Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing.

Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel BEs but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.

Improving decryption quality of optical chaos communication using neural networks.

Optical chaos communication is a promising secure transmission technique because of the advantages of high speed and compatibility with existing fiber-optic systems. The deterioration of chaotic synchronization quality caused by fiber optic transmission impairments affects the quality of recovery of information, especially high-order modulated signals. Here, we demonstrate that the use of a convolutional neural network (CNN) with a bidirectional long short-term memory (LSTM) layer can reduce the decryption BER in an optical chaos communication system based on common-signal-induced semiconductor laser synchronization. The performance of a neural network is investigated as a function of network parameters and chaos synchronization coefficient. Experimental results show that the BER of 16-ary quadrature-amplitude-modulation (16QAM) signal after 100-km fiber transmission is decreased from 3.05 × 10-2 to below the soft-decision forward-error-correction (SD-FEC) threshold of 2.0 × 10-2.

Preoperative serum level of CA153 and a new model to predict the sub-optimal primary debulking surgery in patients with advanced epithelial ovarian cancer.

OBJECTIVE: The aim of this study was to establish a preoperative model to predict the outcome of primary debulking surgery (PDS) for advanced ovarian cancer (AOC) patients by combing Suidan predictive model with HE4, CA125, CA153 and ROMA index. METHODS: 76 AOC Patients in revised 2014 International Federation of Gynecology and Obstetrics (FIGO) stage III-IV who underwent PDS between 2017 and 2019 from Yunnan Cancer Hospital were included. Clinical data including the levels of preoperative serum HE4, CA125, CA153 and mid-lower abdominal CT-enhanced scan results were collected. The logistics regression analysis was performed to find factors associated with sub-optimal debulking surgery (SDS). The receiver operating characteristic curve was used to evaluate the predictive performances of selected variables in the outcome of primary debulking surgery. The predictive index value (PIV) model was constructed to predict the outcome of SDS. RESULTS: Optimal surgical cytoreduction was achieved in 61.84% (47/76) patients. The value for CA125, HE4, CA153, ROMA index and Suidan score was lower in optimal debulking surgery (ODS) group than SDS group. Based on the Youden index, which is widely used for evaluating the performance of predictive models, the best cutoff point for the preoperative serum HE4, CA125, CA153, ROMA index and Suidan score to distinguish SDS were 431.55 pmol/l, 2277 KU/L, 57.19 KU/L, 97.525% and 2.5, respectively. Patients with PIV≥5 may not be able to achieve optimal surgical cytoreduction. The diagnostic accuracy, NPV, PPV and specificity for diagnosing SDS were 73.7%, 82.9%, 62.9% and 72.3%, respectively. In the constructed model, the AUC of the SDS prediction was 0.770 (95% confidence interval: 0.654-0.887), P<0.001. CONCLUSION: Preoperative serum CA153 level is an important non-invasive predictor of primary SDS in advanced AOC, which has not been reported before. The constructed PIV model based on Suidan's predictive model plus HE4, CA125, CA153 and ROMA index can noninvasively predict SDS in AOC patients, the accuracy of this prediction model still needs to be validated in future studies.

Impact of Diagnosis-Related-Group (DRG) payment on variation in hospitalization expenditure: evidence from China.

BACKGROUND: Diagnosis-Related-Group (DRG) payment is considered a crucial means of addressing the rapid increases of medical cost and variation in cost. This paper analyzes the impact of DRG payment on variation in hospitalization expenditure in China. METHOD: Patients with chronic obstructive pulmonary disease (COPD), acute myocardial infarction (AMI) and cerebral infarction (CI) in a Chinese City Z were selected. Patients in the fee-for-service (FFS) payment group and the DRG payment group were used as the control group and intervention group, respectively, and propensity-score-matching (PSM) was conducted. Interquartile distance (IQR), standard deviation (SD) and concentration index were used to analyze variation and trends in terms of hospitalization expenditure across the different groups. RESULTS: After DRG payment reform, the SD of hospitalization expenditure in respect of the COPD, AMI and CI patients in City Z decreased by 11,094, 4,833 and 4,987 CNY, respectively. The concentration indices of hospitalization expenditures for three diseases are all below 0 (statistically significant), with the absolute value tending to increase year by year. CONCLUSION: DRG payment can be seen to guide medical service providers to provide effective treatment that can improve the consistency of medical care services, bringing the cost of medical care closer to its true clinical value.

Identification of Anthocyanin Composition and Functional Analysis of an Anthocyanin Activator in Solanum nigrum Fruits.

Solanum nigrum fruits have been conventionally used in beverages due to their nutritional substances such as minerals, vitamins, amino acids, proteins, sugars, polyphenols, and anthocyanins. The characterization of components and regulatory mechanism of anthocyanins in S. nigrum fruits have rarely been reported. In this study, we determined that the peel and flesh of S. nigrum fruits shared similar HPLC profiles but different contents and total antioxidant activities for anthocyanins. After an efficient purification method, mainly including extraction with pH 1.0 distilled water and then desorption with pH 1.0 95% ethanol after a DM-130 resin adsorption step to obtain more pure anthocyanin extracts, the purity of anthocyanins extracted from S. nigrum fruits reached 56.1%. Moreover, eight anthocyanins from S. nigrum fruit were identified with HPLC-MS/MS for the first time. A typical R2R3-MYB transcription factor gene, SnMYB, was also cloned for the first time by rapid amplification of cDNA ends (RACE)-PCR from S. nigrum. Moreover, the contents of anthocyanins were shown to correlate well (r = 0.93) with the expression levels of SnMYB gene during the fruit's developmental stages. Most significantly, SnMYB gene successfully produced high anthocyanin content (1.03 mg/g) when SnMYB gene was transiently expressed in tobacco leaves. Taken together, S. nigrum fruits are a promising resource for anthocyanin extraction, and SnMYB gene is an activator that positively regulates anthocyanin biosynthesis in S. nigrum.

Study on Micro Production Mechanism of Corner Residual Oil after Polymer Flooding.

To study the microscopic production mechanism of corner residual oil after polymer flooding, microscopic visualization oil displacement technology and COMSOL finite element numerical simulation methods were used. The influence of the viscosity and interfacial tension of the oil displacement system after polymer flooding on the movement mechanism of the corner residual oil was studied. The results show that by increasing the viscosity of the polymer, a portion of the microscopic remaining oil in the corner of the oil-wet property can be moved whereas that in the corner of the water-wet property cannot be moved at all. To move the microscopic remaining oil in the corners with water-wet properties after polymer flooding, the viscosity of the displacement fluid or the displacement speed must be increased by 100-1000 times. Decreasing the interfacial tension of the oil displacement system changed the wettability of the corner residual oil, thus increasing the wetting angle. When the interfacial tension level reached 10-2 mN/m, the degree of movement of the remaining oil in the corner reached a maximum. If the interfacial tension is reduced, the degree of production of the residual oil in the corner does not change significantly. The microscopic production mechanism of the corner residual oil after polymer flooding expands the scope of the displacement streamlines in the corner.

Assessing the quality of primary healthcare for diabetes in China: multivariate analysis using the China Health and Retirement Longitudinal Study (CHARLS) Database.

OBJECTIVE: To assess the quality of primary healthcare (PHC) for patients with diabetes in China from 2011 to 2015. SETTING: This study analysed data on 1006, 1472 and 1771 participants with diabetes who were surveyed in 2011, 2013 and 2015, respectively, in the China Health and Retirement Longitudinal Study, a nationally representative survey conducted in 29 provinces of China. OUTCOME MEASURES: The study measured the proportions of patients with diabetes who received diabetes-related health education, examinations and treatments, as well as the hospital admission rate due to diabetes of these patients. Multilevel logistic regression was used to adjust sociodemographic variables. RESULTS: According to the multivariate analysis, the proportion of patients who received diabetes-related health education decreased significantly (OR=0.74, 95% CI 0.61 to 0.90), and the proportion of those receiving examinations and treatments remained unchanged from 2011 to 2015. Diabetes-related hospitalisation increased from 4.01% in 2011 to 6.08% in 2013 (OR=1.47, 95% CI 0.97 to 2.22), and recurrent hospitalisations increased from 18.87% in 2011 to 28.45% in 2015 (OR=1.78, 95% CI 1.44 to 2.20). The proportions of patients with diabetes-related and recurrent hospitalisations in western China were higher than those in the east (OR=1.80, 95% CI 1.13 to 2.87; OR=1.92, 95% CI 1.50 to 2.45). CONCLUSIONS: Nationally, the analysis of patient-reported process and outcome indicators cannot confirm that the quality of PHC has improved in China during 2011-2015. Regional disparities in primary diabetes care require urgent resource allocation to western China. Establishing a national quality registry for PHC, which transparently reports outcomes by region and social-economic position, is essential for countries sharing the challenge of improving both quality and equity of PHC.