Interpretable machine learning-based clinical prediction model for predicting lymph node metastasis in patients with intrahepatic cholangiocarcinoma.

OBJECTIVE: Prediction of lymph node metastasis (LNM) for intrahepatic cholangiocarcinoma (ICC) is critical for the treatment regimen and prognosis. We aim to develop and validate machine learning (ML)-based predictive models for LNM in patients with ICC. METHODS: A total of 345 patients with clinicopathological characteristics confirmed ICC from Jan 2007 to Jan 2019 were enrolled. The predictors of LNM were identified by the least absolute shrinkage and selection operator (LASSO) and logistic analysis. The selected variables were used for developing prediction models for LNM by six ML algorithms, including Logistic regression (LR), Gradient boosting machine (GBM), Extreme gradient boosting (XGB), Random Forest (RF), Decision tree (DT), Multilayer perceptron (MLP). We applied 10-fold cross validation as internal validation and calculated the average of the areas under the receiver operating characteristic (ROC) curve to measure the performance of all models. A feature selection approach was applied to identify importance of predictors in each model. The heat map was used to investigate the correlation of features. Finally, we established a web calculator using the best-performing model. RESULTS: In multivariate logistic regression analysis, factors including alcoholic liver disease (ALD), smoking, boundary, diameter, and white blood cell (WBC) were identified as independent predictors for LNM in patients with ICC. In internal validation, the average values of AUC of six models ranged from 0.820 to 0.908. The XGB model was identified as the best model, the average AUC was 0.908. Finally, we established a web calculator by XGB model, which was useful for clinicians to calculate the likelihood of LNM. CONCLUSION: The proposed ML-based predicted models had a good performance to predict LNM of patients with ICC. XGB performed best. A web calculator based on the ML algorithm showed promise in assisting clinicians to predict LNM and developed individualized medical plans.

RKHS-based covariate balancing for survival causal effect estimation.

Survival causal effect estimation based on right-censored data is of key interest in both survival analysis and causal inference. Propensity score weighting is one of the most popular methods in the literature. However, since it involves the inverse of propensity score estimates, its practical performance may be very unstable, especially when the covariate overlap is limited between treatment and control groups. To address this problem, a covariate balancing method is developed in this paper to estimate the counterfactual survival function. The proposed method is nonparametric and balances covariates in a reproducing kernel Hilbert space (RKHS) via weights that are counterparts of inverse propensity scores. The uniform rate of convergence for the proposed estimator is shown to be the same as that for the classical Kaplan-Meier estimator. The appealing practical performance of the proposed method is demonstrated by a simulation study as well as two real data applications to study the causal effect of smoking on survival time of stroke patients and that of endotoxin on survival time for female patients with lung cancer respectively.

Exogenous carbon turnover within the soil food web strengthens soil carbon sequestration through microbial necromass accumulation.

Exogenous carbon turnover within soil food web is important in determining the trade-offs between soil organic carbon (SOC) storage and carbon emission. However, it remains largely unknown how soil food web influences carbon sequestration through mediating the dual roles of microbes as decomposers and contributors, hindering our ability to develop policies for soil carbon management. Here, we conducted a 13 C-labeled straw experiment to demonstrate how soil food web regulated the residing microbes to influence the soil carbon transformation and stabilization process after 11 years of no-tillage. Our work demonstrated that soil fauna, as a "temporary storage container," indirectly influenced the SOC transformation processes and mediated the SOC sequestration through feeding on soil microbes. Soil biota communities acted as both drivers of and contributors to SOC cycling, with 32.0% of exogenous carbon being stabilizing in the form of microbial necromass as "new" carbon. Additionally, the proportion of mineral-associated organic carbon and particulate organic carbon showed that the "renewal effect" driven by the soil food web promoted the SOC to be more stable. Our study clearly illustrated that soil food web regulated the turnover of exogenous carbon inputs by and mediated soil carbon sequestration through microbial necromass accumulation.

Ambient Fine Particulate Matter and Cancer: Current Evidence and Future Perspectives.

The high incidence of cancer has placed an enormous health and economic burden on countries around the world. In addition to evidence of epidemiological studies, conclusive evidence from animal experiments and mechanistic studies have also shown that morbidity and mortality of some cancers can be attributed to ambient fine particulate matter (PM2.5) exposure, especially in lung cancer. However, the underlying carcinogenetic mechanisms of PM2.5 remain unclear. Furthermore, in terms of risks of other types of cancer, both epidemiological and mechanistic evidence are more limited and scattered, and the results are also inconsistent. In order to sort out the carcinogenic effect of PM2.5, this paper reviews the association of cancers with PM2.5 based on epidemiological and biological evidence including genetic, epigenetic, and molecular mechanisms. The limitations of existing researches and the prospects for the future are also well clarified in this paper to provide insights for future studies.

Effects of HMW-GSs at Glu-B1 locus on starch-protein interaction and starch digestibility during thermomechanical processing of wheat dough.

BACKGROUND: The composition of glutenin protein significantly affects protein-starch interactions and starch digestion characteristics in wheat dough matrices. To elucidate the effects of high molecular weight glutenin subunits at the Glu-B1 locus on dough processing quality, the detailed structural changes of protein, starch, and their complexes were compared in Mixolab dough samples of two near isogenic lines 7 + 8 and 7 + 9. RESULTS: The results showed that the degree of protein aggregation increased continuously during dough processing, as did the destruction and rearrangement of the gluten network. Compared to 7 + 8, the stronger and more stable protein network formed in 7 + 9 dough induced intensive interactions between protein and starch, primarily through hydrogen bonds and isomeric glycosidic bonds. In 7 + 9 dough, the more compact and extensive protein-starch network significantly inhibited starch gelatinization during dough pasting, while during the dough cooling stage [from C4 (82.8 °C) to C5 (52.8 °C)], more protein-starch complexes composed of monomeric proteins and short-chain starch were generated, which remarkably inhibited starch retrogradation. All protein-starch interactions in the 7 + 9 dough improved the starch digestion resistance, as reflected by the high content of resistant starch. CONCLUSION: The more extensive and intensive protein-starch interactions in the 7 + 9 dough inhibited the gelatinization and enzymatic hydrolysis of starch, thereby producing more slowly digestible starch and resistant starch. These findings demonstrate the feasibility of optimizing the texture and digestibility of wheat-based food products by regulating the behavior and interactions of proteins and starch during dough processing. © 2022 Society of Chemical Industry.

[Molecular markers for predicting the success of micro-TESE in non-obstructive azoospermia].

Non-obstract azoospermia (NOA) is a serious male infertility disease. At present, testicular sperm extraction (micro-TESE) is performed in combination with intracytoplasmic sperm injection (ICSI) technology, NOA patients can have their own consanguine offspring. However, due to the invasiveness and uncertainty of micro-TESE surgery, it is difficult for patients to accept it. Therefore, finding an accurate method to predict the possibility of micro-TESE successful sperm retrival would be beneficial to azoospermia patients. Many genes are transcribed and expressed during spermatogenesis, and molecular assays have irreplaceable sensitivity and specificity in predicting the success sperm retrivel of micro-TESE. This article reviews the methods to predict the success sperm retrivel of micro-TESE including mRNA, non-coding RNA (piRNA, microRNA, cirRNA, tFRNAs) and some protein so far, to provide certain reference value for clinical and subsequent research.

Brønsted Acid-Catalyzed Carbonyl-Olefin Metathesis: Synthesis of Phenanthrenes via Phosphomolybdic Acid as a Catalyst.

Compared with the impressive achievements of catalytic carbonyl-olefin metathesis (CCOM) mediated by Lewis acid catalysts, exploration of the CCOM through Brønsted acid-catalyzed approaches remains quite challenging. Herein, we disclose a synthetic protocol for the construction of a valuable polycycle scaffold through the CCOM with the inexpensive, nontoxic phosphomolybdic acid as a catalyst. The current annulations could realize carbonyl-olefin, carbonyl-alcohol, and acetal-alcohol in situ CCOM reactions and feature mild reaction conditions, simple manipulation, and scalability, making this strategy a promising alternative to the Lewis acid-catalyzed COM reaction.

Identification of the yield traits related haplotype combinations of transcription factor genes TaHDZ34 in common wheat.

A predominant objective in wheat breeding is improving yield-related traits. The homeodomain-leucine zipper (HD-Zip) transcription factor plays a significant role in plant growth and development. In this study, we cloned all homeologs of TaHDZ34, which is a member of the HD-Zip class IV transcription factor family in wheat (Triticum aestivum L.). Sequence polymorphism analysis showed that TaHDZ-A34, TaHDZ-B34, and TaHDZ-D34 formed five, six, and six haplotypes, respectively, and the genes were divided into two main haplotype groups. We also developed functional molecular markers. The TaHDZ34 genes were divided into eight main haplotype combinations. Association analysis and distinct population validation preliminarily indicated that TaHDZ34 genes modulate grain number per spike, effective spikelet number per spike, thousand kernel weight, and flag leaf area per plant in wheat. Hap-ABD was the most effective haplotype combination of TaHDZ34. Subcellular localization showed that TaHDZ-A34 was localized to the nucleus. The interacting proteins of TaHDZ-A34 were involved in protein synthesis/degradation, energy production and transportation, and photosynthesis. Geographic distribution and frequencies of TaHDZ34 haplotype combinations suggested that Hap-Abd and Hap-AbD were preferentially selected in Chinese wheat breeding programs. The high-yield-related haplotype combination Hap-ABD provided beneficial genetic resources for the marker-assisted selection of new wheat cultivars. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01298-5.

Light-Activated Hypoxia-Sensitive Covalent Organic Framework for Tandem-Responsive Drug Delivery.

Covalent organic frameworks (COFs) have received much attention in the biomedical area. However, little has been reported about stimuli-responsive COF for drug delivery. Herein, we synthesized a hypoxia-responsive azo bond-containing COF with nanoscale size and immobilized both photosensitizers chlorin e6 (Ce6) and hypoxia-activated drug tirapazamine (TPZ) into the COFs. When such a COF entered the hypoxic environment and tumor, the COF structure was ruptured and loaded drugs were released from the COF. Together, upon near-infrared (NIR) light irradiation, Ce6 consumed oxygen to produce cytotoxic reactive oxygen species, leading to elevated hypoxia. Such two-step hypoxia stimuli successively induced the deintegration of COF, drug release and activation of TPZ. This promoted the TPZ to generate massive biotoxic oxyradical. In vitro and in vivo evaluation indicated that this two-step hypoxia-activated COF drug delivery system could kill cancer cells and inhibit the growth of tumors effectively.

Transcriptomic Identification of Wheat AP2/ERF Transcription Factors and Functional Characterization of TaERF-6-3A in Response to Drought and Salinity Stresses.

AP2/ERF (APETALA2/ethylene responsive factor) is a family of plant-specific transcription factors whose members are widely involved in many biological processes, such as growth, development, and biotic and abiotic stress responses. Here, 20 AP2/ERF genes were identified based on wheat RNA-seq data before and after drought stress, and classified as AP2, ERF, DREB, and RAV. The analysis of gene structure revealed that about 85% of AP2/ERF family members had lost introns, which are presumed to have been lost during the formation and evolution of the wheat genome. The expression of 20 AP2/ERF family genes could be verified by qRT-PCR, which further supported the validity of the RNA-seq data. Subsequently, subcellular localization and transcriptional activity experiments showed that the ERF proteins were mainly located in the nucleus and were self-activating, which further supports their functions as transcription factors. Furthermore, we isolated a novel ERF gene induced by drought, salt, and cold stresses and named it TaERF-6-3A. TaERF-6-3A overexpression increased sensitivity to drought and salt stresses in Arabidopsis, which was supported by physiological and biochemical indices. Moreover, the expression of stress- and antioxidant-related genes was downregulated in TaERF-6-3A-overexpressing plants. Overall, these results contribute to the further understanding of the TaERF-6-3A gene function in wheat.

Advances in Atroposelectively De Novo Synthesis of Axially Chiral Heterobiaryl Scaffolds.

Axially chiral heterobiaryl frameworks are privileged structures in many natural products, pharmaceutically active molecules, and chiral ligands. Therefore, a variety of approaches for constructing these skeletons have been developed. Among them, de novo synthesis, due to its highly convergent and superior atom economy, serves as a promising strategy to access these challenging scaffolds including C-N, C-C, and N-N chiral axes. So far, several elegant reviews on the synthesis of axially chiral heterobiaryl skeletons have been disclosed, however, atroposelective construction of the heterobiaryl subunits by de novo synthesis was rarely covered. Herein, we summarized the recent advances in the catalytic asymmetric synthesis of the axially chiral heterobiaryl scaffold via de novo synthetic strategies. The related mechanism, scope, and applications were also included.

Pixel-wise body composition prediction with a multi-task conditional generative adversarial network.

The analysis of human body composition plays a critical role in health management and disease prevention. However, current medical technologies to accurately assess body composition such as dual energy X-ray absorptiometry, computed tomography, and magnetic resonance imaging have the disadvantages of prohibitive cost or ionizing radiation. Recently, body shape based techniques using body scanners and depth cameras, have brought new opportunities for improving body composition estimation by intelligently analyzing body shape descriptors. In this paper, we present a multi-task deep neural network method utilizing a conditional generative adversarial network to predict the pixel level body composition using only 3D body surfaces. The proposed method can predict 2D subcutaneous and visceral fat maps in a single network with a high accuracy. We further introduce an interpreted patch discriminator which optimizes the texture accuracy of the 2D fat maps. The validity and effectiveness of our new method are demonstrated experimentally on TCIA and LiTS datasets. Our proposed approach outperforms competitive methods by at least 41.3% for the whole body fat percentage, 33.1% for the subcutaneous and visceral fat percentage, and 4.1% for the regional fat predictions.

The "Dextran-Magnetic Layered Double Hydroxide-Fluorouracil" Drug Delivery System Exerts Its Anti-tumor Effect by Inducing Lysosomal Membrane Permeability in the Process of Cell Death.

The "dextran-magnetic layered double hydroxide-fluorouracil" (DMF) drug delivery system is a new type of pharmaceutic preparation that can cause cancer cell oncosis. In the present study, we used different experimental methods such as 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), cycle assay, reactive oxygen species (ROS) assay, Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI), Giemsa stainings, transmission electron microscopy, immunofluorescence staining and Western blotting to study the mechanism of expansion death by using Hydroxychloroquine (HCQ) as a positive control and 5-Fluorouracil (5-Fu) as reference. The results showed that DMF exhibited a better anti-tumor effect than 5-Fu in the process of cell death, and the pharmacological mechanism of 5-Fu was changed by its preparation DMF. The mechanism of cancer cell death induced by DMF was similar to that of HCQ. But DMF intervention did not cause a large amount of accumulation of mitochondrial reactive oxygen species, and the location of lysosomotropic LysoTracker Red (LTR) staining induced by DMF was closer to the nucleus or nuclear membrane. Lysosomal membrane permeability (LMP) and its subsequent the explosive death of cancer cells may be mainly related to the direct action of DMF with different organelles.

Region of Interest Selection for Functional Features.

Feature selection is a critical component in supervised learning to improve model performance. Searching for the optimal feature candidates can be NP-hard. With limited data, cross-validation is widely used to alleviate overfitting, which unfortunately suffers from high computational cost. We propose a highly innovative strategy in feature selection to reduce the overfitting risk but without cross-validation. Our method selects the optimal sub-interval, i.e., region of interest (ROI), of a functional feature for functional linear regression where the response is a scalar and the predictor is a function. For each candidate sub-interval, we evaluate the overfitting risk by calculating a necessary sample size to achieve a pre-specified statistical power. Combining with a model accuracy measure, we rank these sub-intervals and select the ROI. The proposed method has been compared with other state-of-the-art feature selection methods on several reference datasets. The results show that our proposed method achieves an excellent performance in prediction accuracy and reduces computational cost substantially.

A Wheat TaTOE1-B1 Transcript TaTOE1-B1-3 Can Delay the Flowering Time of Transgenic Arabidopsis.

Flowering time is one of the most important agronomic traits in wheat production. A proper flowering time might contribute to the reduction or avoidance of biotic and abiotic stresses, adjust plant architecture, and affect the yield and quality of grain. In this study, TaTOE1-B1 in wheat produced three transcripts (TaTOE1-B1-1, TaTOE1-B1-2, and TaTOE1-B1-3) by alternative splicing. Compared to the longest transcript, TaTOE1-B1-1, TaTOE1-B1-3 has a deletion in the sixth exon (1219-1264 bp). Under long-day conditions, the heterologous overexpression of the TaTOE1-B1-3 gene delayed flowering, prolonged the vegetative growth time, and enlarged the vegetative body of Arabidopsis, but that of TaTOE1-B1-1 did not. As typical AP2 family members, TaTOE1-B1-1 and TaTOE1-B1-3 are mainly located in the nucleus and have transcriptional activation activities; the transcriptional activation region of TaTOE1-B1-3 is located in the C-terminal. In TaTOE1-B1-3 overexpression lines, the expression of flowering-related AtFT and AtSOC1 genes is significantly downregulated. In addition, this study confirms the protein-protein interaction between TaTOE1-B1-3 and TaPIFI, which may play an important role in flowering inhibition. These results provide a theoretical basis for the precise regulation of wheat flowering time.

Amino Acid Polymorphism in Succinate Dehydrogenase Subunit C Involved in Biological Fitness of Botrytis cinerea.

Succinate dehydrogenase (SDH) is an important respiratory enzyme which participates in the tricarboxylic acid cycle and oxidative phosphorylation. A previous study of the baseline sensitivity of Botrytis cinerea against SDH inhibitors (SDHIs) showed that intrinsic sensitivity of the small population against the SDHIs exhibited significant differences. In the sequencing assay, we found five kinds of amino acid polymorphism in SDH subunit C (SdhC) of B. cinerea isolates which were never exposed to the SDHIs. To validate that amino acid polymorphism in the SdhC of B. cinerea confers intrinsic sensitivity against the SDHIs, the replacement mutants containing each kind of amino acid polymorphism of SdhC exhibited phenotype differences in intrinsic sensitivity to SDHIs, mycelial growth, sporulation, virulence, oxidative stress response, and carbon source utilization. These results indicated that SdhC of B. cinerea experienced positive selection during evolution and resulted in amino acid polymorphism which is involved in intrinsic sensitivity to SDHIs and biological fitness.

The combination of Biochanin A and SB590885 potentiates the inhibition of tumour progression in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is the most aggressive and frequently diagnosed malignancy of the liver. Despite aggressive therapy, life expectancy of many patients in these cases is extended by only a few months. Hepatocellular carcinoma (HCC) has a particularly poor prognosis and would greatly benefit from more effective therapies. METHODS: The CCK-8 assay and colony formation assays were used to test the cell proliferation and viability. The effects of combination Biochanin A and SB590885 on apoptosis and cell cycle arrest of HCC cells were analysed by flow cytometry. The expression of ERK MAPK and PI3K/AKT/mTOR signalling as well as apoptosis and cell cycle-related proteins in HCC cells were tested by western blotting. The HCC cell xenograft model was established to test the tumor proliferation. Serum and plasma were tested for liver and kidney safety markers (ALP, ALT, AST, total bilirubin, creatinine, urea nitrogen) by using SpectraMax i3X. RESULTS: The combination of natural product Biochanin A with the BRAF inhibitor SB590885 synergistically suppressed proliferation, and promoted cell cycle arrest and apoptosis in vitro. Furthermore, we demonstrated that the combination of Biochanin A and SB590885 led to increased impairment of proliferation and HCC tumour inhibition through disrupting of the ERK MAPK and the PI3K/AKT pathways in vitro. The volumes tumors and the weights of tumours were significantly reduced by the combination treatment compared to the control or single treatments in vivo. In addition, we found that there was no significant hepatorenal toxicity with the drug combination, as indicated by the hepatorenal toxicity test. CONCLUSION: The results identify an effective combination therapy for the most aggressive form of HCC and provide the possibility of therapeutic improvement for patients with advanced HCC.

A Dendron-Based Fluorescence Turn-On Probe for Tumor Detection.

Specifically amplifying the emission signals of optical probes in tumors is an effective way to improve the tumor-imaging sensitivity and contrast. In this paper, the first case of dendron-based fluorescence turn-on probes mediated by a Förster resonance energy transfer (FRET) mechanism is reported. Dendrons up to the fourth generation with a hydrophilic oligo(ethylene glycol) scaffold are synthesized by a solid-phase synthesis strategy, and show precise and defect-free chemical structures. To construct the fluorescence turn-on probe, one Cy5.5 molecule is conjugated to the focal of a G3 dendron through a robust linkage and eight Black Hole Quencher 3 (BHQ-3) molecules are conjugated to its periphery through a PEG chain bearing a reductively cleavable disulfide linkage. By in vitro and in vivo experiments, it is demonstrated that the fluorescence of the dendron-based probe can be activated effectively and rapidly in the reductive environments of tumor cells and tissues, and the probe thus exhibits amplified tumor signals and weak normal tissue signals. Compared with the reported nanoscale turn-on probes, the dendron-based probe has several significant advantages, such as well-defined chemical structure, precisely controllable fluorophore/quencher conjugation sites and ratio, desirable chemical stability, and reproducible pharmacokinetic and pharmacological profiles, and is very promising in tumor detection.

Does the sex ratio of singleton births after frozen single blastocyst transfer differ in relation to blastocyst development?

PURPOSE: To investigate the associations between blastocyst development and the sex ratio (male:female) among singleton live births resulting from single-blastocyst frozen embryo transfer (FET) cycles. METHODS: Patients with singleton live births following the first autologous single FET of non- preimplantation genetic testing (PGT) blastocysts in a single reproductive medicine department between January 2015 and February 2019 were included in this retrospective study. The primary outcome measure was the singleton sex ratio. Multivariable logistic regression models were used to estimate the associations between blastocyst quality and singleton sex ratio after adjustment for some potential confounders. RESULTS: There were 638 high-quality and 572 poor-quality single blastocyst FETs, and the blastocysts were conceived via 855 IVF and 355 ICSI treatments. A total of 1210 singleton live births were assessed. High-quality single blastocyst FET resulted in a significantly higher sex ratio than did poor-quality single blastocyst FET (60% vs. 49.7%, P < 0.001). The infertility cause was not associated with sex ratio among singleton live births (P = 0.537). The results of a multivariate analysis revealed that a high-quality blastocyst has a 150% higher probability of being male than a poor-quality blastocyst (adjusted odds ratio (aOR) 1.57; 95% CI 1.24-2, P < 0.001). Among the three blastocyst morphological parameters, Grade B trophectoderm was significantly associated with a higher sex ratio than Grade C (aOR 1.71; 95% CI 1.33-2.21. P < 0.001). Neither expansion degree nor inner cell mass degree were significantly associated with the singleton sex ratio. CONCLUSIONS: A single high-quality blastocyst FET has a higher chance of resulting in a male infant than a female infant. The results demonstrate that grade B trophectoderm confers benefits in improving the implantation potential of male blastocysts.

Influence of humor expression on suicidal ideation among adolescents: mediating effects of depressive emotion and positive emotion.

BACKGROUND: The occurrence and degree of suicidal ideation during the past month in adolescents should be regarded seriously. Several studies have noted that humor expression style and depressive emotion may influence adolescents' suicidal ideation. However, there is insufficient evidence concerning whether positive emotion reduces such suicidal ideation in adolescents. In addition, the relationships among humor expression, depressive emotion, positive emotion and suicidal ideation remain to be confirmed. Therefore, in this study, we aimed to test the mediating roles of depressive emotion and positive emotion in the relationship between humor expression and recent adolescent's suicidal ideation. METHODS: A total of 1551 students in junior high school completed questionnaires. The collected data were analyzed using structural equation modeling (SEM) with LISREL 8.80 and Monte Carlo resampling with R. RESULTS: The results indicate that suicidal ideation in adolescents during the past month was related not only to humor expression but also to depressive emotion and positive emotion. The stronger the depressive emotion felt, the stronger the suicidal ideation; in contrast, the stronger the positive emotion, the weaker the suicidal ideation. Moreover, depressive emotion and positive emotion were found to mediate the relationship between humor expression and suicidal ideation; additionally, positive emotion was found to mediate the relationship between depressive emotion and suicidal ideation. CONCLUSION: These results highlight that depressive emotion and positive emotion may mediate the influence of humor expression on suicidal ideation among adolescents, and positive emotion may mediate the influence of depressive emotion on suicidal ideation. More attention should be paid to decreasing adolescents' self-deprecating humor expression and depressive emotion, whereas more witty response humor expression and positive emotion should be encouraged to prevent their suicidal ideation.