Robust Gaussian Process Regression Method for Efficient Tunneling Pathway Optimization: Application to Surface Processes.

Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, and quantum tunneling phenomena. The most common theoretical approaches involve optimization of reaction pathways, including semiclassical tunneling pathways (called instantons). The computational effort can be demanding, especially for instanton optimizations with an ab initio electronic structure. Recently, machine learning has been applied to accelerate reaction-pathway optimization, showing great potential for a wide range of applications. However, previous methods still suffer from numerical and efficiency issues and were not designed for condensed-phase reactions. We propose an improved framework based on Gaussian process regression for general transformed coordinates, which has improved efficiency and numerical stability, and we propose a descriptor that combines internal and Cartesian coordinates suitable for modeling surface processes. We demonstrate with 11 instanton optimizations in three representative systems that the improved approach makes ab initio instanton optimization significantly cheaper, such that it becomes not much more expensive than a classical transition-state theory rate calculation.

Clinical, Electrodiagnostic, and Ultrasound Findings in 87 Patients With Finger Drop.

BACKGROUND: The inability to extend the fingers at the metacarpophalangeal and interphalangeal joints leads to finger drop. While wrist drop and foot drop are well recognized, the causes of finger drop are poorly understood. AIMS: This study describes the clinical, electrodiagnostic (EDX), and ultrasound (US) features in patients with finger drop. MATERIALS AND METHODS: This is a retrospective study of 87 patients presenting with finger drop and referred for EDX studies during the past 10 years. We analyzed the clinical picture, EDX data, and US findings. The patients were categorized into global (all five digits) or partial (limited to 1-4 digits) finger drop. RESULTS: Fifty-six (64%) patients had global finger drop, while 31 (36%) had partial finger drop. The frequent cause of finger drop was Parsonage-Turner syndrome (PTS) (29 [33%]), followed by trauma (23 [26%]), cervical radiculopathy (16 [18%]), extensor tendon rupture (four [4%]), and compression/entrapment (two [2%]). In 13 (15%) patients, no cause was identified. A total of 13/16 (81%) patients with cervical radiculopathy and four of the patients with tendon rupture had partial finger drop, while 52/64 (81%) with posterior interosseous nerve (PIN) neuropathy had global finger drop. Of the 16 patients who experienced cervical radiculopathy as the cause of the finger drop, 15 patients had C7 and C8 radiculopathy and one patient had C7 radiculopathy. EDX studies of patients with PTS revealed partial axon loss in 18 (62%) patients, conduction block in eight (28%), and total axon loss in four (14%). Enlarged fascicles were observed by US in 40% of patients with PTS. EDX studies of patients who sustained iatrogenic nerve injury causing finger drop demonstrated total axon loss in six (46%) patients, partial axon loss in four (31%), demyelination in two (15%), and conduction block in two (15%). CONCLUSIONS: PIN neuropathy is the most common cause of finger drop, however, lesser-known causes such as cervical radiculopathy and extensor tendon rupture should also be considered. Global finger drop is suggestive of PIN neuropathy, while partial finger drop occurs more often in cervical radiculopathy and tendon rupture. EDX and US studies provide valuable information for localizing the lesion site and may reveal the cause of the finger drop.

AKAP8 promotes ovarian cancer progression and antagonizes PARP inhibitor sensitivity through regulating hnRNPUL1 transcription.

Ovarian cancer (OC) is the highest worldwide cancer mortality cause among gynecologic tumors, but its underlying molecular mechanism remains largely unknown. Here, we report that the RNA binding protein A-kinase anchoring protein 8 (AKAP8) is highly expressed in ovarian cancer and predicts poor prognosis for ovarian cancer patients. AKAP8 promotes ovarian cancer progression through regulating cell proliferation and metastasis. Mechanically, AKAP8 is enriched at chromatin and regulates the transcription of the specific hnRNPUL1 isoform. Moreover, AKAP8 phase separation modulates the hnRNPUL1 short isoform transcription. Ectopic expression of the hnRNPUL1 short isoform could partially rescue the growth inhibition effect of AKAP8-knockdown in ovarian cancer cells. In addition, AKAP8 modulates PARP1 expression through hnRNPUL1, and AKAP8 inhibition enhances PAPR inhibitor cytotoxicity in ovarian cancer. Together, our study uncovers the crucial function of AKAP8 condensation-mediated transcription regulation, and targeting AKAP8 could be potential for improvement of ovarian cancer therapy.

The proteomic analysis uncovers the cellular responses to the African swine fever virus membrane proteins p54, p17, and pB117L.

African swine fever virus (ASFV) infection causes African swine fever (ASF), a highly contagious and fatal disease that poses severe threat to swine production. To gain insights into the host responses to ASFV, we generated recombinant adenovirus Ad5 expressing viral membrane proteins p54, p17, and pB117L individually and infected an alveolar cell line, 3D4/21, with these recombinant viruses. Then, the cell lysates were analyzed using label-free quantification proteomic analysis method. A total of 2158 differentially expressed proteins (DEPs) were identified, of which 817, 466, and 875 proteins were from Ad5-p54-, Ad5-p17-, Ad5-pB117L-infected 3D4/21 cells, respectively. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed distinct yet interconnecting patterns of protein interaction networks. Specifically, the Ad5-p54 virus infection enriched the DEPs primarily involved in the metabolic pathways, endocytosis, adherens junction, and SNARE interactions in vesicular transport. The Ad5-p17 virus infection enriched the DEPs in endocytosis, ubiquitin-mediated proteolysis, N-Glycan biosynthesis, and apoptosis, while the Ad5-pB117L virus infection enriched the DEPs in metabolic pathways, endocytosis, oxidative phosphorylation, and focal adhesion. In summary, these results provide a comprehensive proteinomics analysis of the cellular responses to three ASFV membrane proteins, thus facilitating our understanding of ASFV pathogenesis.

Receptor Ligand-Free Mesoporous Silica Nanoparticles: A Streamlined Strategy for Targeted Drug Delivery across the Blood-Brain Barrier.

Mesoporous silica nanoparticles (MSNs) represent a promising avenue for targeted brain tumor therapy. However, the blood-brain barrier (BBB) often presents a formidable obstacle to efficient drug delivery. This study introduces a ligand-free PEGylated MSN variant (RMSN25-PEG-TA) with a 25 nm size and a slight positive charge, which exhibits superior BBB penetration. Utilizing two-photon imaging, RMSN25-PEG-TA particles remained in circulation for over 24 h, indicating significant traversal beyond the cerebrovascular realm. Importantly, DOX@RMSN25-PEG-TA, our MSN loaded with doxorubicin (DOX), harnessed the enhanced permeability and retention (EPR) effect to achieve a 6-fold increase in brain accumulation compared to free DOX. In vivo evaluations confirmed the potent inhibition of orthotopic glioma growth by DOX@RMSN25-PEG-TA, extending survival rates in spontaneous brain tumor models by over 28% and offering an improved biosafety profile. Advanced LC-MS/MS investigations unveiled a distinctive protein corona surrounding RMSN25-PEG-TA, suggesting proteins such as apolipoprotein E and albumin could play pivotal roles in enabling its BBB penetration. Our results underscore the potential of ligand-free MSNs in treating brain tumors, which supports the development of future drug-nanoparticle design paradigms.

LGCDA: Predicting CircRNA-Disease Association Based on Fusion of Local and Global Features.

CircRNA has been shown to be involved in the occurrence of many diseases. Several computational frameworks have been proposed to identify circRNA-disease associations. Despite the existing computational methods have obtained considerable successes, these methods still require to be improved as their performance may degrade due to the sparsity of the data and the problem of memory overflow. We develop a novel computational framework called LGCDA to predict circRNA-disease associations by fusing local and global features to solve the above mentioned problems. First, we construct closed local subgraphs by using k-hop closed subgraph and label the subgraphs to obtain rich graph pattern information. Then, the local features are extracted by using graph neural network (GNN). In addition, we fuse Gaussian interaction profile (GIP) kernel and cosine similarity to obtain global features. Finally, the score of circRNA-disease associations is predicted by using the multilayer perceptron (MLP) based on local and global features. We perform five- fold cross validation on five datasets for model evaluation and our model surpasses other advanced methods. The code is available at https://github.com/lanbiolab/LGCDA.

Deep Imputation Bi-stochastic Graph Regularized Matrix Factorization for Clustering Single-cell RNA-sequencing Data.

By generating massive gene transcriptome data and analyzing transcriptomic variations at the cell level, single-cell RNA-sequencing (scRNA-seq) technology has provided new way to explore cellular heterogeneity and functionality. Clustering scRNA-seq data could discover the hidden diversity and complexity of cell populations, which can aid to the identification of the disease mechanisms and biomarkers. In this paper, a novel method (DSINMF) is presented for single cell RNA sequencing data by using deep matrix factorization. Our proposed method comprises four steps: first, the feature selection is utilized to remove irrelevant features. Then, the dropout imputation is used to handle missing value problem. Further, the dimension reduction is employed to preserve data characteristics and reduce noise effects. Finally, the deep matrix factorization with bi-stochastic graph regularization is used to obtain cluster results from scRNA-seq data. We compare DSINMF with other state-of-the-art algorithms on nine datasets and the results show our method outperformances than other methods.

Enhanced biosensing of tumor necrosis factor-alpha based on aptamer-functionalized surface plasmon resonance substrate and Goos-Hänchen shift.

Tumor necrosis factor-alpha (TNF-α) serves as a crucial biomarker in various diseases, necessitating sensitive detection methodologies. This study introduces an innovative approach utilizing an aptamer-functionalized surface plasmon resonance (SPR) substrate together with an ultrasensitive measure, the Goos-Hänchen (GH) shift, to achieve sensitive detection of TNF-α. The developed GH-aptasensing platform has shown a commendable figure-of-merit of 1.5 × 104 µm per RIU, showcasing a maximum detectable lateral position shift of 184.7 ± 1.2 µm, as characterized by the glycerol measurement. Employing aptamers as the recognition unit, the system exhibits remarkable biomolecule detection capabilities, including the experimentally obtained detection limit of 1 aM for the model protein bovine serum albumin (BSA), spanning wide dynamic ranges. Furthermore, the system successfully detects TNF-α, a small cytokine, with an experimental detection limit of 1 fM, comparable to conventional SPR immunoassays. This achievement represents one of the lowest experimentally derived detection limits for cytokines in aptamer-based SPR sensing. Additionally, the application of the GH shift marks a ground breaking advancement in aptamer-based biosensing, holding significant promise for pushing detection limits further, especially for small cytokine targets.

Intake of compound probiotics accelerates the construction of immune function and gut microbiome in Holstein calves.

Acquired immunity is an important way to construct the intestinal immune barrier in mammals, which is almost dependent on suckling. To develop a new strategy for accelerating the construction of gut microbiome, newborn Holstein calves were continuously fed with 40 mL of compound probiotics (containing Lactobacillus plantarum T-14, Enterococcus faecium T-11, Saccharomyces cerevisiae T-209, and Bacillus licheniformis T-231) per day for 60 days. Through diarrhea rate monitoring, immune index testing, antioxidant capacity detection, and metagenome sequencing, the changes in diarrhea incidence, average daily gain, immune index, and gut microbiome of newborn calves within 60 days were investigated. Results indicated that feeding the compound probiotics reduced the average diarrhea rate of calves by 42.90%, increased the average daily gain by 43.40%, raised the antioxidant indexes of catalase, superoxide dismutase, total antioxidant capacity, and Glutathione peroxidase by 22.81%, 6.49%, 8.33%, and 13.67%, respectively, and increased the immune indexes of IgA, IgG, and IgM by 10.44%, 4.85%, and 6.12%, respectively. Moreover, metagenome sequencing data showed that feeding the compound probiotics increased the abundance of beneficial strains (e.g., Lactococcus lactis and Bacillus massionigeriensis) and decreased the abundance of some harmful strains (e.g., Escherichia sp. MOD1-EC5189 and Mycobacterium brisbane) in the gut microbiome of calves, thus contributing to accelerating the construction of healthy gut microbiome in newborn Holstein calves. IMPORTANCE: The unstable gut microbiome and incomplete intestinal function of newborn calves are important factors for the high incidence of early diarrhea. This study presents an effective strategy to improve the overall immunity and gut microbiome in calves and provides new insights into the application of compound probiotics in mammals.

Combined collection systems of sewage and rainfall runoff seriously affect the spatial distributions of natural estrogens and their conjugates in river water: Insights from the Pearl River of China.

So far, little has been known about how the combined collection systems of sewage and rainfall runoff (CCSs) affect emerging contaminants in river water. To fill up the knowledge gap, this study was conducted to investigate the spatial distributions of three natural estrogens (NEs, i.e., estrone (E1), 17ß-estradiol (E2) and estriol (E3)) and their conjugates (C-NEs) in the Pearl River in the wet and dry seasons. Results showed that the respective average concentrations of NEs and C-NEs at different locations alongside the Pearl River in the wet season were 7.3 and 1.8 times those in the dry season. Based on estrogen equivalence (EEQ), the average estimated EEQ level in the Pearl River waters in the wet season was nearly 10 times that in the dry season. These seemed to imply that the CCSs in the wet season not only cause untreated sewage into the receiving water body, but greatly decrease the removal efficiency of NEs and C-NEs in wastewater treatment plant. Furthermore, the estimated annual loads of E1, E2, and E3 to the Pearl River in the wet season accounted for about 88.6 %, 100 %, and 99.3 % of the total annual loads. Consequently, this work for the first time demonstrated that the CCSs in cities with high precipitation are unfavorable for controlling of emerging contaminants.

mTOR signaling promotes rapid m6A mRNA methylation to regulate NK-cell activation and effector functions.

Natural killer (NK) cells can be rapidly activated in response to cytokines during host defense against malignant cells or viral infection. However, it remains unclear what mechanisms precisely and rapidly regulate the expression of the numerous genes involved in activating NK cells. In this study, we discovered that NK-cell N6-methyladenosine (m6A) methylation levels were rapidly upregulated upon short-term NK-cell activation and were repressed in the tumor microenvironment. Deficiency of methyltransferase-like 3 (METTL3) or METTL14 moderately influenced NK-cell homeostasis, while double knockout of METTL3/14 significantly impacted NK-cell homeostasis, maturation, and antitumor immunity. This suggests a cooperative role of METTL3 and METTL14 in regulating NK-cell development and effector functions. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we demonstrated that genes involved in NK-cell effector functions, such as Prf1 and Gzmb, were directly modified by m6A methylation. Furthermore, inhibiting mTOR complex 1 (mTORC1) activation prevented m6A methylation levels from increasing when NK cells were activated, and this could be restored by S-adenosylmethionine (SAM) supplementation. Collectively, we have unraveled crucial roles for rapid m6A mRNA methylation downstream of the mTORC1-SAM signal axis in regulating NK-cell activation and effector functions.

[Application of microwave vacuum drying with process management in extract drying of personalized traditional Chinese medicine preparations].

Extracts are important intermediates in the production of traditional Chinese medicines preparations. The drying effect of extracts will directly affect the subsequent production process and the quality of the preparation. To meet the requirements of high drug loading, short time consumption, and simple production process of personalized traditional Chinese medicine preparations, this study explored the application of multi-program microwave vacuum drying process in the extract drying of personalized traditional Chinese medicine preparations. The influencing factors of microwave vacuum drying process were investigated for 5 excipients and 40 prescriptions. Taking the feasibility of drying, drying rate, drying time, and dried extract status as indicators, this study investigated the feeding requirements of microwave vacuum drying. With the dried extract status as the evaluation indicator, the three drying programs(A, B, and C) were compared to obtain the optimal drying condition. The experimental results showed that the optimal feeding conditions for microwave vacuum drying were material layer thickness of 2 cm and C program(a total of 7 drying processes), which solved the problem of easy scorching in microwave drying with process management. Furthermore, the preset moisture content of the dried extract in microwave drying should be 4%-5%, so that the dried extract of traditional Chinese medicine preparation had uniform quality, complete drying, and no scorching. This study lays a foundation for the application of microwave drying in the production of traditional Chinese medicine preparations, promoting the high-quality development of personalized traditional Chinese medicine preparations.

Development and Validation of the Interprofessional Collaboration Practice Competency Scale (IPCPCS) for Clinical Nurses.

Interprofessional collaborative practice is a core competency and is the key to strengthening health practice systems in order to deliver safe and high-quality nursing practice. However, there is no Interprofessional Collaboration Practice Competency Scale (IPCPCS) for clinical nurses in Taiwan. Therefore, the purposes of this study were to develop an IPCPCS and to verify its reliability and validity. This was a psychometric study with a cross-sectional survey using convenience sampling to recruit nurses from the seven hospitals of a medical foundation. A self-designed structured IPCPCS was rolled out via a Google survey. The data were analyzed using descriptive statistics, principal-axis factoring (PAF) with Promax rotation, Pearson correlation, reliability analysis, and one-way ANOVA. PAF analysis found that three factors could explain 77.76% of cumulative variance. These were collaborative leadership and interprofessional conflict resolution, interprofessional communication and team functioning, and role clarification and client-centered care. The internal consistency of the three factors (Cronbach's α) was between 0.970 to 0.978, and the Pearson correlation coefficients were between 0.814 to 0.883. Significant differences were presented in the IPCPCS score by age, education level, total years of work experience, position on the nursing clinical ladder, and participation in interprofessional education. In conclusion, the three factors used in the IPCPCS have good reliability and construct validity. This scale can be used as an evaluation tool of in-service interprofessional education courses for clinical nurses.

Deficiency of Cbfß in articular cartilage leads to osteoarthritis-like phenotype through Hippo/Yap, TGFß, and Wnt/ß-catenin signaling pathways.

Osteoarthritis (OA) is the most prevalent degenerative joint disorder, causing physical impairments among the elderly. Core binding factor subunit ß (Cbfß) has a critical role in bone homeostasis and cartilage development. However, the function and mechanism of Cbfß in articular cartilage and OA remains unclear. We found that Cbfßf/fAggrecan-CreERT mice with Cbfß-deficiency in articular cartilage developed a spontaneous osteoarthritis-like phenotype with articular cartilage degradation. Immunofluorescence staining showed that Cbfßf/fAggrecan-CreERT mice exhibited a significant increase in the expression of articular cartilage degradation markers and inflammatory markers in the knee joints. RNA-sequencing analysis demonstrated that Cbfß orchestrated Hippo/Yap, TGFß/Smad, and Wnt/ß-catenin signaling pathways in articular cartilage, and Cbfß deficiency resulted in the abnormal expression of downstream genes involved in maintaining articular cartilage homeostasis. Immunofluorescence staining results showed Cbfß deficiency significantly increased active ß-catenin and TCF4 expression while reducing Yap, TGFß1, and p-Smad 2/3 expression. Western blot and qPCR validated gene expression changes in hip articular cartilage of Cbfß-deficient mice. Our results demonstrate that deficiency of Cbfß in articular cartilage leads to an OA-like phenotype via affecting Hippo/Yap, TGFß, and Wnt/ß-catenin signaling pathways, disrupting articular cartilage homeostasis and leading to the pathological process of OA in mice. Our results indicate that targeting Cbfß may be a potential therapeutic target for the design of novel and effective treatments for OA.

A bibliometric study on trends in chiropractic research from 1920 to 2023.

OBJECTIVE: An increasing body of evidence suggests a positive role of chiropractic in the treatment of neuro-musculoskeletal disorders. This study aims to explore current research hotspots and trends, providing insights into the broad prospects of this field. METHODS: A bibliometric review was conducted on all chiropractic articles included in the Web of Science Core Collection before December 31, 2023. RESULTS: Over the past century, the volume of research in the field of chiropractic has been fluctuating annually, with four peaks observed in total. The United States, Canada, Australia, and the United Kingdom are leading countries. Chu, Eric Chun-Pu is the author with the most publications, while Bronfort, Gert has the highest total citation count. The University of Southern Denmark has produced the most publications, while Queens University - Canada is the most central institution. The Journal of Manipulative and Physiological Therapeutics is the journal with the most publications and citations, while the Journal of the American Medical Association is the most central journal. The two most-cited articles were both authored by Eisenberg DM. Emerging keywords include "chronic pain" and "skills". The theoretical mechanisms and scientific basis of chiropractic, its clinical practice and safety, education and training, integration with other disciplines, and patient experiences and satisfaction are the frontiers and hotspots of research. CONCLUSION: This study integrates bibliometric analysis to summarize the current state of research and global network centers in the field of chiropractic, further highlighting the hotspots and trends in this field. However, Individual and national rankings should be interpreted with caution due to our focus on Web of Science rather than PubMed.

Interaction between HTR2A rs3125 and negative life events in suicide attempts among patients with major depressive disorder: a cross-sectional study.

BACKGROUND: Both genetic and environmental factors play crucial roles in the development of major depressive disorder (MDD) and suicide attempts (SA). However, the interaction between both items remains unknown. This study aims to explore the interactions between the genetic variants of the serotonin 2 A receptor (HTR2A) and the nitric oxide synthase 1 (NOS1) and environmental factors in patients who experience MDD and SA. METHODS: A total of 334 patients with MDD and a history of SA (MDD-SA) were recruited alongside 518 patients with MDD with no history of SA (MDD-NSA), and 716 healthy controls (HC). The demographic data and clinical characteristics were collected. Sequenom mass spectrometry was used to detect eight tag-single nucleotide polymorphisms (tagSNPs) in HTR2A (rs1328683, rs17068986, and rs3125) and NOS1 (rs1123425, rs2682826, rs3741476, rs527590, and rs7959232). Generalized multifactor dimensionality reduction (GMDR) was used to analyze the gene-environment interactions. RESULTS: Four tagSNPs (rs17068986, rs3125, rs527590, and rs7959232) exhibited significant differences between the three groups. However, these differences were not significant between the MDD-SA and MDD-NSA groups after Bonferroni correction. A logistic regression analysis revealed that negative life events (OR = 1.495, 95%CI: 1.071-2.087, P = 0.018), self-guilt (OR = 2.263, 95%CI: 1.515-3.379, P < 0.001), and negative cognition (OR = 2.252, 95%CI: 1.264-4.013, P = 0.006) were all independently associated with SA in patients with MDD. Furthermore, GMDR analysis indicated a significant interaction between HTR2A rs3125 and negative life events. Negative life events in conjunction with the HTR2A rs3125 CG + GG genotype were associated with a higher SA risk in patients with MDD when compared to the absence of negative life events in conjunction with the CC genotype (OR = 2.547, 95% CI: 1.264-5.131, P = 0.009). CONCLUSION: Several risk factors and a potential interaction between HTR2A rs3125 and negative life events were identified in patients with SA and MDD. The observed interaction likely modulates the risk of MDD and SA, shedding light on the pathogenesis of SA in patients with MDD.

Aloperine-Type Alkaloids with Antiviral and Antifungal Activities from the Seeds of Sophora alopecuroides L.

As a continuous flow investigation of novel pesticides from natural quinolizidine alkaloids, the chemical compositions of the seeds of Sophora alopecuroides were thoroughly researched. Fifteen new aloperine-type alkaloids (1-15) as well as six known aloperine-type alkaloids (16-21) were obtained from the extract of S. alopecuroides. The structures of 1-21 were confirmed via HRESIMS, NMR, UV, IR, ECD calculations, and X-ray diffraction. The antiviral activities of 1-21 against tobacco mosaic virus (TMV) were detected following the improved method of half-leaf. Compared with ningnanmycin (protective: 69.7% and curative: 64.3%), 15 exhibited excellent protective (71.7%) and curative (64.6%) activities against TMV. Further biological studies illustrated that 15 significantly inhibited the transcription of the TMV-CP gene and increased the activities of polyphenol oxidase (PPO), peroxidase (POD), superoxide dismutase (SOD), and phenylalanine ammonia-lyase (PAL). The antifungal activities of 1-21 against Phytophythora capsica, Botrytis cinerea, Alternaria alternata, and Gibberella zeae were screened according to a mycelial inhibition test. Compound 13 displayed excellent antifungal activity against B. cinerea (EC50: 7.38 µg/mL). Moreover, in vitro antifungal mechanism studies displayed that 13 causes accumulation of reactive oxygen species and finally leads to mycelia cell membrane damage and cell death in vitro.

Effects of Nutrient Solution Application Rates on Yield, Quality, and Water-Fertilizer Use Efficiency on Greenhouse Tomatoes Using Grown-in Coir.

The yield, quality, and water-fertilizer use efficiency of crops are important parameters for assessing rational water and fertilizer management. For an optimal water and fertilizer system with respect to the nutrient solution irrigation of greenhouse tomatoes using cultivation substrates, a two-year greenhouse cultivation experiment was conducted from 2022 to 2023. Three drip fertigation treatments (T1, T2, and T3) were implemented in the experiment, where nutrient solutions were supplied when the substrate's water content reached 60%, 70%, and 80%. The frequency of nutrient solution applications is based on weighing coconut coir strips in the morning and evening at 7:00 to determine the daily water consumption of plants. Nutrient solutions were supplied when the substrate's water content reached the lower limit, and the upper limit for nutrient supply was set at 100% of the substrate water content. The nutrient solution application was carried out multiple times throughout the day, avoiding the midday heat. The nutrient solution formula used was the soilless tomato cultivation formula from South China Agricultural University. The results show that plant height and the leaf area index rapidly increased in the early and middle stages, and later growth tended to stabilize; the daily transpiration of tomatoes increased with an increase in nutrient solution supply, and it was the greatest in the T3 treatment. Between the amount of nutrient solution application and the number of years, the yield increased with the increase of the amount of nutrient solution, showing T3 > T2 > T1. Although the average yield of the T2 treatment was slightly lower than that of the T3 treatment by 3.65%, the average irrigation water use efficiency, water use efficiency, and partial fertilizer productivity of the T2 treatment were significantly higher than those of the T3 treatment by 29.10%, 19.99%, and 28.89%, respectively (p < 0.05). Additionally, soluble solid, vitamin C, and soluble sugar contents and the sugar-acid ratio of tomatoes in the T2 treatment were greater than those in the other two treatments (p < 0.05). Using the TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) method, it was concluded that the nutrient solution application rate of 70% can significantly increase water and fertilizer use efficiency and markedly improve the nutritional and flavor quality of the fruit without a significant reduction in yield. This finding provides significant guidance for the high-yield, high-quality, and efficient production of coconut coir-based cultivated tomatoes in greenhouses.

MRUNet-3D: A multi-stride residual 3D UNet for lung nodule segmentation.

Obtaining an accurate segmentation of the pulmonary nodules in computed tomography (CT) images is challenging. This is due to: (1) the heterogeneous nature of the lung nodules; (2) comparable visual characteristics between the nodules and their surroundings. A robust multi-scale feature extraction mechanism that can effectively obtain multi-scale representations at a granular level can improve segmentation accuracy. As the most commonly used network in lung nodule segmentation, UNet, its variants, and other image segmentation methods lack this robust feature extraction mechanism. In this study, we propose a multi-stride residual 3D UNet (MRUNet-3D) to improve the segmentation accuracy of lung nodules in CT images. It incorporates a multi-slide Res2Net block (MSR), which replaces the simple sequence of convolution layers in each encoder stage to effectively extract multi-scale features at a granular level from different receptive fields and resolutions while conserving the strengths of 3D UNet. The proposed method has been extensively evaluated on the publicly available LUNA16 dataset. Experimental results show that it achieves competitive segmentation performance with an average dice similarity coefficient of 83.47 % and an average surface distance of 0.35 mm on the dataset. More notably, our method has proven to be robust to the heterogeneity of lung nodules. It has also proven to perform better at segmenting small lung nodules. Ablation studies have shown that the proposed MSR and RFIA modules are fundamental to improving the performance of the proposed model.

THAP3 recruits SMYD3 to OXPHOS genes and epigenetically promotes mitochondrial respiration in hepatocellular carcinoma.

Mitochondria harbor the oxidative phosphorylation (OXPHOS) system to sustain cellular respiration. However, the transcriptional regulation of OXPHOS remains largely unexplored. Through the cancer genome atlas (TCGA) transcriptome analysis, transcription factor THAP domain-containing 3 (THAP3) was found to be strongly associated with OXPHOS gene expression. Mechanistically, THAP3 recruited the histone methyltransferase SET and MYND domain-containing protein 3 (SMYD3) to upregulate H3K4me3 and promote OXPHOS gene expression. The levels of THAP3 and SMYD3 were altered by metabolic cues. They collaboratively supported liver cancer cell proliferation and colony formation. In clinical human liver cancer, both of them were overexpressed. THAP3 positively correlated with OXPHOS gene expression. Together, THAP3 cooperates with SMYD3 to epigenetically upregulate cellular respiration and liver cancer cell proliferation.