intervention, demonstrating the great innovation capacity of genome engineering. Large epi-chromosomal DNA structures were established in Escherichia coli cells, but some of these methods were inconvenient, using heterologous systems, or relied on engineered E. coli strains. RESULTS: The wild-type model bacterium E. coli has a single circular chromosome. In this work, a novel method was developed to split the original chromosome of wild-type E. coli. With this method, novel E. coli strains containing two chromosomes of 0.10 Mb and 4.54 Mb, and 2.28 Mb and 2.36 Mb were created respectively, designated as E. coli0.10/4.54 and E. coli2.28/2.36. The new chromosomal arrangement was proved by PCR amplification of joint regions as well as a combination of Nanopore and Illumina sequencing analysis. While E. coli0.10/4.54 was quite stable, the two chromosomes of E. coli2.28/2.36 population recombined into a new chromosome (Chr.4.64MMut), via recombination. Both engineered strains grew slightly slower than the wild-type, and their cell shapes were obviously elongated. CONCLUSION: Finally, we successfully developed a simple CRISPR-based genome engineering technique for the construction of multi-chromosomal E. coli strains with no heterologous genetic parts. This technique might be applied to other prokaryotes for synthetic biology studies and applications in the future.

Complete genome sequence of a novel mitovirus isolated from the fungus Fusarium equiseti causing potato dry rot.

In this study, a novel mitovirus was isolated from the fungus Fusarium equiseti causing potato dry rot and tentatively designated as "Fusarium equiseti mitovirus 1" (FeMV1). The full-length genome sequence of FeMV1 consists of 2,459 nucleotides with a predicted A + U content of 69.5%. Using the mold mitochondrial genetic code, an open reading frame (ORF) of 725 amino acids (aa) was predicted to encode an RNA-dependent RNA polymerase (RdRp). The RdRp protein contains six conserved motifs, with the highly conserved GDD in motif IV, and the 5'-untranslated region (UTR) and 3'-UTR of FeMV1 have the potential to fold into stem-loop secondary structures and a panhandle structure, both of which are typical characteristics of members of the family Mitoviridae. Results of a BLASTp search showed that the RdRp aa sequence of FeMV1 shared the highest sequence similarity with that of Fusarium poae mitovirus 2 (FpMV2) (76.84% identity, E-value = 0.0). Phylogenetic analysis based on the complete aa sequence of RdRp further suggested that FeMV1 is a new member of the family Mitoviridae. This is the first report of the complete genome sequence analysis of a mitovirus associated with F. equiseti.

Downregulation of SUN2 promotes metastasis of colon cancer by activating BDNF/TrkB signalling by interacting with SIRT1.

Distant metastasis is the major cause of colon cancer (CC) treatment failure. SAD1/UNC84 domain protein-2 (SUN2) is a key component of linker of the nucleoskeleton and cytoskeleton (LINC) complexes that may be relevant for metastasis in several cancers. Here, we first confirmed that SUN2 levels were significantly lower in primary CC tissues and distant metastasis than in normal colon tissues, and high SUN2 expression predicted good overall survival. Overexpression of SUN2 or knockdown of SUN2 inhibited or promoted cell migration and invasion in vitro, respectively. Moreover, silencing of SUN2 promoted metastasis in vivo. Mechanistically, we showed that SUN2 exerts its tumour suppressor functions by decreasing the expression of brain derived neurotrophic factor (BDNF) to inhibit BDNF/tropomyosin-related kinase B (TrkB) signalling. Additionally, SUN2 associated with SIRT1 and increased the acetylation of methyl-CpG binding protein 2 (MeCP2) to increase its occupancy at the BDNF promoter. Taken together, our findings indicate that SUN2 is a key component in CC progression that acts by inhibiting metastasis and that novel SUN2-SIRT1-MeCP2-BDNF signalling may prove to be useful for the development of new strategies for treating patients with CC. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Rapid Inference of Nitrogen Oxide Emissions Based on a Top-Down Method with a Physically Informed Variational Autoencoder.

Accurate timely estimation of emissions of nitrogen oxides (NOx) is a prerequisite for designing an effective strategy for reducing O3 and PM2.5 pollution. The satellite-based top-down method can provide near-real-time constraints on emissions; however, its efficiency is largely limited by efforts in dealing with the complex emission-concentration response. Here, we propose a novel machine-learning-based method using a physically informed variational autoencoder (VAE) emission predictor to infer NOx emissions from satellite-retrieved surface NO2 concentrations. The computational burden can be significantly reduced with the help of a neural network trained with a chemical transport model, allowing the VAE emission predictor to provide a timely estimation of posterior emissions based on the satellite-retrieved surface NO2 concentration. The VAE emission predictor successfully corrected the underestimation of NOx emissions in rural areas and the overestimation in urban areas, resulting in smaller normalized mean biases (reduced from -0.8 to -0.4) and larger R2 values (increased from 0.4 to 0.7). The interpretability of the VAE emission predictor was investigated using sensitivity analysis by modulating each feature, indicating that NO2 concentration and planetary boundary layer (PBL) height are important for estimating NOx emissions, which is consistent with our common knowledge. The advantages of the VAE emission predictor in efficiency, flexibility, and accuracy demonstrate its great potential in estimating the latest emissions and evaluating the control effectiveness from observations.

RNA-seq Analysis of Rhizoctonia solani AG-4HGI Strain BJ-1H Infected by a New Viral Strain of Rhizoctonia solani Partitivirus 2 Reveals a Potential Mechanism for Hypovirulence.

Rhizoctonia solani partitivirus 2 (RsPV2), in the genus Alphapartitivirus, confers hypovirulence on R. solani AG-1-IA, the causal agent of rice sheath blight. In this study, a new strain of RsPV2 obtained from R. solani AG-4HGI strain BJ-1H, the causal agent of black scurf on potato, wasidentified and designated as Rhizoctonia solani partitivirus 2 strain BJ-1H (RsPV2-BJ). An RNA sequencing analysis of strain BJ-1H and the virus RsPV2-BJ-free strain BJ-1H-VF derived from strain BJ-1H was conducted to investigate the potential molecular mechanism of hypovirulence induced by RsPV2-BJ. In total, 14,319 unigenes were obtained, and 1,341 unigenes were identified as differentially expressed genes (DEGs), with 570 DEGs being down-regulated and 771 being up-regulated. Notably, several up-regulated DEGs were annotated to cell wall degrading enzymes, including ß-1,3-glucanases. Strain BJ-1H exhibited increased expression of ß-1,3-glucanase after RsPV2-BJ infection, suggesting that cell wall autolysis activity in R. solani AG-4HGI strain BJ-1H might be promoted by RsPV2-BJ, inducing hypovirulence in its host fungus R. solani AG-4HGI. To the best of our knowledge, this is the first report on the potential mechanism of hypovirulence induced by a mycovirus in R. solani.

Mimicking atmospheric photochemical modelling with a deep neural network.

Fast and accurate prediction of ambient ozone (O3) formed from atmospheric photochemical processes is crucial for designing effective O3 pollution control strategies in the context of climate change. The chemical transport model (CTM) is the fundamental tool for O3 prediction and policy design, however, existing CTM-based approaches are computationally expensive, and resource burdens limit their usage and effectiveness in air quality management. Here we proposed a novel method (noted as DeepCTM) that using deep learning to mimic CTM simulations to improve the computational efficiency of photochemical modeling. The well-trained DeepCTM successfully reproduces CTM-simulated O3 concentration using input features of precursor emissions, meteorological factors, and initial conditions. The advantage of the DeepCTM is its high efficiency in identifying the dominant contributors to O3 formation and quantifying the O3 response to variations in emissions and meteorology. The emission-meteorology-concentration linkages implied by the DeepCTM are consistent with known mechanisms of atmospheric chemistry, indicating that the DeepCTM is also scientifically reasonable. The DeepCTM application in China suggests that O3 concentrations are strongly influenced by the initialized O3 concentration, as well as emission and meteorological factors during daytime when O3 is formed photochemically. The variation of meteorological factors such as short-wave radiation can also significantly modulate the O3 chemistry. The DeepCTM developed in this study exhibits great potential for efficiently representing the complex atmospheric system and can provide policymakers with urgently needed information for designing effective control strategies to mitigate O3 pollution.

Mastering the D-Band Center of Iron-Series Metal-Based Electrocatalysts for Enhanced Electrocatalytic Water Splitting.

The development of non-noble metal-based electrocatalysts with high performance for hydrogen evolution reaction and oxygen evolution reaction is highly desirable in advancing electrocatalytic water-splitting technology but proves to be challenging. One promising way to improve the catalytic activity is to tailor the d-band center. This approach can facilitate the adsorption of intermediates and promote the formation of active species on surfaces. This review summarizes the role and development of the d-band center of materials based on iron-series metals used in electrocatalytic water splitting. It mainly focuses on the influence of the change in the d-band centers of different composites of iron-based materials on the performance of electrocatalysis. First, the iron-series compounds that are commonly used in electrocatalytic water splitting are summarized. Then, the main factors affecting the electrocatalytic performances of these materials are described. Furthermore, the relationships among the above factors and the d-band centers of materials based on iron-series metals and the d-band center theory are introduced. Finally, conclusions and perspectives on remaining challenges and future directions are given. Such information can be helpful for adjusting the active centers of catalysts and improving electrochemical efficiencies in future works.