scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution.

SUMMARY: Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA-seq datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 175 samples, 663 857 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, scCancer2 integrated a module to process the spatial transcriptomic data and analyze the spatial features of TME. AVAILABILITY AND IMPLEMENTATION: The package and user documentation are available at http://lifeome.net/software/sccancer2/ and https://doi.org/10.5281/zenodo.10477296.

Development of a risk assessment model for cardiac injury in patients newly diagnosed with acute myeloid leukemia based on a multicenter, real-world analysis in China.

BACKGROUND: Studies have revealed that acute myeloid leukemia (AML) patients are prone to combined cardiac injury. We aimed to identify hematological risk factors associated with cardiac injury in newly diagnosed AML patients before chemotherapy and develop a personalized predictive model. METHODS: The population baseline, blood test, electrocardiogram, echocardiograph, and genetic and cytogenetic data were collected from newly diagnosed AML patients. The data were subdivided into training and validation cohorts. The independent risk factors were explored by univariate and multivariate logistic regression analysis respectively, and data dimension reduction and variable selection were performed using the least absolute shrinkage and selection operator (LASSO) regression models. The nomogram was generated and the reliability and generalizability were verified by receiver operating characteristic (ROC) curves, the area under the curve (AUC) and calibration curves in an external validation cohort. RESULTS: Finally, 499 AML patients were included. After univariate logistic regression, LASSO regression and multivariate logistic regression analysis, abnormal NT-proBNP, NPM1 mutation, WBC, and RBC were independent risk factors for cardiac injury in AML patients (all P < 0.05). The nomogram was constructed based on the above four variables with high accuracy. The area under the curve was 0.742, 0.750, and 0.706 in the training, internal validation, and external validation cohort, respectively. The calibration curve indicated that the model has good testing capability. The Kaplan-Meier curve showed that the higher the risk of combined cardiac injury in AML patients, the lower their probability of survival. CONCLUSIONS: This prediction nomogram identifies hematological risk factors associated with cardiac injury in newly diagnosed AML patients and can help hematologists identify the risk and provide precise treatment options.

Study on leukapheresis of hyperleukocytic acute myeloid leukemia through in vitro centrifugation.

Respiratory failure, intracranial hemorrhage and infection were more common in hyperleukocytic acute myeloid leukemia patients than in non-hyperleukocytic leukemia patients. Compared with non-apheresis treatment, the white blood cells decreased significantly and the infection rate decreased after apheresis treatment. However, the treatment time of leukapheresis in patients with hyperleukocytic leukemia is very long, while it is more damaging to cells. In this study, which conducted a retrospective analysis on patients with hyperleukocytic acute myeloid leukemia, the process of centrifugation of normal cells and patients' cells by apheresis machine was simulated in vitro. Through selecting 5 healthy persons and 11 patients with hyperleukocytic acute myeloid leukemia, extracting their blood samples and performing in vitro centrifugation at different speeds or duration, we observed the changes of the numbers and morphology of peripheral blood cells in healthy people and patients, so as to explore the optimal centrifugation parameters during leukapheresis. The cells obtained by the optimal centrifugation parameters were cryopreserved and two groups of mice (10 mice in each group) were used to establish leukemia animal models. Through the research, it is found that when the centrifugal speed is below 6000 rpm, the damage to blood cells in healthy people and in patients with hyperleukocytic leukemia is not obvious. When the centrifugal speed is above 6000 rpm, the platelets will be damaged significantly. The cells obtained under the optimal centrifugation parameters can be successfully cryopreserved and used to establish leukemia animal models. This study is of great significance for improving the efficiency and reducing the side effects of leukapheresis, and is helpful to improve the treatment of white blood cells reduction.

Age differences in interbrain synchronization during peer cooperation: an EEG hyperscanning study.

Healthy peer relationships could provide emotional and social support for adolescents experiencing dramatic physical and environmental changes. Examining age differences in cognitive neural processing during peer interaction provides insight into adolescent interpersonal contact and "social brain" development. The present study compared the age differences between adolescents and adults by examining the behavior and interbrain synchronization of pairs in a cooperative computer game task. 32 pairs of adolescents and 31 pairs of adults were recruited as participants. The reaction times and interbrain synchronization of the participants were measured. The results revealed that interbrain synchronization activation following the onset of the "ready signal" was primarily detected in low-frequency bands such as delta and theta. Adolescent pairs' interbrain synchronization activations were significantly higher than those of adult pairs in the anterior and central brain regions, such as the frontal, frontal-central, and parietal lobes. Correlation analysis indicated a positive correlation between occipital region interbrain synchronization and behavioral performance. The findings provide behavioral and neurophysiological evidence for the characteristics of adolescent interpersonal cognitive processing and point to the significance of low-frequency interbrain synchronization in interpersonal coordination.

Combined transcriptomics and metabolomics analysis reveals salinity stress specific signaling and tolerance responses in the seagrass Zostera japonica.

KEY MESSAGE: Multiple regulatory pathways of Zostera japonica to salt stress were identified through growth, physiological, transcriptomic and metabolomic analyses. Seagrasses are marine higher submerged plants that evolved from terrestrial monocotyledons and have fully adapted to the high saline seawater environment during the long evolutionary process. As one of the seagrasses growing in the intertidal zone, Zostera japonica not only has the ability to quickly adapt to short-term salt stress but can also survive at salinities ranging from the lower salinity of the Yellow River estuary to the higher salinity of the bay, making it a good natural model for studying the mechanism underlying the adaptation of plants to salt stress. In this work, we screened the growth, physiological, metabolomic, and transcriptomic changes of Z. japonica after a 5-day exposure to different salinities. We found that high salinity treatment impeded the growth of Z. japonica, hindered its photosynthesis, and elicited oxidative damage, while Z. japonica increased antioxidant enzyme activity. At the transcriptomic level, hypersaline stress greatly reduced the expression levels of photosynthesis-related genes while increasing the expression of genes associated with flavonoid biosynthesis. Meanwhile, the expression of candidate genes involved in ion transport and cell wall remodeling was dramatically changed under hypersaline stress. Moreover, transcription factors signaling pathways such as mitogen-activated protein kinase (MAPK) were also significantly influenced by salt stress. At the metabolomic level, Z. japonica displayed an accumulation of osmolytes and TCA mediators under hypersaline stress. In conclusion, our results revealed a complex regulatory mechanism in Z. japonica under salt stress, and the findings will provide important guidance for improving salt resistance in crops.

Prevalence trends of anemia impairment in adolescents and young adults with HIV/AIDS.

BACKGROUND: Anemia is a common complication of HIV/AIDS, particularly in adolescents and young adults across various countries and regions. However, little is known about the changing prevalence trends of anemia impairment in this population over time. METHODS: Data on anemia in adolescents and young adults with HIV/AIDS from 1990 to 2019 were collected from the Global Burden of Disease. Prevalence was calculated by gender, region, and country for individuals aged 10-24, and trends were measured using estimating annual percentage changes (EAPC). RESULTS: Globally, the prevalence of adolescents and young adults with HIV/AIDS increased from 103.95 per 100,000 population in 1990 to 203.78 in 2019. However, anemia impairment has decreased over the past three decades, with a global percentage decreasing from 70.6% in 1990 to 34.7% in 2019, mainly presenting as mild to moderate anemia and significantly higher in females than males. The largest decreases were observed in Central Sub-Saharan Africa, North America, and Eastern Sub-Saharan Africa, with EAPCs of -2.8, -2.34, and -2.17, respectively. Tajikistan (78.76%) and Madagascar (74.65%) had the highest anemia impairment percentage in 2019, while China (16.61%) and Iceland (13.73%) had the lowest. Anemia impairment was closely related to sociodemographic index (SDI) levels, with a high proportion of impairment in low SDI regions but a stable decreasing trend (EAPC = -0.37). CONCLUSION: Continued anemia monitoring and management are crucial for patients with HIV, especially in high-prevalence regions and among females. Public health policies and interventions can improve the quality of life and reduce morbidity and mortality.

Association between the triglyceride-glucose index and left ventricular global longitudinal strain in patients with coronary heart disease in Jilin Province, China: a cross-sectional study.

BACKGROUND: This study aimed to investigate the association between the triglyceride-glucose (TyG) index and left ventricular global longitudinal strain (GLS) in patients with coronary heart disease and to examine the role of left ventricular GLS in detecting early changes in cardiac function in patients with coronary heart disease in the subclinical stage. METHODS: A cross-sectional study involving 178 participants with symptomatic coronary artery disease excluding myocardial infarction or left ventricular dysfunction was conducted in Jilin Province, China. Basic clinical, biochemical, and echocardiographic data were obtained from all participants. Myocardial strain parameters were compared between patients with higher TyG index and those with lower TyG index, and the association between the gradually elevated TyG index and on subclinical cardiac function in patients with coronary heart disease was evaluated. RESULTS: The GLS of left ventricle was lower in the higher TyG index group than in the lower TyG index group. As the TyG index increases, the GLS progressively decreases. The results remained stable after adjusting for confounding factors. CONCLUSIONS: A higher TyG index maybe independently associated with subclinical left ventricular dysfunction in patients with coronary heart disease.

Downregulation of miR-892b inhibits the progression of osteoarthritis via targeting cyclin D1 and cyclin D2.

BACKGROUNDS: Osteoarthritis (OA) is an orthopedic inflammatory disease which can cause functional disability and chronic pain. MiRNAs are known to play important roles in OA. To identify the targets for the treatment of OA, bioinformatics analysis was performed to explore differentially expressed miRNAs between OA and normal samples. METHODS: Bioinformatics analysis was conducted to identify differentially expressed miRNAs. To mimic OA in vitro, primary chondrocytes were stimulated with IL-1ß. Meanwhile, flow cytometry was performed to detect the cell apoptosis and cycle distribution. In addition, protein and mRNA expressions were detected by Western blot and RT-qPCR, respectively. Finally, in vivo model of OA was constructed to investigate the function of miR-892b in OA. RESULTS: The data indicated that miR-892b was identified to be upregulated in OA samples. Additionally, miR-892b antagomir markedly reversed IL-1ß-induced growth decline of chondrocytes via inhibiting the apoptosis. IL-1ß notably elevated the expressions of MMP1 and MMP13 and downregulated the level of Aggrecan in chondrocytes, while miR-892b antagomir reversed these phenomena. Meanwhile, cyclin D1 and cyclin D2 were the direct targets of miR-892b. In addition, IL-1ß-induced G1 phase arrest in chondrocytes was partially abolished by of miR-892b antagomir. In vivo study indicated miR-892b antagomir could significantly alleviate the symptom of OA in a rat model. CONCLUSION: MiR-892b antagomir inhibits the progression of OA via targeting Cyclin D1 and Cyclin D2. Thus, our finding might supply a novel target for OA treatment.

Light-Driven Polarity Switching of the Chromatographic Stationary Phase with Photoreversibility.

Regrettably, conventional chromatographic columns have immutable polarity, resulting in requirements of at least two columns with polarity difference and sophisticated mechanical switching valves, which hinders the development of "micro-smart" multidimensional tandem chromatography. In this work, light-driven polarity switching was realized in a single capillary column based on the reversible trans-cis isomerization of 4-[3-(triethoxysilyl)propoxy]azobenzene as the stationary phase under light irradiation, with the change in dipole moment. As a result, the stationary phase offers precise and dynamic control of polarity based on the cis-trans azobenzene ratio, which depends on irradiation wavelength and time. Thus, the continuous adjustment of polarity enables diversified chromatographic separation modes, for example, step-polarity gradient and polarity-conversion separation modes, taking advantage of the superior freedom of polarity switching in time and spatial dimensions. The photosensitive column also shows good reproducibility of polarity photoreversibility and high separation efficiency. The present study might offer brand new insight into developing miniaturization and intellectualization of multidimensional chromatography via designing smart responsive switching valves or stationary phases, besides mechanical means.

A novel strategy for creating a new system of third-generation hybrid rice technology using a cytoplasmic sterility gene and a genic male-sterile gene.

Heterosis utilization is the most effective way to improve rice yields. The cytoplasmic male-sterility (CMS) and photoperiod/thermosensitive genic male-sterility (PTGMS) systems have been widely used in rice production. However, the rate of resource utilization for the CMS system hybrid rice is low, and the hybrid seed production for the PTGMS system is affected by the environment. The technical limitations of these two breeding methods restrict the rapid development of hybrid rice. The advantages of the genic male-sterility (GMS) rice, such as stable sterility and free combination, can fill the gaps of the first two generations of hybrid rice technology. At present, the third-generation hybrid rice breeding technology is being used to realize the application of GMS materials in hybrid rice. This study aimed to use an artificial CMS gene as a pollen killer to create a smart sterile line for hybrid rice production. The clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) technology was used to successfully obtain a CYP703A3-deficient male-sterile mutant containing no genetically modified component in the genetic background of indica 9311. Through young ear callus transformation, this mutant was transformed with three sets of element-linked expression vectors, including pollen fertility restoration gene CYP703A3, pollen-lethality gene orfH79 and selection marker gene DsRed2. The maintainer 9311-3B with stable inheritance was obtained, which could realize the batch breeding of GMS materials. Further, the sterile line 9311-3A and restorer lines were used for hybridization, and a batch of superior combinations of hybrid rice was obtained.

An integrated strategy for the identification and screening of anti-allergy components from natural products based on calcium fluctuations and cell extraction coupled with HPLC-Q-TOF-MS.

Allergic diseases are a significant public health problem worldwide. Traditional Chinese medicines (TCMs) with reported anti-allergy effects may be important sources for the development of new anti-allergy drugs. Thus, establishing an analytical method that can simultaneously identify and screen anti-allergic compounds in TCMs is important. The increased concentrations of intracellular calcium ions resulting in mast cell degranulation releasing active mediators play a key role in allergic diseases, which can be used as a potential index to identify anti-allergic herbs and compounds. In this study, we provide a new strategy that was applied to screening natural anti-allergic compounds based on fluorescence calcium ion (Ca2+) fluctuation integrated with cell extract and high-performance liquid chromatography-mass spectrometry (HPLC-MS). A low-cost, convenient fluorescence detection Ca2+ signaling method was established and successfully applied to identify three herbs. Then, the method was integrated with biospecific cell fishing and HPLC-MS to screen potential active components that have the effect of stabilizing the cell membrane of rat basophilic leukemia granulocytes (RBL-2H3). Seven components, namely, albiflorin and paeoniflorin from Radix Paeoniae Alba, ononin and formononetin from Radix Astragali, cimifugin, 4'-O-ß-D-glucosyl-5-O-methylvisamminol, and prim-O-glucosylcimifugin from Radix Saposhnikoviae were fished. These seven compounds have the effect of inhibiting cell Ca2+ influx. 4'-O-ß-D-Glucosyl-5-O-methylvisamminol, prim-O-glucosylcimifugin, paeoniflorin, ononin, and formononetin significantly inhibit the release of ß-hexosaminidase, which is equivalent to the positive drug. In conclusion, the integrated strategy of fluorescence detection calcium ion kinetic method binding with biospecific cell fishing was an effective mode to identify and screen natural anti-allergic compounds.

Vanishing quantum oscillations in Dirac semimetal ZrTe5.

One of the characteristics of topological materials is their nontrivial Berry phase. Experimental determination of this phase largely relies on a phase analysis of quantum oscillations. We study the angular dependence of the oscillations in a Dirac material [Formula: see text] and observe a striking spin-zero effect (i.e., vanishing oscillations accompanied with a phase inversion). This indicates that the Berry phase in [Formula: see text] remains nontrivial for arbitrary field direction, in contrast with previous reports. The Zeeman splitting is found to be proportional to the magnetic field based on the condition for the spin-zero effect in a Dirac band. Moreover, it is suggested that the Dirac band in [Formula: see text] is likely transformed into a line node other than Weyl points for the field directions at which the spin zero occurs. The results underline a largely overlooked spin factor when determining the Berry phase from quantum oscillations.

[Mechanism of Xiaoyao San in treatment of depression,breast hyperplasia,and functional dyspepsia based on network pharmacology].

This study aimed to explore the mechanism of Xiaoyao San(XYS) in the treatment of three diseases of liver depression and spleen deficiency, ie, depression, breast hyperplasia, and functional dyspepsia, and to provide a theoretical basis for the interpretation of the scientific connotation of "treating different diseases with the same method" of traditional Chinese medicines. Traditional Chinese medicine systems pharmacology database and analysis platform(TCMSP) was used to screen the active components of XYS which underwent principal component analysis(PCA) with the available drugs for these three diseases to determine the corresponding biological activities. The targets of XYS on depression, breast hyperplasia, and functional dyspepsia were obtained from GeneCards, TTD, CTD, and DrugBank databases. Cytoscape was used to plot the "individual herbal medicine-active components-potential targets" network. The resulting key targets were subjected to Kyoto encyclopedia of genes and genomes(KEGG) pathway analysis and gene ontology(GO) enrichment analysis. A total of 121 active components of XYS and 38 common targets in the treatment of depression, breast hyperplasia, and functional dyspepsia were collected. The key biological pathways were identified, including advanced glycation and products(AGEs)-receptor for advanced glycation and products(RAGE) signaling pathway in diabetic complications, HIF-1 signaling pathway, and cancer-related pathways. The key targets of XYS in the treatment of depression, breast hyperplasia, and functional dyspepsia included IL6, IL4, and TNF, and the key components were kaempferol, quercetin, aloe-emodin, etc. As revealed by the molecular docking, a strong affinity was observed between the key components and the key targets, which confirmed the results. The therapeutic efficacy of XYS in the treatment of diseases of liver depression and spleen deficiency was presumedly achieved by reducing the inflammatory reactions. The current findings are expected to provide novel research ideas and approaches to classify the scientific connotation of "treating different diseases with the same method" of Chinese medicines, as well as a theoretical basis for understanding the mechanism of XYS and exploring its clinical applications.

A Discrete-Time Neurodynamic Approach to Sparsity-Constrained Nonnegative Matrix Factorization.

Sparsity is a desirable property in many nonnegative matrix factorization (NMF) applications. Although some level of sparseness of NMF solutions can be achieved by using regularization, the resulting sparsity depends highly on the regularization parameter to be valued in an ad hoc way. In this letter we formulate sparse NMF as a mixed-integer optimization problem with sparsity as binary constraints. A discrete-time projection neural network is developed for solving the formulated problem. Sufficient conditions for its stability and convergence are analytically characterized by using Lyapunov's method. Experimental results on sparse feature extraction are discussed to substantiate the superiority of this approach to extracting highly sparse features.

Pericentral hepatocytes produce insulin-like growth factor-2 to promote liver regeneration during selected injuries in mice.

Liver regeneration (LR) happens after various types of injuries. Unlike the well-studied LR caused by partial hepatectomy (PHx), there is accumulating evidence suggesting that LR during other injuries may result from unknown mechanisms. In this study, we found that insulin-like growth factor 2 (IGF-2) was drastically induced following the liver injuries caused by tyrosinemia or long-term treatments of CCl4 . However, this was not observed during the early phase of acute liver injuries after PHx or single treatment of CCl4 . Remarkably, most IGF-2-expressing hepatocytes were located at the histological area around the central vein of the liver lobule after the liver injuries caused either in fumarylacetoacetate hydrolase-deficient mice or in CCl4 chronically treated mice. Hepatocyte proliferation in vivo was significantly promoted by induced IGF-2 overexpression, which could be inhibited by adeno-associated virus-delivered IGF-2 short hairpin RNAs or linsitinib, an inhibitor of IGF-2 signaling. Proliferating hepatocytes in vivo responded to IGF-2 through both insulin receptor and IGF-1 receptor. IGF-2 also significantly promoted DNA synthesis of primary hepatocytes in vitro. More interestingly, the significantly induced IGF-2 was also found to colocalize with glutamine synthetase in the region enriched with proliferating hepatocytes for the liver samples from patients with liver fibrosis. CONCLUSION: IGF-2 is produced by pericentral hepatocytes to promote hepatocyte proliferation and repair tissue damage in the setting of chronic liver injury, which is distinct from the signaling that occurs post-PHx. (Hepatology 2017;66:2002-2015).

Direct measurement of the quantum state of photons in a cavity.

We propose a scheme to measure the quantum state of photons in a cavity. The proposal is based on the concept of quantum weak values and applies equally well to both the solid-state circuit and atomic cavity quantum electrodynamics (QED) systems. The proposed scheme allows us to access directly the superposition components in Fock state basis, rather than the Wigner function as usual in phase space. Moreover, the separate access feature held in the direct scheme does not require a global reconstruction for the quantum state, which provides a particular advantage beyond the conventional method of quantum state tomography.

The Cost and Cost-utility of Three Public Health HIV Case-finding Strategies: Evidence from Rhode Island, 2012-2014.

To evaluate three testing strategies to identify new HIV diagnoses in Rhode Island (RI). RI deployed three testing strategies, by using rapid HIV tests at clinical settings, community-based organization (CBO) settings, and the Partner Notification Services (PNS) program from 2012 to 2014. We reviewed the rapid HIV test results and confirmatory test results to identify new diagnoses, and conducted a cost-utility analysis. The average cost per new diagnosis was $33,015 at CBO settings, $5446 at clinical settings, and $33,818 at the PNS program. The cost-utility analysis showed the state-wide program was cost-saving; testing was cost-saving at clinical settings, and cost-effective at CBO settings and the PNS program. Further analyses showed that cost-effectiveness varied widely across CBOs. The HIV testing expansion program in RI was cost-saving overall. The heterogeneity of cost-effectiveness across settings should provide guidance to officials for allocation of future resources to HIV testing.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N2CO photodissociation.

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N2CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N2CO photodissociation at λ > 335 nm is an ultrafast process and the two C-N bonds are broken in a stepwise way, giving birth to CO and N2 as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C-N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.

Improved master equation approach to quantum transport: from Born to self-consistent Born approximation.

Beyond the second-order Born approximation, we propose an improved master equation approach to quantum transport under self-consistent Born approximation. The basic idea is to replace the free Green's function in the tunneling self-energy diagram by an effective reduced propagator under the Born approximation. This simple modification has remarkable consequences. It not only recovers the exact results for quantum transport through noninteracting systems under arbitrary voltages, but also predicts the challenging nonequilibrium Kondo effect. Compared to the nonequilibrium Green's function technique that formulates the calculation of specific correlation functions, the master equation approach contains richer dynamical information to allow more efficient studies for such as the shot noise and full counting statistics.