The regulatory role of m6A modification in the maintenance and differentiation of embryonic stem cells.

As the most prevalent and reversible internal epigenetic modification in eukaryotic mRNAs, N 6-methyladenosine (m6A) post-transcriptionally regulates the processing and metabolism of mRNAs involved in diverse biological processes. m6A modification is regulated by m6A writers, erasers, and readers. Emerging evidence suggests that m6A modification plays essential roles in modulating the cell-fate transition of embryonic stem cells. Mechanistic investigation of embryonic stem cell maintenance and differentiation is critical for understanding early embryonic development, which is also the premise for the application of embryonic stem cells in regenerative medicine. This review highlights the current knowledge of m6A modification and its essential regulatory contribution to the cell fate transition of mouse and human embryonic stem cells.

Provincial Maternal and Child Information System in Inner Mongolia, China: Descriptive Implementation Study.

BACKGROUND: After the implementation of 2- and 3-child policies, the rising proportion of high-age and high-risk pregnancies put enormous pressure on maternal and child health (MCH) services for China. This populous nation with an increasing population flow imperatively required the support of large-scale information systems for management. Municipal MCH information systems were commonly applied in developed cities of eastern provinces in China. However, implementation of provincial MCH information systems in relatively low-income areas is lacking. In 2020, the implementation of a regional maternal and child information system (RMCIS) in Inner Mongolia filled this gap. OBJECTIVE: This paper aimed to demonstrate the construction process and evaluate the implementation effect of an RMCIS in improving the regional MCH in Inner Mongolia. METHODS: We conducted a descriptive study for the implementation of an RMCIS in Inner Mongolia. Based on the role analysis and information reporting process, the system architecture design had 10 modules, supporting basic health care services, special case management, health support, and administration and supervision. Five-color management was applied for pregnancy risk stratification. We collected data on the construction cost, key characteristics of patients, and use count of the main services from January 1, 2020, to October 31, 2022, in Inner Mongolia. Descriptive analysis was used to demonstrate the implementation effects of the RMCIS. RESULTS: The construction and implementation of the RMCIS cost CNY 8 million (US $1.1 million), with a duration of 13 months. Between 2020 and 2022, the system recorded 221,772 registered pregnant women, with a 44.75% early pregnancy registry rate and 147,264 newborns, covering 278 hospitals and 225 community health care centers in 12 cities. Five-color management of high-risk pregnancies resulted in 76,975 (45.45%) pregnancies stratified as yellow (general risk), 36,627 (21.63%) as orange (relatively high risk), 156 (0.09%) as red (high risk), and 3888 (2.30%) as purple (infectious disease). A scarred uterus (n=28,159, 36.58%), BMI≥28 (n=14,164, 38.67%), aggressive placenta praevia (n=32, 20.51%), and viral hepatitis (n=1787, 45.96%) were the top factors of high-risk pregnancies (yellow, orange, red, and purple). In addition, 132,079 pregnancies, including 65,018 (49.23%) high-risk pregnancies, were registered in 2022 compared to 32,466 pregnancies, including 21,849 (67.30%) high-risk pregnancies, registered in 2020. CONCLUSIONS: The implementation of an RMCIS in Inner Mongolia achieved the provincial MCH data interconnection for basic services and obtained both social and economic benefits, which could provide valuable experience to medical administration departments, practitioners, and medical informatics constructors worldwide.

Expression, purification, characterization and crystallization of Panax quinquefolius ginsenoside glycosyltransferase Pq3-O-UGT2.

Pq3-O-UGT2, derived from Panax quinquefolius, functions as a ginsenoside glucosyltransferase, utilizing UDP-glucose (UDPG) as the sugar donor to catalyze the glycosylation of Rh2 and F2. An essential step in comprehending its catalytic mechanism involves structural analysis. In preparation for structural analysis, we expressed Pq3-O-UGT2 in the Escherichia coli (E. coli) strain Rosetta (DE3). The recombinant Pq3-O-UGT2 was purified through Ni-NTA affinity purification, a two-step ion exchange chromatography, and subsequently size-exclusion chromatography (SEC). Notably, the purified Pq3-O-UGT2 showed substantial activity toward Rh2 and F2, catalyzing the formation of Rg3 and Rd, respectively. This activity was discernible within a pH range of 4.0-9.0 and temperature range of 30-55 °C, with optimal conditions observed at pH 7.0-8.0 and 37 °C. The catalytic efficiency of Pq3-O-UGT2 toward Rh2 and F2 was 31.43 s-1 mΜ-1 and 169.31 s-1 mΜ-1, respectively. We further crystalized Pq3-O-UGT2 in both its apo form and co-crystalized forms with UDPG, Rh2 and F2, respectively. High-quality crystals were obtained and X-ray diffraction data was collected for all co-crystalized samples. Analysis of the diffraction data revealed that the crystal of Pq3-O-UGT2 co-crystalized with UDP-Glc belonged to space group P1, while the other two crystals belonged to space group P212121. Together, this study has laid a robust foundation for subsequent structural analysis of Pq3-O-UGT2.

Cut-off values of haemoglobin and clinical outcomes in incident peritoneal dialysis: the PDTAP study.

BACKGROUND: To explore the cut-off values of haemoglobin (Hb) on adverse clinical outcomes in incident peritoneal dialysis (PD) patients based on a national-level database. METHODS: The observational cohort study was from the Peritoneal Dialysis Telemedicine-assisted Platform (PDTAP) dataset. The primary outcomes were all-cause mortality, major adverse cardiovascular events (MACE) and modified MACE (MACE+). The secondary outcomes were the occurrences of hospitalization, first-episode peritonitis and permanent transfer to haemodialysis (HD). RESULTS: A total of 2591 PD patients were enrolled between June 2016 and April 2019 and followed up until December 2020. Baseline and time-averaged Hb <100 g/l were associated with all-cause mortality, MACE, MACE+ and hospitalizations. After multivariable adjustments, only time-averaged Hb <100 g/l significantly predicted a higher risk for all-cause mortality {hazard ratio [HR] 1.83 [95% confidence interval (CI) 1.19-281], P = .006}, MACE [HR 1.99 (95% CI 1.16-3.40), P = .012] and MACE+ [HR 1.77 (95% CI 1.15-2.73), P = .010] in the total cohort. No associations between Hb and hospitalizations, transfer to HD and first-episode peritonitis were observed. Among patients with Hb ≥100 g/l at baseline, younger age, female, use of iron supplementation, lower values of serum albumin and renal Kt/V independently predicted the incidence of Hb <100 g/l during the follow-up. CONCLUSION: This study provided real-world evidence on the cut-off value of Hb for predicting poorer outcomes through a nation-level prospective PD cohort.

SBRT vs. Y90: HCC Treatment Outcomes and Costs.

OBJECTIVES: Stereotactic Body Radiotherapy (SBRT) and Yttrium-90 (Y90) are among the ablative therapies used as treatment options for localized hepatocellular carcinoma (HCC). To date, direct comparisons of the 2 modalities' outcomes and costs are lacking. This study aimed to analyze demographic, treatment, and cost information for patients with HCC treated with SBRT and Y90. METHODS: Patients with HCC treated with SBRT or Y90 radioembolization between January 2018 and January 2020 at one institution were retrospectively reviewed. Demographic and treatment data were compared utilizing χ 2 tests. Kaplan-Meier curves and log-rank tests were applied to compare overall survival and progression-free survival in different treatment groups. Cox proportional hazard models were applied to analyze the unadjusted and adjusted survival differences. Ten SBRT and 10 Y90 patients were randomly selected for Medicare cost analysis. RESULTS: Sixty-three patients received Y90, and 21 received SBRT. On univariable and multivariable analysis, there was no significant difference in overall survival or progression-free survival between the Y90 and SBRT cohorts. SBRT patients had higher American Joint Committee on Cancer staging ( P =0.039), greater tumor size (4.07 vs. 2.96 cm, P =0.013), and greater rates of prior liver-directed therapy (71.4% SBRT vs. 12.7% Y90, P <0.001). The average cost for SBRT was $15,148, and Y90 was $41,360. CONCLUSIONS: SBRT and Y90 are effective therapies in the treatment of HCC, specifically having similar overall survival and progression-free survival. Y90 was found to have a significantly higher cost than SBRT. This study demonstrates the need for prospective studies to assess these modalities in treating HCC.

Growth mechanism prediction for nanoparticles via structure matching polymerization.

Exploring structural and component evolution remains a challenging scientific problem for nanoscience. We propose a novel approach called principle of minimization of structure matching polymerization (SMP) change to rapidly explore the global minimum structure on the potential energy surface (PES). The new method can map low-dimensional stable structures to high-dimensional local minima, and this will make it possible for us to study the growth mechanisms of nanoparticles. Some new lowest-energy structures were found by SMP methods for sulfuric acid (SA)-dimethylamine (DMA) systems relative to previous studies. Additionally, we found that the growth process of boron clusters is mainly that the small-size boron clusters are continuously added to large-size boron clusters by structure matching for Bn (n = 2-36) systems, Bm + Bk → Bn, where m + k = n and 1 ≤ k ≤ 3. The SMP approach can greatly improve the search efficiency of other unbiased global optimization algorithms, such as basin-hopping (BH) and genetic algorithm (GA), with an enhancement of up to 19- and 7-fold relative to traditional BH and GA algorithms for searching the global minima of Bn (n = 14-22) systems. The SMP approach is general and flexible and can be applied to different kinds of problems, such as material structure design, crystal structure prediction, and new drug generation.

Structure-function and engineering of plant UDP-glycosyltransferase.

Natural products synthesized by plants have substantial industrial and medicinal values and are therefore attracting increasing interest in various related industries. Among the key enzyme families involved in the biosynthesis of natural products, uridine diphosphate-dependent glycosyltransferases (UGTs) play a crucial role in plants. In recent years, significant efforts have been made to elucidate the catalytic mechanisms and substrate recognition of plant UGTs and to improve them for desired functions. In this review, we presented a comprehensive overview of all currently published structures of plant UGTs, along with in-depth analyses of the corresponding catalytic and substrate recognition mechanisms. In addition, we summarized and evaluated the protein engineering strategies applied to improve the catalytic activities of plant UGTs, with a particular focus on high-throughput screening methods. The primary objective of this review is to provide readers with a comprehensive understanding of plant UGTs and to serve as a valuable reference for the latest techniques used to improve their activities.

New Multicomponent Optimization Scheme for Equiatomic Vanadium-Titanium Nanoparticle Study.

We present a new multicomponent structure prediction method named MRS-Swap searching, which is inspired by space symmetry and swap of different atomic species. For the pure titanium cluster, a new ground-state structure of the Ti20 cluster with higher symmetry relative to a previous study was found by our method. Based on the structural analysis of Tin (n = 2k, k = 2-11), Vn (n = 2k, k = 2-11), and TinVm (n = m = 2-11) systems, we found that the lowest energy structures of these three systems are very similar, which indicates that equiatomic vanadium-titanium-mixed clusters do not change their ground-state structure relative to the same size pure vanadium and titanium cluster. According to the structure-activity relationship, we conclude that the yield strength (σ) of macro vanadium-titanium alloy is between pure titanium and pure vanadium metal, and this can be expressed through σ(Ti) > σ(TiV) > σ(V). The X-ray diffraction results show that the V2Nb, TiVNb, and Ti2Nb alloys also have the same BCC structure, which may be related to their microstructure. Our method and results can be helpful for future multicomponent alloy design.

A polarization image enhancement method for glioma.

Polarization imaging technique (PIT) based on a backward scattering 3 × 3 Mueller matrix polarization imaging experimental setup is able to study the optical information and microstructure of glioma and non-glioblastoma tissues from clinical treatment. However, the image contrast of Mueller Matrix Elements (MME) is far from sufficient to provide supplemental information in the clinic, especially in off-diagonal MME. The aim of this work is to propose an innovative method to improve the contrast and quality of PIT images of glioma and non-glioma tissues. The work first confirms the robustness of the method by evaluating the enhanced images and assessment coefficients on ex vivo unstained glioma and non-glioma sample bulks, then the optimal enhancement results are tested and presented based on the multi-sample tests. This PIT image enhancement method can greatly improve the contrast and detailed texture information of MMEs images, which can provide more useful clinical information, and further be used to identify glioma and residues in the intraoperative environment with PIT.

Theoretical Study of the Gas-Phase Hydrolysis of Formaldehyde to Produce Methanediol and Its Implication to New Particle Formation.

Aldehydes were speculated to be important precursor species in new particle formation (NPF). The direct involvement of formaldehyde (CH2O) in sulfuric acid and water nucleation is negligible; however, whether its atmospheric hydrolysate, methanediol (CH2(OH)2), which contains two hydroxyl groups, participates in NPF is not known. This work investigates both CH2O hydrolysis and NPF from sulfuric acid and CH2(OH)2 with quantum chemistry calculations and atmospheric cluster dynamics modeling. Kinetic calculation shows that reaction rates of the gas-phase hydrolysis of CH2O catalyzed by sulfuric acid are 11-15 orders of magnitude faster than those of the naked path at 253-298 K. Based on structures and the calculated formation Gibbs free energies, the interaction between sulfuric acid/its dimer/its trimer and CH2(OH)2 is thermodynamically favorable, and CH2(OH)2 forms hydrogen bonds with sulfuric acid/its dimer/its trimer via two hydroxyl groups to stabilize clusters. Our further cluster kinetic calculations suggested that the particle formation rates of the system are higher than those of the binary system of sulfuric acid and water at ambient low sulfuric acid concentrations and low relative humidity. In addition, the formation rate is found to present a negative temperature dependence because evaporation rate constants contribute significantly to it. However, cluster growth is essentially limited by the weak formation of the largest clusters, which implies that other stabilizing vapors are required for stable cluster formation and growth.

Local Therapies for Hepatocellular Carcinoma and Role of MRI-Guided Adaptive Radiation Therapy.

Hepatocellular carcinoma (HCC) is the most common liver tumor, with a continually rising incidence. The curative treatment for HCC is surgical resection or liver transplantation; however, only a small portion of patients are eligible due to local tumor burden or underlying liver dysfunction. Most HCC patients receive nonsurgical liver-directed therapies (LDTs), including thermal ablation, transarterial chemoembolization (TACE), transarterial radioembolization (TARE), and external beam radiation therapy (EBRT). Stereotactic ablative body radiation (SABR) is a specific type of EBRT that can precisely deliver a high dose of radiation to ablate tumor cells using a small number of treatments (or fractions, typically 5 or less). With onboard MRI imaging, MRI-guided SABR can improve therapeutic dose while minimizing normal tissue exposure. In the current review, we discuss different LDTs and compare them with EBRT, specifically SABR. The emerging MRI-guided adaptive radiation therapy has been reviewed, highlighting its advantages and potential role in HCC management.

Experiment-theory hybrid method for studying the formation mechanism of atmospheric new particle formation.

Atmospheric aerosols have a significant influence on climate change through their effect on the cloud lifetime and the radiative balance of the Earth's atmosphere. Despite its importance, the mechanism of aerosol nucleation is still poorly understood. Based on the low-energy structure of cluster molecules, quantum chemical (QC) computations can help us to directly calculate the formation mechanism of atmospheric clusters and formation rates at the molecular level. However, deciphering the formation mechanism of pre-nucleated clusters, especially those close to the critical size (∼1.7 nm), remains extremely challenging because many millions of configuration spaces might need to be explored to find the low-energy structure. We present a new idea that establishes a comprehensive experimental and computational hybrid calculation protocol to integrate experimental data, isomer distributions, hydrogen bond interactions, and interaction sites for exploring the configuration spaces and clarifying the nucleation mechanism of acid-base clusters, whose maximum size can exceed 1.7 nm. This protocol can effectively and accurately explore the configuration space of complex large nucleation clusters on the potential energy surface (PES). The consistency of the cluster concentration and the formation rate between the experiment and the in situ measurement is much better than that of the previous studies and proves its accuracy. In addition, we found that malic acid (MA) can enhance sulfuric acid-dimethylamine (SA-DMA)-based particle formation rates in the atmospheric boundary layer, for example, in Shanghai and Beijing in the summer, with an enhancement of up to 700- and 135-fold, respectively. The enhancement in atmospheric particle formation by MA is critical for new particle formation in the boundary layer with relatively low SA and DMA concentrations and at high temperature. This model greatly improves our understanding of the complex aerosol nucleation mechanism of large-scale multicomponent cluster molecules.

Ion formation mechanism of cortisone molecules and clusters in charged nanodroplets.

Mass spectrometry measurements coupled with classical molecular dynamics (MD) simulations have been conducted in recent years to understand the final stage of ion formation in electrospray ionization (ESI). Here, to characterize the ion formation mechanism in the recently developed droplet-assisted ionization (DAI) source, MD simulations with various conditions (solute number, temperature, ions, composition) were performed to help explain DAI-based measurements. The specific binding ability of cortisone with preformed ions (ions of sodium, cesium and iodide) in evaporating nanodroplets makes the ion formation process characteristic of both the ion evaporation and charge residue models (IEM and CRM, respectively). Most preformed ions are ejected with dozens of solvent molecules to form gas-phase ions by IEM, while clusters of one or more cortisone molecules with one or more preformed ions remain in the evaporating droplet to form gas-phase ions by CRM. As the ratio of cortisone molecules to preformed ions increases, the number of preformed ions held in the droplet without ejection by the IEM increases. In other words, increasing the molecular solute to preformed ion ratio in the droplet increases the fraction of gas-phase ions formed by CRM relative to IEM. The increase in CRM relative to IEM is accompanied by an increase in the calculated activation energy barrier, which can explain the activation energy measurements by DAI, where droplets without preformed ions exhibit higher activation energies for gas-phase ion formation than droplets containing large numbers of preformed ions.

Towards fully ab initio simulation of atmospheric aerosol nucleation.

Atmospheric aerosol nucleation contributes to approximately half of the worldwide cloud condensation nuclei. Despite the importance of climate, detailed nucleation mechanisms are still poorly understood. Understanding aerosol nucleation dynamics is hindered by the nonreactivity of force fields (FFs) and high computational costs due to the rare event nature of aerosol nucleation. Developing reactive FFs for nucleation systems is even more challenging than developing covalently bonded materials because of the wide size range and high dimensional characteristics of noncovalent hydrogen bonding bridging clusters. Here, we propose a general workflow that is also applicable to other systems to train an accurate reactive FF based on a deep neural network (DNN) and further bridge DNN-FF-based molecular dynamics (MD) with a cluster kinetics model based on Poisson distributions of reactive events to overcome the high computational costs of direct MD. We found that previously reported acid-base formation rates tend to be significantly underestimated, especially in polluted environments, emphasizing that acid-base nucleation observed in multiple environments should be revisited.

GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing.

BACKGROUND: The main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug-disease relationships. Although many computational models have been proposed recently, it is still difficult to reliably predict drug-disease associations from a variety of sources of data. RESULTS: In order to identify potential drug-disease associations, this paper introduces a novel end-to-end model called Graph convolution network based on a multimodal attention mechanism (GCMM). In particular, GCMM incorporates known drug-disease relations, drug-drug chemical similarity, drug-drug therapeutic similarity, disease-disease semantic similarity, and disease-disease target-based similarity into a heterogeneous network. A Graph Convolution Network encoder is used to learn how diseases and drugs are embedded in various perspectives. Additionally, GCMM can enhance performance by applying a multimodal attention layer to assign various levels of value to various features and the inputting of multi-source information. CONCLUSION: 5 fold cross-validation evaluations show that the GCMM outperforms four recently proposed deep-learning models on the majority of the criteria. It shows that GCMM can predict drug-disease relationships reliably and suggests improvement in the desired metrics. Hyper-parameter analysis and exploratory ablation experiments are also provided to demonstrate the necessity of each module of the model and the highest possible level of prediction performance. Additionally, a case study on Alzheimer's disease (AD). Four of the five medications indicated by GCMM to have the highest potential correlation coefficient with AD have been demonstrated through literature or experimental research, demonstrating the viability of GCMM. All of these results imply that GCMM can provide a strong and effective tool for drug development and repositioning.

Sulfuric acid-dimethylamine particle formation enhanced by functional organic acids: an integrated experimental and theoretical study.

Atmospheric new particle formation (NPF), which has been observed globally in clean and polluted environments, is an important source of boundary-layer aerosol particles and cloud condensation nuclei, but the fundamental mechanisms leading to multi-component aerosol formation have not been well understood. Here, we use experiments and quantum chemical calculations to better understand the involvement of carboxylic acids in initial NPF from gas phase mixtures of carboxylic acid, sulfuric acid (SA), dimethylamine, and water. A turbulent flow tube coupled to an ultrafine condensation particle counter with particle size magnifier has been set up to measure NPF. Experimental results show that pyruvic acid (PA), succinic acid (SUA), and malic acid (MA) can enhance sulfuric acid-dimethylamine nucleation in the order PA < SUA < MA with a greater enhancement observed at lower SA concentrations. Computational results indicate that the carboxylic and hydroxyl groups are related to the enhancement. This experiment-theory study shows the formation of multi-component aerosol particles and the role of the organic functional group, which may aid in understanding the role of organics in aerosol nucleation and growth in polluted areas, and help to choose organic molecules of specific structures for simulation.

Telemedicine and Clinical Outcomes in Peritoneal Dialysis: A Propensity-Matched Study.

INTRODUCTION: Telemedicine (TM) has shown to provide potential benefits on clinical outcomes in patients with chronic kidney disease but limited evidences published in the peritoneal dialysis (PD) population. This study aimed to explore the long-term effects of TM on the mortality and technique failure. METHODS: The Peritoneal Dialysis Telemedicine-assisted Platform Cohort Study (PDTAP Study) was conducted prospectively in 27 hospitals in China since 2016. Patient and practice data were collected through the doctor-end of the TM app (Manburs) for all participants. TM including self-monitoring records, on-line education materials, and real-time physician-patient contact was only performed for the patient-end users of the Manburs. The primary outcome was all-cause mortality. The secondary outcomes were cause-specific mortality and all-cause and cause-specific permanent transfer to hemodialysis. RESULTS: A total of 7,539 PD patients were enrolled between June 2016 and April 2019, with follow-up till December 2020. Patients were divided into two cohorts: TM group (39.1%) and non-TM group (60.9%). A propensity score was used to create 2,160 matched pairs in which the baseline covariates were well-balanced. There were significantly lower risks of all-cause mortality (HR 0.59 [0.51, 0.67], p < 0.001), CVD mortality (HR 0.59 [0.49, 0.70], p < 0.001), all-cause transfer to hemodialysis (0.57 [0.48, 0.67], p < 0.001), transfer to hemodialysis from PD-related infection (0.67 [0.51, 0.88], p = 0.003), severe fluid overload (0.40 [0.30, 0.55], p < 0.001), inadequate solute clearance (0.49 [0.26, 0.92], p = 0.026), and catheter-related noninfectious complications (0.41 [0.17, 0.97], p = 0.041) in the TM group compared with the non-TM group. CONCLUSION: This study indicated real-world associations between TM usage and reduction in patient survival and technique survival through a multicenter prospective cohort.

Engineering of triterpene metabolism and overexpression of the lignin biosynthesis gene PAL promotes ginsenoside Rg3 accumulation in ginseng plant chassis.

The ginsenoside Rg3 found in Panax species has extensive pharmacological properties, in particular anti-cancer effects. However, its natural yield in Panax plants is limited. Here, we report a multi-modular strategy to improve yields of Rg3 in a Panax ginseng chassis, combining engineering of triterpene metabolism and overexpression of a lignin biosynthesis gene, phenylalanine ammonia lyase (PAL). We first performed semi-rational design and site mutagenesis to improve the enzymatic efficiency of Pq3-O-UGT2, a glycosyltransferase that directly catalyzes the biosynthesis of Rg3 from Rh2 . Next, we used clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing to knock down the branch pathway of protopanaxatriol-type ginsenoside biosynthesis to enhance the metabolic flux of the protopanaxadiol-type ginsenoside Rg3 . Overexpression of PAL accelerated the formation of the xylem structure, significantly improving ginsenoside Rg3 accumulation (to 6.19-fold higher than in the control). We combined overexpression of the ginsenoside aglycon synthetic genes squalene epoxidase, Pq3-O-UGT2, and PAL with CRISPR/Cas9-based knockdown of CYP716A53v2 to improve ginsenoside Rg3 accumulation. Finally, we produced ginsenoside Rg3 at a yield of 83.6 mg/L in a shake flask (7.0 mg/g dry weight, 21.12-fold higher than with wild-type cultures). The high-production system established in this study could be a potential platform to produce the ginsenoside Rg3 commercially for pharmaceutical use.