Interpretable machine learning identifies metabolites associated with glomerular filtration rate in type 2 diabetes patients.

Objective: The co-occurrence of kidney disease in patients with type 2 diabetes (T2D) is a major public health challenge. Although early detection and intervention can prevent or slow down the progression, the commonly used estimated glomerular filtration rate (eGFR) based on serum creatinine may be influenced by factors unrelated to kidney function. Therefore, there is a need to identify novel biomarkers that can more accurately assess renal function in T2D patients. In this study, we employed an interpretable machine-learning framework to identify plasma metabolomic features associated with GFR in T2D patients. Methods: We retrieved 1626 patients with type 2 diabetes (T2D) in Liaoning Medical University First Affiliated Hospital (LMUFAH) as a development cohort and 716 T2D patients in Second Affiliated Hospital of Dalian Medical University (SAHDMU) as an external validation cohort. The metabolite features were screened by the orthogonal partial least squares discriminant analysis (OPLS-DA). We compared machine learning prediction methods, including logistic regression (LR), support vector machine (SVM), random forest (RF), and eXtreme Gradient Boosting (XGBoost). The Shapley Additive exPlanations (SHAP) were used to explain the optimal model. Results: For T2D patients, compared with the normal or elevated eGFR group, glutarylcarnitine (C5DC) and decanoylcarnitine (C10) were significantly elevated in GFR mild reduction group, and citrulline and 9 acylcarnitines were also elevated significantly (FDR<0.05, FC > 1.2 and VIP > 1) in moderate or severe reduction group. The XGBoost model with metabolites had the best performance: in the internal validate dataset (AUROC=0.90, AUPRC=0.65, BS=0.064) and external validate cohort (AUROC=0.970, AUPRC=0.857, BS=0.046). Through the SHAP method, we found that C5DC higher than 0.1µmol/L, Cit higher than 26 µmol/L, triglyceride higher than 2 mmol/L, age greater than 65 years old, and duration of T2D more than 10 years were associated with reduced GFR. Conclusion: Elevated plasma levels of citrulline and a panel of acylcarnitines were associated with reduced GFR in T2D patients, independent of other conventional risk factors.

Explainable Machine Learning-Based Prediction Model for Diabetic Nephropathy.

The aim of this study is to analyze the effect of serum metabolites on diabetic nephropathy (DN) and predict the prevalence of DN through a machine learning approach. The dataset consists of 548 patients from April 2018 to April 2019 in the Second Affiliated Hospital of Dalian Medical University (SAHDMU). We select the optimal 38 features through a least absolute shrinkage and selection operator (LASSO) regression model and a 10-fold cross-validation. We compare four machine learning algorithms, including extreme gradient boosting (XGB), random forest, decision tree, and logistic regression, by AUC-ROC curves, decision curves, and calibration curves. We quantify feature importance and interaction effects in the optimal predictive model by Shapley additive explanation (SHAP) method. The XGB model has the best performance to screen for DN with the highest AUC value of 0.966. The XGB model also gains more clinical net benefits than others, and the fitting degree is better. In addition, there are significant interactions between serum metabolites and duration of diabetes. We develop a predictive model by XGB algorithm to screen for DN. C2, C5DC, Tyr, Ser, Met, C24, C4DC, and Cys have great contribution in the model and can possibly be biomarkers for DN.

Radiomic advances in the transarterial chemoembolization related therapy for hepatocellular carcinoma.

Radiomics is a hot topic in the research on customized oncology treatment, efficacy evaluation, and tumor prognosis prediction. To achieve the goal of mining the heterogeneity information within the tumor tissue, the image features concealed within the tumoral images are turned into quantifiable data features. This article primarily describes the research progress of radiomics and clinical-radiomics combined model in the prediction of efficacy, the choice of treatment modality, and survival in transarterial chemoembolization (TACE) and TACE combination therapy for hepatocellular carcinoma.

A Metabolism-Based Interpretable Machine Learning Prediction Model for Diabetic Retinopathy Risk: A Cross-Sectional Study in Chinese Patients with Type 2 Diabetes.

The burden of diabetic retinopathy (DR) is increasing, and the sensitive biomarkers of the disease were not enough. Studies have found that the metabolic profile, such as amino acid (AA) and acylcarnitine (AcylCN), in the early stages of DR patients might have changed, indicating the potential of metabolites to become new biomarkers. We are amid to construct a metabolite-based prediction model for DR risk. This study was conducted on type 2 diabetes (T2D) patients with or without DR. Logistic regression and extreme gradient boosting (XGBoost) prediction models were constructed using the traditional clinical features and the screening features, respectively. Assessing the predictive power of the models in terms of both discrimination and calibration, the optimal model was interpreted using the Shapley Additive exPlanations (SHAP) to quantify the effect of features on prediction. Finally, the XGBoost model incorporating AA and AcylCN variables had the best comprehensive evaluation (ROCAUC = 0.82, PRAUC = 0.44, Brier score = 0.09). C18 : 1OH lower than 0.04 µmol/L, C18 : 1 lower than 0.70 µmol/L, threonine higher than 27.0 µmol/L, and tyrosine lower than 36.0 µmol/L were associated with an increased risk of developing DR. Phenylalanine higher than 52.0 µmol/L was associated with a decreased risk of developing DR. In conclusion, our study mainly used AAs and AcylCNs to construct an interpretable XGBoost model to predict the risk of developing DR in T2D patients which is beneficial in identifying high-risk groups and preventing or delaying the onset of DR. In addition, our study proposed possible risk cut-off values for DR of C18 : 1OH, C18 : 1, threonine, tyrosine, and phenylalanine.

Identification of predictive factors for post-transarterial chemoembolization liver failure in hepatocellular carcinoma patients: A retrospective study.

BACKGROUND: Post-transarterial chemoembolization (TACE) liver failure occurs frequently in hepatocellular carcinoma (HCC) patients. The identification of predictors for post-TACE liver failure is of great importance for clinical decision-making in this population. AIM: To investigate the occurrence rate and predictive factors of post-TACE liver failure in this retrospective study to provide clues for decision-making regarding TACE procedures in HCC patients. METHODS: The clinical records of HCC patients treated with TACE therapy were reviewed. Baseline clinical characteristics and laboratory parameters of these patients were extracted. Logistic models were used to identify candidates to predict post-TACE liver failure. RESULTS: A total of 199 HCC patients were enrolled in this study, and 70 patients (35.2%) developed post-TACE liver failure. Univariate and multivariate logistic models indicated that microspheres plus gelatin embolization and main tumor size > 5 cm were risk predictors for post-TACE liver failure [odds ratio (OR): 4.4, 95% confidence interval (CI): 1.2-16.3, P = 0.027; OR: 2.3, 95%CI: 1.05-5.3, P = 0.039, respectively]. Conversely, HCC patients who underwent tumor resection surgery before the TACE procedure had a lower risk for post-TACE liver failure (OR: 0.4, 95%CI: 0.2-0.95, P = 0.039). CONCLUSION: Microspheres plus gelatin embolization and main tumor size might be risk factors for post-TACE liver failure in HCC patients, while prior tumor resection could be a favorable factor reducing the risk of post-TACE liver failure.

Effects of shikonin on the development of ovarian follicles and female germline stem cells.

OBJECTIVE: To investigate the effects and potential mechanism of action of shikonin (SHK) on the development of ovarian follicles and female germline stem cells (FGSCs). METHODS: Female Kunming adult mice were administered SHK (0, 20 and 50 mg/kg) by oral gavage. Cultures of FGSCs were treated with SHK 32 µmol/l for 24 h. The ovarian index in mouse ovaries was calculated. Numbers of primordial, primary and atretic follicles were counted. Germline stem cell markers and apoptosis were examined. Levels of glutathione (GSH), superoxide dismutase (SOD) and reactive oxygen species (ROS) were measured. RESULTS: Both doses of SHK significantly decreased the ovarian index, the numbers of primordial follicles, primary follicles and antral follicles in mice. SHK significantly increased the numbers of atretic follicles and atretic corpora lutea. SHK promoted apoptosis in vivo and in vitro. SHK significantly decreased the levels of the germline stem cell markers. SHK significantly lowered GSH levels and the activity of SOD in the peripheral blood from mice, whereas SHK significantly elevated cellular ROS content in FGSCs. CONCLUSIONS: These current results suggested that follicular development and FGSCs were suppressed by SHK through the induction of apoptosis and oxidative stress might be involved in this pathological process.

[Seedlings regenerative dynamics of dominant trees in a secondary forest in montane region of eastern Liaoning Province, China]. / è¾½ä¸œå±±åŒºæ¬¡ç”Ÿæž—ä¹”æœ¨ä¼˜åŠ¿æ ‘ç§å¹¼è‹—æ›´æ–°åŠ¨æ€.

To reveal the seedlings dynamics of dominant trees and their response to canopy changes (as indicated by changes in leaf area index), we analyzed the seedlings dynamics of dominant trees and canopy structure during forest regeneration based on three-year (2014 to 2016) censuses and hemispherical photography in a 4 hm2 forest dynamics monitoring plot. The results showed that canopy LAI first decreased and then increased during the survey period, with significant interannual difference. The seedlings of 12 dominant tree species showed notable response to the change of canopy structure, with the response varying among different tree species. The relative abundance or frequency of seedlings for neutral tree species generally increased with the decreases of canopy LAI. The relative abundance or frequency of seedlings of light-demanding tree species generally decreased with the increases of canopy LAI. In multi-response permutation procedures by analyzing the numeric composition and distribution of dominant tree seedlings, there was significant difference among the three censuses. Such interannual difference gradually decreased from 2014 to 2016. Significant change occurred in the indicator species of dominant tree seedlings, reflecting their responses to the changes of canopy structure.

Regulation of Mesenchymal Stem to Transit-Amplifying Cell Transition in the Continuously Growing Mouse Incisor.

In adult tissues and organs with high turnover rates, the generation of transit-amplifying cell (TAC) populations from self-renewing stem cells drives cell replacement. The role of stem cells is to provide a renewable source of cells that give rise to TACs to provide the cell numbers that are necessary for cell differentiation. Regulation of the formation of TACs is thus fundamental to controlling cell replacement. Here, we analyze the properties of a population of mesenchymal TACs in the continuously growing mouse incisor to identify key components of the molecular regulation that drives proliferation. We show that the polycomb repressive complex 1 acts as a global regulator of the TAC phenotype by its direct action on the expression of key cell-cycle regulatory genes and by regulating Wnt/ß-catenin-signaling activity. We also identify an essential requirement for TACs in maintaining mesenchymal stem cells, which is indicative of a positive feedback mechanism.

[Spatial pattern and interspecific spatial association of tree seedlings in a secondary forest in montane region of eastern Liaoning Province, China.] / è¾½ä¸œå±±åŒºæ¬¡ç”Ÿæž—ä¹”æœ¨å¹¼è‹—åˆ†å¸ƒæ ¼å±€ä¸Žç§é—´ç©ºé—´å ³è”æ€§.

We established a 4 hm2(200 m×200 m) temperate secondary forest plot in the montane region of eastern Liaoning Province, China, and analyzed the spatial patterns and interspecific spatial associations of tree seedlings at scales of 0-50 m. The results showed that under complete spatial randomness null model, 95% of the species at the scale of 0-20 m showed a significant aggregation pattern, and 19 species at the scale of 0-16 m showed an aggregation pattern. The proportion of species exhibiting aggregated patterns decreased with the spatial scale. At the scale of 50 m, the random distribution pattern became the main form of tree species distribution. Underheterogeneous Poisson process null model, 5% of the species at the scale of 0-24 m showed a significant aggregation pattern, and 42% and 58% of the species at the scale of 26-50 m showed a random distribution and regularity patterns, respectively. Under complete spatial randomness null model, the proportion of species pairs of positive correlation was the highest, and at the scale of 50 m, the proportion of species pairs showed positive correlation, uncorrelated and negative correlation tended to be equal. Under heterogeneous Poisson process null model, species pairs mainly showed negative correlation, and the proportion of species pairs exhibiting negative correlation increased with spatial scale. The results implied that seed dispersal limitation and habitat heterogeneity could explain the aggregation pattern of tree seedlings. The strong aggregation of tree seedlings also contributed to close interspecific spatial associations and poor stability of the regeneration community.

Anti-inflammatory and blood stasis activities of essential oil extracted from Artemisia argyi leaf in animals.

Artemisia argyi leaf is a well-known species in traditional Chinese medicine. However, the anti-inflammatory and activating blood stasis activities of its essential oil (AAEO) have not been explored in vivo. The present study measured the contents of three chemical components by gas chromatography (GC). The anti-acute inflammatory effects of AAEO were investigated in dimethyl benzene, glacial acetic acid and carrageenan-induced animals through skin administration or by oral gavage, respectively. The effects of AAEO on haemorheology were studied in a rat acute blood stasis model. The contents of eucalyptol, camphor and borneol in AAEO were 254.4, 51.6 and 58.7 mg/g, respectively. All dosages of AAEO by skin administration significantly decreased the swelling in dimethyl benzene-induced ear oedema and carrageenan-induced paw oedema, and reduced the permeability in glacial acetic acid-induced abdominal blood capillary (p < 0.01). Meanwhile, haemorheology indexes such as whole blood viscosity and the erythrocyte aggregation index significantly decreased only in the high dosage group. In addition, the effects of AAEO by oral gavage were weaker than skin administration at the medium dose in the experiments. It suggests that AAEO has better absorption bioavailability and pharmacological effects through skin administration due to the better skin permeability of essential oil than gastrointestinal absorption.

Uncertainty analysis of primary water pollutant control in China's pulp and paper industry.

The total emission control target of water pollutants (e.g., COD and NH4-N) for a certain industrial sector can be predicted and analysed using the popular technology-based bottom-up modelling. However, this methodology has obvious uncertainty regarding the attainment of mitigation targets. The primary uncertainty comes from macro-production, pollutant reduction roadmap, and technical parameters. This research takes the paper and pulp industry in China as an example, and builds 5 mitigation scenarios via different combinations of raw material structure, scale structure, procedure mitigation technology, and end-of-pipe treatment technology. Using the methodology of uncertainty analysis via Monte Carlo, random sampling was conducted over a hundred thousand times. According to key parameters, sensitive parameters that impact total emission control targets such as industrial output, technique structure, cleaner production technology, and end-of-pipe treatment technology are discussed in this article. It appears that scenario uncertainty has a larger influence on COD emission than NH4-N, hence it is recommended that a looser total emission control target for COD is necessary to increase its feasibility and availability while maintaining the status quo of NH4-N. Consequently, from uncertainty analysis, this research recognizes the sensitive products, techniques, and technologies affecting industrial water pollution.

The consumption and recycling collection system of PET bottles: a case study of Beijing, China.

After studying the recycling collection system of polyethylene terephthalate (PET) bottles worldwide, the authors conducted an intercept survey in Beijing. Two separate questionnaires were issued, one questionnaire to PET bottle consumers and one to PET bottle recyclers. In this study, consumers are defined as people that consume PET-bottled beverages in their daily life. Recyclers were defined as those involved in the collection and recycling of PET bottles. These include scavengers, itinerant waste buyers, small community waste-buying depots, medium/large redemption depots, and recycling companies. In total, 580 surveys were completed, including 461 by consumers and 119 by recyclers. The authors found that consumption of PET bottles in Beijing was nearly 100,000 tonnes in 2012. Age, occupation, gender, and education were identified as significant factors linked to PET-bottled beverage consumption, while income was not a significant factor. 90% Of post-consumed PET bottles were collected by informal collectors (i.e., scavengers and itinerant waste buyers). The survey also found that nearly all PET bottles were reprocessed by small factories that were not designed with pollution control equipment, which allows them to offer higher prices for waste recyclable bottles. As Beijing is trying to build a formal recycling collection system for recyclables, subsidies should be given to the formal recycling sector rather than being charged land use fees, and attention should also be given to informal recyclers that make their living from the collection of recyclables. Informal and formal sectors may work together by employing the scavengers and itinerant waste buyers for the formal sectors. In addition to the recycling of PET bottles, concern should also be allocated to reduce consumption, especially among young people, as they, compared to other groups, have a stronger demand for PET-bottled beverages and will be the main body of society.

[Method for environmental management in paper industry based on pollution control technology simulation].

To evaluate the reduction potential of industrial water pollutant emissions and to study the application of technology simulation in pollutant control and environment management, an Industrial Reduction Potential Analysis and Environment Management (IRPAEM) model was developed based on coupling of "material-process-technology-product". The model integrated bottom-up modeling and scenario analysis method, and was applied to China's paper industry. Results showed that under CM scenario, the reduction potentials of waster water, COD and ammonia nitrogen would reach 7 x 10(8) t, 39 x 10(4) t and 0.3 x 10(4) t, respectively in 2015, 13.8 x 10(8) t, 56 x 10(4) t and 0.5 x 10(4) t, respectively in 2020. Strengthening the end-treatment would still be the key method to reduce emissions during 2010-2020, while the reduction effect of structure adjustment would be more obvious during 2015-2020. Pollution production could basically reach the domestic or international advanced level of clean production in 2015 and 2020; the index of wastewater and ammonia nitrogen would basically meet the emission standards in 2015 and 2020 while COD would not.

Rectal adenocarcinoma metastatic to the tonsil; PET-CT observations with pathological confirmation: A case report.

Metastasis of rectal adenocarcinoma develops by lymphatic or hematogenous spread. The usual sites of metastasis from rectal adenocarcinoma include local and distant lymph nodes, the liver and the lungs. The current case report presents a unique case of a mass that was identified in the tonsil by positron emission tomography-computed tomography (PET-CT), indicating a metastasis from rectal adenocarcinoma. Metastatic tumor to the tonsil is extremely rare and to the best of our knowledge, no previous studies have reported a case of tonsil metastasis from rectal adenocarcinoma. PET-CT scanners represent an important evolution in technology that is helping to bring anatomical imaging togeother with functional imaging in cancer diagnosis and therapy. Written informed consent was obtained from the patient.

Stanniocalcin-1 protects bovine intestinal epithelial cells from oxidative stress-induced damage

Chronic enteritis can produce an excess of reactive oxygen species resulting in cellular damage. Stanniocalcin-1(STC-1) reportedly possesses anti-oxidative activity, the aim of this study was to define more clearly the direct contribution of STC-1 to anti-oxidative stress in cattle. In this study, primary intestinal epithelial cells (IECs) were exposed to hydrogen peroxide (H2O2) for different time intervals to mimic chronic enteritis-induced cellular damage. Prior to treatment with 200 microM H2O2, the cells were transfected with a recombinant plasmid for 48 h to over-express STC-1. Acridine orange/ethidium bromide (AO/EB) double staining and trypan blue exclusion assays were then performed to measure cell viability and apoptosis of the cells, respectively. The expression of STC-1 and apoptosis-related proteins in the cells was monitored by real-time PCR and Western blotting. The results indicated that both STC-1 mRNA and protein expression levels positively correlated with the duration of H2O2 treatment. H2O2 damaged the bovine IECs in a time-dependent manner, and this effect was attenuated by STC-1 over-expression. Furthermore, over-expression of STC-1 up-regulated Bcl-2 protein expression and slightly down-regulated caspase-3 production in the damaged cells. Findings from this study suggested that STC-1 plays a protective role in intestinal cells through an antioxidant mechanism.

[Study on moxa sticks burning temperature-time-space curves].

OBJECTIVE: To study the burning characteristics of moxa stick. METHODS: A self-designed moxa stick burning temperature measuring device, which was assembled with ALTEC intelligence digital setter and SJ-600 thermocouple, was used to conduct next four experiences: 1) embedding a thermocouple inside a moxa stick to measure peak burning temperature; 2) pulling a thermocouple embedded in the moxa stick at the proper rate to detect combustion stability; 3) elucidating temperature distribution of transverse section by measuring the temperature in the center, radius midpoint and lateral; 4) drawing temperature-time-space curves by pulling the thermocouples in the former three observation points. RESULTS: The experiment indicated that the burning temperature peak of three-year moxa stick (Hubei Herbal Medicine St. Qichun Technology Co., Ltd.) was 848 degrees C which had good combustion stability. Furthermore, the temperature in the center, radius midpoint and lateral of transverse section were 843 degrees C, 731 degrees C and 410 degrees C, respectively, and its burning temperature-time-space curves was drawn, which showed the real-time burning temperature and the peak burning temperature and were regarded as ultimate indice to integrate the formers. CONCLUSION: The measuring system elaborately reflecting the burning features of moxa stick may provide reference for manufacture industry of moxa stick quality criteria for its convenience and accuracy.

A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.).

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.

Study on moxa sticks burning temperature-time-space curves / 中国针灸

<p><b>OBJECTIVE</b>To study the burning characteristics of moxa stick.</p><p><b>METHODS</b>A self-designed moxa stick burning temperature measuring device, which was assembled with ALTEC intelligence digital setter and SJ-600 thermocouple, was used to conduct next four experiences: 1) embedding a thermocouple inside a moxa stick to measure peak burning temperature; 2) pulling a thermocouple embedded in the moxa stick at the proper rate to detect combustion stability; 3) elucidating temperature distribution of transverse section by measuring the temperature in the center, radius midpoint and lateral; 4) drawing temperature-time-space curves by pulling the thermocouples in the former three observation points.</p><p><b>RESULTS</b>The experiment indicated that the burning temperature peak of three-year moxa stick (Hubei Herbal Medicine St. Qichun Technology Co., Ltd.) was 848 degrees C which had good combustion stability. Furthermore, the temperature in the center, radius midpoint and lateral of transverse section were 843 degrees C, 731 degrees C and 410 degrees C, respectively, and its burning temperature-time-space curves was drawn, which showed the real-time burning temperature and the peak burning temperature and were regarded as ultimate indice to integrate the formers.</p><p><b>CONCLUSION</b>The measuring system elaborately reflecting the burning features of moxa stick may provide reference for manufacture industry of moxa stick quality criteria for its convenience and accuracy.</p>