CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism.

MOTIVATION: Due to the varying delivery methods of mRNA vaccines, codon optimization plays a critical role in vaccine design to improve the stability and expression of proteins in specific tissues. Considering the many-to-one relationship between synonymous codons and amino acids, the number of mRNA sequences encoding the same amino acid sequence could be enormous. Finding stable and highly expressed mRNA sequences from the vast sequence space using in silico methods can generally be viewed as a path-search problem or a machine translation problem. However, current deep learning-based methods inspired by machine translation may have some limitations, such as recurrent neural networks, which have a weak ability to capture the long-term dependencies of codon preferences. RESULTS: We develop a BERT-based architecture that uses the cross-attention mechanism for codon optimization. In CodonBERT, the codon sequence is randomly masked with each codon serving as a key and a value. In the meantime, the amino acid sequence is used as the query. CodonBERT was trained on high-expression transcripts from Human Protein Atlas mixed with different proportions of high codon adaptation index codon sequences. The result showed that CodonBERT can effectively capture the long-term dependencies between codons and amino acids, suggesting that it can be used as a customized training framework for specific optimization targets. AVAILABILITY AND IMPLEMENTATION: CodonBERT is freely available on https://github.com/FPPGroup/CodonBERT.

Basic Transcription Factor 3 Like 4 Enhances Malignant Phenotypes through Modulating Tumor Cell Function and Immune Microenvironment in Glioma.

Recent investigations into the tumor microenvironment have provided insights into the limited response of glioma progression to immunotherapy. However, the specific involvement of basic transcription factor 3 like 4 (BTF3L4) in glioma progression and its correlation with immune cell infiltration remain areas of uncertainty that require further exploration. In the current study, BTF3L4 expression was delineated by using gene expression profiling/interactive analysis and multiplex-immunohistologic staining of tissue microarrays. The prognostic value of BTF3L4 was then assessed by using Cox regression models and Kaplan-Meier methods, and in vitro experiments were conducted to investigate how BTF3L4 protein affects the proliferation, migration, and invasion capabilities of glioma cells. Furthermore, the CIBERSORT and ESTIMATE methods were used to quantify immune cells that correlate to BTF3L4 expression, and multiplex-immunohistologic staining was applied to investigate its correlation with infiltrated immune cells in glioma tissues. These findings revealed higher BTF3L4 expression in glioma tissues compared with non-tumor brain tissues, which correlated with clinical characteristics and worse patient prognosis. Furthermore, the down-regulation of BTF3L4 protein in the glioma cell line had a detrimental effect on cell migration, invasion, and proliferation. In addition, the association between BTF3L4 and key immune molecules in glioma, particularly with the infiltration of CD66B+ neutrophils and programmed death ligand 1 expression, was identified. These results highlight the prognostic significance of BTF3L4 and propose BTF3L4 as a potential target for glioma immune therapy.

Double-atom dealloying-derived Frank partial dislocations in cobalt nanocatalysts boost metal-air batteries and fuel cells.

Oxygen reduction reaction (ORR), an essential reaction in metal-air batteries and fuel cells, still faces many challenges, such as exploiting cost-effective nonprecious metal electrocatalysts and identifying their surface catalytic sites. Here we introduce bulk defects, Frank partial dislocations (FPDs), into metallic cobalt to construct a highly active and stable catalyst and demonstrate an atomic-level insight into its surface terminal catalysis. Through thermally dealloying bimetallic carbide (Co3ZnC), FPDs were in situ generated in the final dealloyed metallic cobalt. Both theoretical calculations and atomic characterizations uncovered that FPD-driven surface terminations create a distinctive type of surface catalytic site that combines concave geometry and compressive strain, and this two-in-one site intensively weakens oxygen binding. When being evaluated for the ORR, the catalyst exhibits onset and half-wave potentials of 1.02 and 0.90 V (versus the reversible hydrogen electrode), respectively, and negligible activity decay after 30,000 cycles. Furthermore, zinc-air batteries and H2-O2/air fuel cells built with this catalyst also achieve remarkable performance, making it a promising alternative to state-of-the-art Pt-based catalysts. Our findings pave the way for the use of bulk defects to upgrade the catalytic properties of nonprecious electrocatalysts.

SCARB2 associates with tumor-infiltrating neutrophils and predicts poor prognosis in breast cancer.

BACKGROUND: The tumor microenvironment (TME) plays a crucial role in various aspects of breast cancer development and metastasis. Nevertheless, the expression, prognostic significance, and correlation with clinical features of SCARB2 in breast cancer, as well as the infiltrative characteristics of TME, remain largely unknown. METHODS: We analyzed the differential presentation of SCARB2 mRNA in breast cancer tissues and nontumorous breast tissues and prognosis by The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Additionally, the Tumor Immunity Estimation Resource (TIMER) was taken to evaluate the correlation between SCARB2 mRNA presence and tumor-infiltrating immune cells and immune checkpoints in the TME in breast cancer. We performed multiple immunohistochemical staining to verify the SCARB2 protein expression in breast cancer tissues and its relationship to immune cells and checkpoints and clinicopathological features. RESULTS: We identified elevated SCARB2 expression in breast cancer tissues, and high SCARB2 protein presentation was associated with advanced clinical stage and unfavorable prognosis. In addition, enhanced SCARB2 protein presence was closely correlated with up-regulation CD66b+ neutrophils infiltration in tumor tissues (r = 0.210, P < 0.05) and CD68 + CD163+ M2 macrophages in the interstitium (r = 0.233, P < 0.05), as well as the immune checkpoints, including PD-1 (r = 0.314, P < 0.01) protein expression. CONCLUSION: SCARB2 holds promise for predicting the clinical outcome of breast cancer patients and could serve as a potential therapeutic target.

HCRNet: high-throughput circRNA-binding event identification from CLIP-seq data using deep temporal convolutional network.

Identifying genome-wide binding events between circular RNAs (circRNAs) and RNA-binding proteins (RBPs) can greatly facilitate our understanding of functional mechanisms within circRNAs. Thanks to the development of cross-linked immunoprecipitation sequencing technology, large amounts of genome-wide circRNA binding event data have accumulated, providing opportunities for designing high-performance computational models to discriminate RBP interaction sites and thus to interpret the biological significance of circRNAs. Unfortunately, there are still no computational models sufficiently flexible to accommodate circRNAs from different data scales and with various degrees of feature representation. Here, we present HCRNet, a novel end-to-end framework for identification of circRNA-RBP binding events. To capture the hierarchical relationships, the multi-source biological information is fused to represent circRNAs, including various natural language sequence features. Furthermore, a deep temporal convolutional network incorporating global expectation pooling was developed to exploit the latent nucleotide dependencies in an exhaustive manner. We benchmarked HCRNet on 37 circRNA datasets and 31 linear RNA datasets to demonstrate the effectiveness of our proposed method. To evaluate further the model's robustness, we performed HCRNet on a full-length dataset containing 740 circRNAs. Results indicate that HCRNet generally outperforms existing methods. In addition, motif analyses were conducted to exhibit the interpretability of HCRNet on circRNAs. All supporting source code and data can be downloaded from https://github.com/yangyn533/HCRNet and https://doi.org/10.6084/m9.figshare.16943722.v1. And the web server of HCRNet is publicly accessible at http://39.104.118.143:5001/.

Automated exploitation of deep learning for cancer patient stratification across multiple types.

MOTIVATION: Recent frameworks based on deep learning have been developed to identify cancer subtypes from high-throughput gene expression profiles. Unfortunately, the performance of deep learning is highly dependent on its neural network architectures which are often hand-crafted with expertise in deep neural networks, meanwhile, the optimization and adjustment of the network are usually costly and time consuming. RESULTS: To address such limitations, we proposed a fully automated deep neural architecture search model for diagnosing consensus molecular subtypes from gene expression data (DNAS). The proposed model uses ant colony algorithm, one of the heuristic swarm intelligence algorithms, to search and optimize neural network architecture, and it can automatically find the optimal deep learning model architecture for cancer diagnosis in its search space. We validated DNAS on eight colorectal cancer datasets, achieving the average accuracy of 95.48%, the average specificity of 98.07%, and the average sensitivity of 96.24%, respectively. Without the loss of generality, we investigated the general applicability of DNAS further on other cancer types from different platforms including lung cancer and breast cancer, and DNAS achieved an area under the curve of 95% and 96%, respectively. In addition, we conducted gene ontology enrichment and pathological analysis to reveal interesting insights into cancer subtype identification and characterization across multiple cancer types. AVAILABILITY AND IMPLEMENTATION: The source code and data can be downloaded from https://github.com/userd113/DNAS-main. And the web server of DNAS is publicly accessible at 119.45.145.120:5001.

THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model.

MOTIVATION: Quantitative determination of protein thermodynamic stability is a critical step in protein and drug design. Reliable prediction of protein stability changes caused by point variations contributes to developing-related fields. Over the past decades, dozens of structure-based and sequence-based methods have been proposed, showing good prediction performance. Despite the impressive progress, it is necessary to explore wild-type and variant protein representations to address the problem of how to represent the protein stability change in view of global sequence. With the development of structure prediction using learning-based methods, protein language models (PLMs) have shown accurate and high-quality predictions of protein structure. Because PLM captures the atomic-level structural information, it can help to understand how single-point variations cause functional changes. RESULTS: Here, we proposed THPLM, a sequence-based deep learning model for stability change prediction using Meta's ESM-2. With ESM-2 and a simple convolutional neural network, THPLM achieved comparable or even better performance than most methods, including sequence-based and structure-based methods. Furthermore, the experimental results indicate that the PLM's ability to generate representations of sequence can effectively improve the ability of protein function prediction. AVAILABILITY AND IMPLEMENTATION: The source code of THPLM and the testing data can be accessible through the following links: https://github.com/FPPGroup/THPLM.

A Fluorination Strategy and Low-Acidity Anchoring Group in Self-Assembled Molecules for Efficient and Stable Inverted Perovskite Solar Cells.

Herein, we synthesized two donor-acceptor (D-A) type small organic molecules with self-assembly properties, namely MPA-BT-BA and MPA-2FBT-BA, both containing a low acidity anchoring group, benzoic acid. After systematically investigation, it is found that, with the fluorination, the MPA-2FBT-BA demonstrates a lower highest occupied molecular orbital (HOMO) energy level, higher hole mobility, higher hydrophobicity and stronger interaction with the perovskite layer than that of MPA-BT-BA. As a result, the device based-on MPA-2FBT-BA displays a better crystallization and morphology of perovskite layer with larger grain size and less non-radiative recombination. Consequently, the device using MPA-2FBT-BA as hole transport material achieved the power conversion efficiency (PCE) of 20.32 % and remarkable stability. After being kept in an N2 glove box for 116 days, the unsealed PSCs' device retained 93 % of its initial PCE. Even exposed to air with a relative humidity range of 30±5 % for 43 days, its PCE remained above 91 % of its initial condition. This study highlights the vital importance of the fluorination strategy combined with a low acidity anchoring group in SAMs, offering a pathway to achieve efficient and stable PSCs.

CircBIRC6 facilitates the malignant progression via miR-488/GRIN2D-mediated CAV1-autophagy signal axis in gastric cancer.

Circular RNAs (circRNAs) represent a novel class of non-coding RNAs that play significant roles in tumorigenesis and tumor progression. High-throughput sequencing of gastric cancer (GC) tissues has identified circRNA BIRC6 (circBIRC6) as a potential circRNA derived from the BIRC6 gene, exhibiting significant upregulation in GC tissues. The expression of circBIRC6 is notably elevated in GC patients. Functionally, it acts as a molecular sponge for miR-488, consequently upregulating GRIN2D expression and promoting GC proliferation, migration, and invasion. Moreover, overexpression of circBIRC6 leads to increased GRIN2D expression, which in turn enhances caveolin-1 (CAV1) expression, resulting in autophagy deficiency due to miR-488 sequestration. This cascade of events significantly influences tumorigenesis in vivo. Our findings collectively illustrate that the CircBIRC6-miR-488-GRIN2D axis fosters CAV1 expression in GC cells, thereby reducing autophagy levels. Both circBIRC6 and GRIN2D emerge as potential targets for treatment and independent prognostic factors for GC patients.

Identification of a novel waikavirus infecting Pittosporum tobira in China.

A novel waikavirus, tentatively named "Pittosporum tobira waikavirus" (PtWV), was identified in Pittosporum tobira plants exhibiting mosaic and ringspot symptoms on foliage in Yunnan, China. The full-length genomic sequence was determined by high-throughput sequencing and rapid amplification of cDNA ends. The genome of PtWV is 12,709 nt in length and has a large open reading frame (ORF) of 11,010 nt, encoding a polyprotein, and a small ORF that encodes a 13.2-kDa bellflower vein chlorosis virus (BVCV)-like protein. Phylogenetic analysis and sequence alignment revealed that PtWV is closely related to actinidia yellowing virus 1 (AcYV1), which shares the highest amino acid (aa) sequence similarity (50.1% identity) in the Pro-RdRp region. To the best of our knowledge, this is the first report of a novel waikavirus in P. tobira.

Qingfei Tongluo Mixture Attenuates Bleomycin-Induced Pulmonary Inflammation and Fibrosis through mTOR-Dependent Autophagy in Rats.

As an interstitial fibrosis disease characterized by diffuse alveolitis and structural alveolar disorders, idiopathic pulmonary fibrosis (IPF) has high lethality but lacks limited therapeutic drugs. A hospital preparation used for the treatment of viral pneumonia, Qingfei Tongluo mixture (QFTL), is rumored to have protective effects against inflammatory and respiratory disease. This study aims to confirm whether it has a therapeutic effect on bleomycin-induced IPF in rats and to elucidate its mechanism of action. Male SD rats were randomly divided into the following groups: control, model, CQ + QFTL (84 mg/kg chloroquine (CQ) + 3.64 g/kg QFTL), QFTL-L, M, H (3.64, 7.28, and 14.56 g/kg, respectively) and pirfenidone (PFD 420 mg/kg). After induction modeling and drug intervention, blood samples and lung tissue were collected for further detection. Body weight and lung coefficient were examined, combined with hematoxylin and eosin (H&E) and Masson staining to observe lung tissue lesions. The enzyme-linked immunosorbent assay (ELISA) and the hydroxyproline (HYP) assay kit were used to detect changes in proinflammatory factors (transforming growth factor-ß (TGF-ß), tumor necrosis factor-α (TNF-α), and interleukin-1ß (IL-1ß)) and HYP. Immunohistochemistry and Western blotting were performed to observe changes in proteins related to pulmonary fibrosis (α-smooth muscle actin (α-SMA) and matrix metalloproteinase 12 (MMP12)) and autophagy (P62 and mechanistic target of rapamycin (mTOR)). Treatment with QFTL significantly improved the adverse effects of bleomycin on body weight, lung coefficient, and pathological changes. Then, QFTL reduced bleomycin-induced increases in proinflammatory mediators and HYP. The expression changes of pulmonary fibrosis and autophagy marker proteins are attenuated by QFTL. Furthermore, the autophagy inhibitor CQ significantly reversed the downward trend in HYP levels and α-SMA protein expression, which QFTL improved in BLM-induced pulmonary fibrosis rats. In conclusion, QFTL could effectively attenuate bleomycin-induced inflammation and pulmonary fibrosis through mTOR-dependent autophagy in rats. Therefore, QFTL has the potential to be an alternative treatment for IPF in clinical practice.

First Report of Leek Yellow Stripe Virus Infecting Allium cepa in China.

Onion (Allium cepa), a member of the genus Allium, is widely cultivated throughout the world including China (Zhang et al. 2022). In July 2022, stunted onion (A. cepa 'Weiwang') plants showing typical symptoms of yellow stripe and leaves distortion (Fig. S1) were observed in a vegetable garden in Hohhot, Inner Mongolia, China. The garden is approximately 0.24 ha with around 20,000 onion plants, out of which 140 plants were symptomatic. Diagnosis of the symptomatic plants using negative stain electron microscopy revealed the association of long flexuous virus particles measuring about 11 to 12 nm × 820 to 1000 nm (Fig. S2), which was suggestive of the presence of potyvirus (Chen et al. 2002). Subsequently, the pathogen was identified as the leek yellow stripe virus through RT-PCR combined with Sanger sequencing as described below. The total RNA of each sample was extracted using the MiniBEST plant RNA extraction kit (TaKaRa, Dalian, China), serving as template for synthesis of cDNA using the ABScriptIII RT master mix (ABclonal Biotechnology, Wuhan, China). We then amplified a fragment at the 3' terminus of LYSV using a M5 Hiper superluminal mix (Mei5 Biotechnology, Beijing, China) with the primer pair LYSV-F / LYSV-R (Santosa and Ertunc 2020) which flank the partial NIb gene, the complete coat protein gene and partial 3' untranslated region of LYSV. A unique PCR product of about 1 kb was seen for 10 out of the 140 samples. Five out of the 10 PCR products were randomly selected and cloned using a Zero Background pTOPO-TA cloning kit (Aidlab Technologies, Beijing, China) and E. coli JM109 competent cells were then transformed. Positive colonies were screened by PCR detection of the insert fragments using the primers LYSV-F/-R, and the inserts were sequenced at BGI Genomics (Beijing) using the M13(-21) Forward and M13 Reverse primers. All the obtained sequences were 1032 nt in length, and shared nucleotide sequence identities of 99.2% to 100% (two out of the five sequences were identical to each other). The query sequences were submitted to BLASTn to retrieve homologous sequences from NCBI GenBank databases, and the results showed that the four sequences were homologous to LYSV, suggesting the occurrence of LYSV on onions in Inner Mongolia, China. The sequences were then deposited in GenBank under accession numbers of OQ969953-56, named LYSV isolate Hohhot-1, -2, -3, and -4. In comparison with other published LYSV isolates, the LYSV Hohhot-1, -2, -3, and -4 had the highest nucleotide sequence identity of 87.23%, 86.97%, 87.33%, and 87.23% with LYSV G66 (GenBank accession no. MN059493), respectively, which infects garlic in China. Phylogeny analysis was performed based on 41 complete sequences of the CP gene of LYSV, including the four in this work and another 37 from GenBank of which six isolates were discovered in onions in Turkey (MN070124, MN070126, MN070130, MN070131, MN864794 and MN864795) and the others 31 isolates were from garlics or leeks in 15 different countries (Argentina, Australia, Brazil, China, Ethiopia, Germany, India, Iran, Japan, Mexico, Netherlands, New Zealand, Serbia, South Korea, and Spain), while the CP gene of onion yellow dwarf virus (AJ510223) was employed as an outgroup reference. The tree was reconstructed using the neighbor-joining method of MEGA11 with a bootstrap value of 1,000 replicates. On the tree (Fig. S3), the LYSV Hohhot-1, -2, -3, and -4 were closely related to each other and were distinct from other LYSV isolates including the six isolates in onions in Turkey, suggesting a specific genetic variation of the LYSV isolates in Hohhot. According to Santosa et al. (2023), LYSV Hohhot-1, -2, -3, and -4 were within the S-type lineage. This was the first record of LYSV infecting onions in China, expanding the natural host range of LYSV in China, which offered important information for the management of onion diseases.

First Report of Powdery Mildew caused by Erysiphe astragali on Sphaerophysa salsula.

Sphaerophysa salsula (Pall.) DC., also known as Yang Liao Pao, belongs to the Leguminosae family and is the only existing species in the Sphaerophysa genus. S. salsula is tolerance to cold, high salt, and alkaline soil, it is widely cultivated in China as a forage crop, and used as a Chinese folk medicine to treat hypertension (Ma et al., 2002). In 2023, signs and symptoms similar to powdery mildew were found on S. salsula planted in Tumd left (40.515°N, 110.424°E), Baotou City, Inner Mongolia Autonomous Region, China. The white powdery substance covered 90% of the leaf area, and the infected plants showed weak growth and senescence. More than 80% of plants (n=200) had these powdery mildew-like symptoms. Hyphal appressoria are solitary, conidiophores have few branches and septa. Conidia are cylindrical to clavate, 25-32 µm long and 8-15 µm wide (n=30), conidia form single subapical germ tubes, straight to curved-sinuous, with swollen apex or distinctly lobed conidial appressorium. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Schmidt and Braun 2020). Fungal structures were isolated from diseased leaves, and genomic DNA of the pathogen was extracted using the method described by Zhu et al. (2022). The internal transcribed spacer (ITS) region was amplified by PCR using the primers PMITS1/PMITS2 (Cunnington et al. 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The powdery mildew strain, named as KMD (GenBank accession no.: PP267067), showed an identity of 100% (645/645bp) with Erysiphe astragali, a powdery mildew reported on Astragalus glycyphyllos in Golestan, Iran (GenBank: OP806834) and identity of 99.6% (643/645bp) with Erysiphe astragali (GenBank: MW142495), a powdery mildew reported on A. scaberrimus in Inner Mongolia, China (Sun et al. 2023). Pathogenicity tests were conducted by brushing the conidia from infected S. salsula leaves onto leaves of four healthy plants, while four control plants were brushed in the same manner. All the treated plants were placed in separate growth chambers maintained at 19°C and 65% humidity, with a 16 h light/8 h dark photoperiod. Nine days after inoculation, the treated plants showed powdery mildew symptoms, while the control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was reisolated and identified as E. astragali based on morphological and molecular analysis, thereby fulfilling Koch's postulates. No report on the occurrence of powdery mildew on S. salsula plants has been found previously. The occurrence of this destructive powdery mildew may adversely affect the cultivation of S. salsula. Identifying the pathogen of powdery mildew will support future efforts to control and manage powdery mildew on S. salsula.

Factors Associated with the e-Health Literacy Among Older Adults with Chronic Obstructive Pulmonary Disease: A Cross-Sectional Study.

Background: The telemanagement model in chronic diseases needs older patients to have a certain level of e-Health literacy. According to Electronic Health Literacy model, factors associated with the e-Health literacy among older patients could be comprehensively investigated from individual, situational, and environmental aspects. Objectives: To investigate the e-Health literacy levels among older patients with chronic obstructive pulmonary disease (COPD) and explore associated factors. Methods: A cross-sectional study was conducted among older patients with COPD. The e-Health Literacy Scale was used to measure individuals' e-Health literacy. The multiple linear regression was applied to identify factors associated with e-Health literacy. Results: A total of 230 responses were included in the final analysis. The average score of e-Health literacy for older COPD patients was 24.66 (6.86). After adjusting the model, the results of multiple linear regression demonstrated that aging attitudes (B = 0.067, p < 0.001), technophobia (B = -0.285, p < 0.001), and self-efficacy (B = 0.431, p < 0.001) accounted for 68.3% (p < 0.001) of the total variation in e-Health literacy. Conclusion: This study identifies significant correlations of technophobia, aging attitudes, and self-efficacy, respectively, with e-Health literacy, and self-efficacy and technophobia may be constant predictive factors of e-Health literacy. In the future, intervention research on e-Health literacy should be conducted from a social psychology perspective, with particular emphasis on addressing negative aging attitudes and technophobia. That will promote the tele-management model of chronic diseases. Trial Registration: Chinese Clinical Trial Registry (ChiCTR): ChiCTR1900028563; http://apps.who.int/trialsearch/default.aspx.

Symmetry-Breaking Induced Dipole Enhancement for Efficient Spiro-Type Hole Transporting Materials: Easy Synthesis with High Stability.

Spiral cores are crucial for designing efficient hole transporting materials (HTMs) for perovskite solar cells (PSCs), owing to their no-planar 3D architecture, high thermal stability, good solubility, and beneficial solid-state morphology. A lack of facile synthetic procedures for the spiral core limited the development of novel and stable spiral HTMs. In this regard, a one-step reaction is adopted to produce several novel acceptor-embedded spiral cores containing electron-withdrawing carbonyl group embedded orthogonal spiral conformation. After coupling with triphenylamine donors, symmetry-breaking spiral HTMs with uneven charge distribution can be obtained, bearing the advantages of adjustable dipole moment and enhanced structural stability. A combined theoretical and experimental study shows that the HTM with a stronger dipole moment can easily adsorb on the surface of perovskite via electrostatic potential, and the closer distance promoted facile hole transfer from perovskite to HTMs. In the end, PSCs based on strongly polarized spiro-BC-OMe achieved efficient hole extraction and thus an improved fill factor, promoting a power conversion efficiency (PCE) of 22.15%, and a module-based PCE of 18.61% with an active area of 16.38 cm2 . This study provides a new avenue for designing HTMs with strong dipole moments for efficient PSCs.

An Analysis of the Potential and Cost of the U.S. Refinery Sector Decarbonization.

In 2019, U.S. petroleum refineries emitted 196 million metric tons (MT) of CO2, while the well-to-gate and the full life cycle CO2 emissions were significantly higher, reaching 419 and 2843 million MT of CO2, respectively. This analysis examines decarbonization opportunities for U.S. refineries and the cost to achieve both refinery-level and complete life-cycle CO2 emission reductions. We used 2019 life-cycle CO2 emissions from U.S. refineries as a baseline and identified three categories of decarbonization opportunity: (1) switching refinery energy inputs from fossil to renewable sources (e.g., switch hydrogen source); (2) carbon capture and storage of CO2 from various refining units; and (3) changing the feedstock from petroleum crude to biocrude using various blending levels. While all three options can reduce CO2 emissions from refineries, only the third can reduce emissions throughout the life cycle of refinery products, including the combustion of fuels (e.g., gasoline and diesel) during end use applications. A decarbonization approach that combines strategies 1, 2, and 3 can achieve negative life-cycle CO2 emissions, with an average CO2 avoidance cost of $113-$477/MT CO2, or $54-$227/bbl of processed crude; these costs are driven primarily by the high cost of biocrude feedstock.

Restriction of photoinduced electron transfer as a mechanism for the aggregation-induced emission of a trityl-functionalised maleimide fluorophore.

The restriction of intramolecular motion (RIM) and restricted access to a conical intersection (RACI) have been accepted as general working mechanisms for aggregation-induced emission (AIE) phenomena. However, as the family of AIE molecules grows, the RIM and RACl mechanisms cannot be used to fully understand some AIE phenomena. Herein, the restriction of the photoinduced electron transfer (RPET) state is proposed to rationalize the AIE phenomena of trityl-functionalised maleimide molecule based on density functional theory calculations. The "state-crossing from a locally excited to an electron transfer state" (SLEET) model was employed to predict the ON/OFF molecular PET in solution and solid states. According to the SLEET model, we showed that a non-emissive electron transfer excited state leads to the fluorescence quenching of trityl-functionalised maleimide in solution. However, due to the reduced polarity of the environment in aggregates, the electron transfer state is thermodynamically inaccessible, and a low-lying locally excited state exhibits intense emission. These findings provide a theoretical foundation to understand the working mechanisms of AIE molecules and the design of new AIEgens. We expect that the RPET mechanism can be used to screen potential AIEgens using the SLEET model.

Kisspeptin regulates the proliferation and apoptosis of ovary granulosa cells in polycystic ovary syndrome by modulating the PI3K/AKT/ERK signalling pathway.

BACKGROUND: The development of polycystic ovary syndrome (PCOS) is closely correlated with apoptosis and oxidative stress in ovarian granulosa cells. Kisspeptin plays an important role in reproductive organ function. This study aimed to explore the role of kisspeptin in PCOS and oxidative stress-triggered apoptosis of ovarian granular cells. METHODS: A PCOS rat model was established by injecting dehydroepiandrosterone (DHEA) and feeding the rats a high-fat diet. The RNA and protein levels of kisspeptin were analysed by quantitative PCR, western blotting, and histological staining. Tissue damage was evaluated using haematoxylin and eosin (H&E) staining. The viability and proliferation of human granulosa cell KGN were measured using the cell counting kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assays. Cell cycle and apoptosis were analysed by flow cytometry. Oxidative stress was analysed by measuring reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), and catalase (CAT) levels. RESULTS: Kisspeptin was downregulated in the ovarian granulosa cells of PCOS rats compared to those of control rats. Kisspeptin overexpression enhanced KGN cell proliferation and inhibited apoptosis. ROS generation was suppressed by kisspeptin, along with decreased levels of MDA and increased levels of the antioxidants GSH, SOD, and CAT. Kisspeptin activates PI3K/AKT and ERK signalling, and inactivation of ERK1/2 suppresses the protective role of kisspeptin in ovarian granulosa cells. CONCLUSION: Kisspeptin improves proliferation and alleviates apoptosis and oxidative stress in ovarian granulosa cells by activating PI3K/AKT and ERK signalling.

Occurrence of Powdery Mildew Caused by Erysiphe astragali on Astragalus scaberrimus in Inner Mongolia, China.

Astragalus scaberrimus Bunge, a perennial herb, is widely distributed in North and central China, Russia, and Mongolia (POWO, 2023). Due to its tolerance to drought, cold, high salt, low nutrients and alkaline soil, this plant is widely cultivated in China as a forage crop, for water and soil conservation, and for its medicinal properties (Meng, 2015). In 2022, powdery mildew-like signs and symptoms were seen on leaves of A. scaberrimuns cultivated on the campus of Inner Mongolia Agricultural University, Hohhot, Inner Mongolia China. White powder-like masses covered up to 99% of the leaf area with infected plants showing weak growth and senescence. More than 70% of plants (n = 180) exhibited these powdery mildew-infected symptoms. Conidiophores were 70-120 µm long (n = 20) and composed of a basal foot cell, followed by two cells and a conidium. Cylindrical- or ovoid-shaped conidia were 30-45µm long by 9-15 µm wide (n = 20). Brown or light-brown chasmothecia were 100-140 µm in diameter, with flexuous appendages. Based on these morphological characteristics, the fungus was tentatively identified as an Erysiphe sp. (Braun and Cook, 2012; Schmidt and Braun, 2020). Fungal structures were isolated from diseased leaves and genomic DNA of the pathogen was extracted utilizing the method described by Zhu et al. (2022). The internal transcribed spacer (ITS) region was amplified by PCR employing the primers PMITS1/PMITS2 (Cunnington et al., 2003) and the amplicon sequenced by Invitrogen (Shanghai, China). The sequence for the powdery mildew fungus (GenBank accession no.: MW142495) showed 100% identity (645/645 bp) with Erysiphe astragali, which was reported on A. glycyphyllos in Golestan province, Iran (accession no. OP806834). Pathogenicity tests were conducted by brushing the conidia from infected A. scaberrimus leaves onto leaves of four healthy plants, while, the four control plants were brushed in the same manner. All the treated plants were placed in separate growth chambers maintained at 19℃, 65% humidity, with 16 h light/8 h dark photoperiod. Nine days post inoculation, powdery mildew disease signs appeared on inoculated plants, whereas control plants remained asymptomatic. The same results were obtained for two repeated pathogenicity experiments. The powdery mildew fungus was reisolated and identified as E. astragali based on morphological and molecular analysis, thereby fulfilling Koch's postulates. E. astragali causing powdery mildew on A. glycyphyllus were previously reported in Germany with Genbank accesion number of MZ265150 and MZ265151 (Bradshaw et al., 2022). This, to our knowledge, is the first report of powdery mildew caused by E. astragali on A. scaberrimus. The severe occurrence of this destructive powdery mildew disease on A. scaberrimus may adversely affect the utility of the plant for soil conservation or cultivation for medicinal purposes. Identifying the causal agent of powdery mildew will support efforts for the future control and management of diseases on A. scaberrimus.

The intricate role of annexin A2 in kidney: a comprehensive review.

Annexin A2 (Anxa2) is a calcium (Ca2+)-regulated phospholipid binding protein composed of a variable N-terminus and a conserved core domain. This protein has been widely found in many tissues and fluids, including tubule cells, glomerular epithelial cells, renal vessels, and urine. In acute kidney injury, the expression level of this protein is markedly elevated in response to acute stress. Moreover, Anxa2 is a novel biomarker and potential therapeutic target with prognostic value in chronic kidney disease. In addition, Anxa2 is associated not only with clear-cell renal cell carcinoma differentiation but also the formation of calcium-related nephrolithiasis. In this review, we discuss the characteristics and functions of Anxa2 and focus on recent reports on the role of Anxa2 in the kidney, which may be useful for future research.