Development and initial results of 320 GHz interferometer system in Heliotron J

A new 320 GHz solid-state source interferometer is installed in the Heliotron J helical device to explore the physics of high-density plasmas (ne > 2-3 × 10¹⁹ m^-3, typically) realized with advanced fueling techniques. This interferometry system is of the Michelson type and is based on the heterodyne principle, with two independent solid-state sources that can deliver an output power of up to 50 mW. A high time resolution measurement of <1 µs can be derived by tuning the frequency of one source in the frequency range of 312-324 GHz on the new system, which can realize the fluctuation measurement. We successfully measured the line-averaged electron density in high-density plasma experiments. The measured density agreed well with a microwave interferometer measurement using a different viewing chord, demonstrating that the new system can be used for routine diagnostics of electron density in Heliotron J.

Distribution of lipid levels and prevalence of hyperlipidemia: data from the NHANES 2007-2018

Background

Lipid-lowering therapy is important, and the distribution of lipid levels and the incidence of hyperlipidemia may vary in different subgroups of the population. We aimed to explore the distribution of lipid levels and the prevalence of hyperlipidemia in subpopulations with subgroup factors, including age, sex, race, and smoking status.

Methods

Our study used data from the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2018, ultimately enrolling and analyzing 15,499 participants. A cross-sectional analysis was performed to assess the distribution of lipids and prevalence of hyperlipidemia in subpopulations, and multifactorial logistic regression analyses were performed for the prevalence of hyperlipidemia, adjusted for age, sex, race and smoking status.

Results

Blacks had significantly lower mean serum total cholesterol and triglycerides and higher serum high-density lipoprotein cholesterol (HDL-C) than whites (P < 0.001). In contrast, Mexican Americans had markedly higher mean serum triglycerides and lower serum HDL-C than whites (P < 0.001). Furthermore, the prevalence of hypercholesterolemia and hypertriglyceridemia was lower in blacks than in whites (P = 0.003 and P < 0.001, respectively), while the prevalence of hypertriglyceridemia was significantly higher in Mexican Americans than in whites (P = 0.002). In addition, total cholesterol and triglyceride levels were significantly higher in women aged 65 years or older and markedly higher than in men in the same age group (P < 0.001). In addition, overall mean total cholesterol, triglyceride, and low-density lipoprotein cholesterol (LDL-C) levels were higher in smokers than in nonsmokers (P = 0.01, P < 0.001, and P = 0.005, respectively).

Conclusion

Based on NHANES data, the mean lipid levels and prevalence of hyperlipidemia differed by sex, age, race, and smoking status.

Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy

Autophagy is a major contributor to anti-cancer therapy resistance. Many efforts have been made to understand and overcome autophagy-mediated therapy resistance, but these efforts have been unsuccessful in clinical applications. In this study, we establish an autophagy signature to estimate tumor autophagy status. We then classify approximately 10,000 tumor samples across 33 cancer types from The Cancer Genome Atlas into autophagy score-high and autophagy score-low groups. We characterize the associations between multi-dimensional molecular features and tumor autophagy, and further analyse the effects of autophagy status on drug response. In contrast to the conventional view that the induction of autophagy serves as a key resistance mechanism during cancer therapy, our analysis reveals that autophagy induction may also sensitize cancer cells to anti-cancer drugs. We further experimentally validate this phenomenon for several anti-cancer drugs in vitro and in vivo, and reveal that autophagy inducers potentially sensitizes tumor cells to etoposide through downregulating the expression level of DDIT4. Our study provides a comprehensive landscape of molecular alterations associated with tumor autophagy and highlights an opportunity to leverage multi-omics analysis to utilize multiple drug sensitivity induced by autophagy.

Direct Measurement of Resonances in ^{7}Be(α,γ)^{11}C Relevant to νp-Process Nucleosynthesis

We have performed the first direct measurement of two resonances of the ^{7}Be(α,γ)^{11}C reaction with unknown strengths using an intense radioactive ^{7}Be beam and the DRAGON recoil separator. We report on the first measurement of the 1155 and 1110 keV resonance strengths of 1.73±0.25(stat)±0.40(syst)  eV and 125_{-25}^{+27}(stat)±15(syst)  meV, respectively. The present results have reduced the uncertainty in the ^{7}Be(α,γ)^{11}C reaction rate to ∼9.4%-10.7% over T=1.5-3  GK, which is relevant for nucleosynthesis in the neutrino-driven outflows of core-collapse supernovae (νp process). We find no effect of the new, constrained reaction rate on νp-process nucleosynthesis.

Meta-Analysis of Matrix Metalloproteinases in the Risk of Cardiovascular and Neurodegenerative Diseases

Objective

To investigate the risk of cardiovascular and neurodegenerative diseases induced by matrix metalloproteinases (MMPs) by meta-analysis.

Methods

Relevant literature was searched from Wanfang Medical Center, CNQI, VIP, PubMed, and other domestic and foreign literature databases for the research direction, and the risk of cardiovascular and neurodegenerative diseases induced by MMPs was meta-analyzed using the fixed-effect model and random-effect model.

Results

MMP-1 and MMP-9 were risk factors for cardiovascular diseases by fixed and random-effect model analysis, respectively, while MMP-2 and MMP-9 were risk factors for increased neurodegenerative diseases by random-effect model analysis.

Conclusion

MMP-1 and MMP-9 are risk factors for cardiovascular diseases, and MMP-2 and MMP-9 are major factors for increased risk of neurodegenerative diseases. MMP-1, MMP-2, and MMP-9 can be used as new targets for clinical diagnosis, treatment, and research of subsequent cardiovascular and neurodegenerative diseases.

Pathogenicity of Beauveria bassiana PfBb and Immune Responses of a Non-Target Host, Spodoptera frugiperda (Lepidoptera: Noctuidae)

Exploring the pathogenicity of a new fungus strain to non-target host pests can provide essential information on a large scale for potential application in pest control. In this study, we tested the pathogenicity of Beauveria bassiana PfBb on the important agricultural pest Spodoptera frugiperda (Lepidoptera: Noctuidae) by determining the relative activities of protective enzymes and detoxifying enzymes in different larval instars. Our results show that the B. bassiana PfBb strain could infect all six larval instars of S. frugiperda, and its virulence to S. frugiperda larvae gradually increased with an increase in spore concentration. Seven days after inoculation, the LC₅₀ of B. bassiana PfBb was 7.7 × 10⁵, 5.5 × 10⁶, 2.2 × 10⁷, 3.1 × 10⁸, 9.6 × 10⁸, and 2.5 × 10¹¹ spores/mL for first to sixth instars of S. frugiperda, respectively, and the LC₅₀ and LC₉₀ of B. bassiana PfBb for each S. frugiperda instar decreased with infection time, indicating a significant dose effect. Furthermore, the virulence of B. bassiana PfBb to S. frugiperda larvae gradually decreased with an increase in larval instar. The activities of protective enzymes (i.e., catalase, peroxidase, and superoxide dismutase) and detoxifying enzymes (i.e., glutathione S-transferases, carboxylesterase, and cytochrome P450) in S. frugiperda larvae of the first three instars infected with B. bassiana PfBb changed significantly with infection time, but such variations were not obvious in the fifth and sixth instars. Additionally, after being infected with B. bassiana PfBb, the activities of protective enzymes and detoxification enzymes in S. frugiperda larvae usually lasted from 12 to 48 h, which was significantly longer than the control. These results indicate that the pathogenicity of B. bassiana PfBb on the non-target host S. frugiperda was significant but depended on the instar stage. Therefore, the findings of this study suggest that B. bassiana PfBb can be used as a bio-insecticide to control young larvae of S. frugiperda in an integrated pest management program.

High Sclerotinia sclerotiorum resistance in rapeseed plant has been achieved by OsPGIP6

Sclerotinia sclerotiorum, a worldwide distributed fungal pathogen, causes serious adverse effects on the yield and seed quality of rapeseed. Polygalacturonase-inhibiting proteins (PGIPs) can protect the cell wall from degradation by pathogen-secreted polygalacturonases (PGs). The present study found several PGIPs from Oryza sativa, especially OsPGIP6 and 3 have much higher inhibitory activities to SsPGs than BnPGIP2 from Brassica napus. Among them, OsPGIP1, 4, 6 can significantly elevate the resistance of transgenic Arabidopsis to S. sclerotiorum. Subsequently, OsPGIP1, 3, 4, 6 were subjected to SSR resistance assay in transgenic rapeseed plants. Among which, OsPGIP6 showed the highest resistance to S. sclerotiorum. At 48 h after detached leaves inoculation, the lesion area of OE-OsPGIP6 rapeseed plants is only 17.93% of the non-transgenic line, and 22.17, 21.32, 52.78, 56.47%, compared to OE-BnPGIP2, OE-OsPGIP1, OE-OsPGIP2, OE-OsPGIP4, respectively. Furthermore, the lesion area of OE-OsPGIP6 reached 10.11% compared to WT at 72 hpi. Also, the lesion length on the stem of OE-OsPGIP6 plants was reduced by 36.83% compared to WT. These results reveal that OsPGIP family, especially OsPGIP6, has a great potential in rapeseed S. sclerotiorum-resistance breeding.

ICBatlas: A comprehensive resource for depicting immune checkpoint blockade therapy characteristics from transcriptome profiles

Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. Much work is currently being conducted to investigate the mechanisms of ICB therapy at the transcriptional level. Integrating the data produced by these studies will help us give more insight into the transcriptomic features of ICB therapy. We collected the transcriptome and clinical data of ICB-treated patient samples from the GEO, ArrayExpress, TCGA, and dbGaP databases. Based on the clinical information, all samples are initially classified into response/non-response or pre-treatment/on-treatment groups. Differential expression, pathway enrichment, and immune cell infiltration analyses are performed between the samples from different groups. We also introduce the Response Score (RS) calculated by integrating the variability degree and the frequency of the dysregulated genes in the responders to evaluate the impact of gene expression on the response. Finally, all the abovementioned contents are integrated into the ICBatlas database. ICBatlas provides the transcriptome features of ICB therapy through the analysis of 1515 ICB-treated samples from 25 studies across nine cancer types. The data in ICBatlas include clinical outcomes, treatment-related genes, biological pathways, and immune cell infiltration. Users can investigate the abovementioned transcriptome features in the Response (R vs. NR) or Treatment (Pre vs. On) modules at the dataset, cancer type, or immune checkpoint level and compare the degree of gene impact on the response in the RS module. ICBatlas is the first database to show the transcriptome features on ICB therapy in human cancers and freely available at http://bioinfo.life.hust.edu.cn/ICBatlas/.

Identification, Genetic Diversity, and Chemical Control of Xanthomonas arboricola pv. pruni in China

Peach bacterial spot caused by Xanthomonas arboricola pv. pruni has become widespread in most peach-producing areas of China and has caused devastating losses to the peach industry. However, little is known about the population biology and epidemiology of X. arboricola pv. pruni in China, thus no effective management strategy is available. Altogether, 321 symptomatic samples of peach bacterial spot from 12 provinces in China were collected from which 612 bacterial isolates were obtained. Based on 16S rDNA sequence comparison in GenBank, the obtained isolates were identified as Pantoea spp. (514) and Xanthomonas spp. (98). The pathogenicity test demonstrated that the causal agent of the peach bacterial spot was the Xanthomonas spp. instead of the Pantoea spp. Based on morphological observation, physiological and biochemical characterization, and molecular identification, the Xanthomonas spp. were further identified to be X. arboricola pv. pruni. Then, 41 X. arboricola pv. pruni isolates representing different populations were selected and analyzed with repetitive element sequence based-PCR and intersimple sequence repeat markers to understand the genetic diversity and population structure along with four X. arboricola pv. pruni isolates from plum and three isolates of X. arboricola pv. juglandis as comparison. A total of 98 polymorphic alleles were identified, with a mean value of percentage of polymorphic loci of 14. Genetic diversity and phylogenetic analysis revealed the profound heterogeneity between X. arboricola pv. juglandis and X. arboricola pv. pruni, moderate genetic differentiation within X. arboricola pv. pruni, and obvious host specificity but weak geographical differentiation in X. arboricola population. Finally, the efficiency of bactericides on X. arboricola pv. pruni was evaluated in vitro and in vivo. The parallel repeated field trials in two orchards demonstrated that 80% Mancozeb (1:800) and 47% Kocide (1:800, 1:1,500, and 1:2,000) had excellent control efficacies for X. arboricola pv. pruni, especially as the control efficacy of Kocide could even reach 90%. This study conducted a systematic investigation for the occurrence, population variance, and chemical control of X. arboricola pv. pruni. It improved the understanding of the pathogen populations of peach bacterial spot in China and provided solid theoretical and practical guidance for X. arboricola pv. pruni control.

Physicochemical Heterogeneity in Silicon Anodes from Cycled Lithium-Ion Cells

The severe capacity fade of lithium-ion cells with silicon-dominant anodes has hindered their widescale commercialization. In this work, we link cell capacity fade to the heterogeneous physicochemical evolution of silicon anodes during battery cycling. Through a multilength scale characterization approach, we demonstrate that silicon particles near the anode surface react differently from those near the copper current collector. In particular, near the anode surface we find an amorphized wispy silicon encased in a highly fluorinated matrix of electrolyte-reduction products. In contrast, closer to the current collector, the silicon retains more of its initial morphology and structure, suggesting the presence of isolated particles. The results show that the accessibility of active silicon to lithium ions varies across the anode matrix. Material and cell designs, which minimize electrode expansion resulting from the in-filling of pores with the solid electrolyte interphase (SEI), are needed to enhance anode homogeneity during the electrochemical cycling.

Virulence-Associated Genes of Calonectria ilicola, Responsible for Cylindrocladium Black Rot

The Cylindrocladium black rot caused by Calonectria ilicicola is a destructive disease affecting a broad range of crops. Herein, we study virulence-associated genes of C. ilicicolaCi14017 isolated from diseased peanut roots (Arachis hypogaea L.). Ci14017 was identified via phylogenetic analysis of the internal transcribed spacer region and standard Koch’s postulate testing. Virulence-associated genes were based on genome analyses and comparative analysis of transcriptome and proteome profiles of sensitive and resistant peanut cultivars. Ci14017 identified as C. ilicicola has a 66 Mb chromosome with 18,366 predicted protein-coding genes. Overall, 46 virulence-associated genes with enhanced expression levels in the sensitive cultivars were identified. Sequence analysis indicated that the 46 gene products included two merops proteins, eight carbohydrate-active enzymes, seven cytochrome P450 enzymes, eight lipases, and 20 proteins with multi-conserved enzyme domains. The results indicate a complex infection mechanism employed by Ci14017 for causing Cylindrocladium black rot in peanuts.

Three Isomeric Non-Fullerene Acceptors Comprising a Mono-Brominated End-Group for Efficient Organic Solar Cells

Non-fullerene acceptors (NFAs) carrying a 1,1-dicyanomethylene-3-indanone (IC) end-group are the most powerful ones to boost the power conversion efficiency of organic solar cells (OSCs). However, the well-known Knoevenagel condensation of the mono-halogenated IC end-group will result in an NFA isomeric effect, a chemical issue that needs to be addressed. Herein, facile preparations and separations of three well-defined mono-brominated isomers BTzIC-2Br-δ, BTzIC-2Br-γ, and BTzIC-2Br-δγ via column chromatography with a well-chosen mixing solvent were demonstrated for Knoevenagel condensation, and their structures were verified by NMR spectra and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) mass spectra. It is the first time that an asymmetric isomer BTzIC-2Br-δγ is reported, and the regioisomeric effect on optoelectronic properties can be investigated based on all three isomers. Moreover, the single-crystal structure was successfully achieved for the symmetric molecule BTzIC-2Br-γ. With benzodithiophene (BDT)-free PFBT4T-T20 as an easily accessible and low-cost polymer donor, the three isomers could show differentiated device performances, with a power conversion efficiency order of BTzIC-2Br-γ (16.00%) > BTzIC-2Br-δγ (15.81%) > BTzIC-2Br-δ (15.29%). The best efficiency of 16.00% achieved with BTzIC-2Br-γ is among the highest ones for binary OSCs based on the low-cost BDT-free donors. The facile and complete synthesis of isomeric NFAs with mono-halogenated IC end-groups would promote the elucidation of the structure-property relationship.

Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut

The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.

Lasiodiplodia fici sp. nov., Causing Leaf Spot on Ficus altissima in China

High temperatures and the seasonality in tropical ecosystems favours plant pathogens, which result in many fungal diseases. Among these, diseases caused by Botryosphaeriaceae species are prominent as dieback, canker and leaf spots. In this research, we isolated one leaf-spot-causing Botryosphaeriaceae species from Ficus altissima leaves, which were collected in Guangzhou, Guangdong Province, China. Isolation and identification of the pathogen were based on morphological and molecular aspects. Based on multigene phylogenetic analysis of combined internal transcribed spacer (ITS), translation elongation factor 1-α gene (tef1) and beta-tubulin gene (tub2), the fungus associated with leaf spots on F. altissima is described as Lasiodiplodia fici, a novel species. Pathogenicity assays were conducted by inoculating the fungus onto detached shoots and plants under controlled environmental conditions. The results revealed that the L. fici isolates can infect the plant tissues under stress conditions by developing disease symptoms on detached shoots within three days. However, when it was inoculated onto the leaves of the host and grown in natural conditions, the progression of the disease was slow. The putative pathogen was re-isolated, and Koch's assumptions were satisfied. This is the first report of Lasiodiplodia species causing disease on Ficus altissima. Results from the present study will provide additional knowledge on fungal pathogens associated with forest and ornamental plant species.

[Effects of menopause on depressive and anxiety symptoms in community women in Beijing]

Objective: To determine the effects of menopausal stage, age and other associated risk factors on symptoms of anxiety and depression among women in a community in Beijing. Methods: This study was a community-based prospective cohort. Participants who had transitioned through natural menopause, completed two or more depressive and anxiety symptoms evaluations, aged 35 to 64 years, and did not use hormone therapy were selected from the Peking Union Medical College Hospital aging longitudinal cohort of women in midlife to this analysis. The primary outcome variables were depressive and anxiety symptoms, assessed by hospital anxiety and depression scale (HADS). The generalized estimation equation was used in the statistical analysis. Results: Followed up from 2006 to 2014, 430 women and 2 533 HADS assessments were retained in the cohort. Depressive symptoms were more common than anxiety symptoms during all menopausal stages. The incidences of depressive and anxiety symptoms were 14.5% (19/191) and 3.1% (4/191) in the premenopausal -3 stage, respectively. The incidence increased in both menopausal transition and postmenopausal stage, with the highest incidence in the +1c stage [20.6% (155/751) and 8.8% (66/751), respectively]. However, these differences were not statistically significant (all P>0.05). Depressive symptoms were highest in the ≥60-<65 age group [20.8% (74/355)], and anxiety symptoms were highest in the ≥50-<55 age group [8.2% (62/754)]; but there were no statistical significances between different age groups and depressive and anxiety symptoms (all P>0.05). Multivariable analysis showed that high body mass index, low education status, and poor health status were independently associated with depressive symptoms (all P<0.05), and that poor health status, trouble falling asleep, and early awakening were independently associated with anxiety symptoms (all P<0.01). Conclusions: Depressive and anxiety symptoms are more common during menopausal transition and postmenopausal stage compared with reproductive stage. Depressive symptoms are more common than anxiety symptoms. To screen and assess depressive and anxiety symptoms in perimenopausal women is essential, especially for women with high risk factors.

Effect of PM2.5 exposure on gestational hypertension, fetal size in preeclampsia-like rats

Studies have shown intriguing associations between gestational PM_2.5 exposure and preeclampsia (PE), as well as fetal growth restriction (FGR). This study investigated the impact of PM_2.5 exposure on gestational hypertension and fetal outcome in a preeclampsia-like rat model. Pregnant Sprague Dawley rats were exposed to either filtered (FA) or PM_2.5-contaminated air during the whole pregnancy period. A PE-like rat model was established by intraperitoneal injection of L-NAME (300 mg/kg) from gestational day (GD) 12 to until GD20. Systolic blood pressure (SBP), weight gain, pup weight and placental weight were measured. The percentages of rat Treg/Th17 cells and Th17-related cytokines were examined by flow cytometry. Gene expression profiles were analyzed by microarray, and the expression of differentially expressed genes was validated by qRT-PCR. The results showed that maternal PM_2.5 exposure had no effect on SBP but was associated with low birth weight (LBW) and a higher labyrinth/basal zone ratio. The percentages of splenic Th17 cells from the PM_2.5 group of PE-like rats were higher than those from the FA or PM_2.5 groups of healthy controls. A significantly decreased Treg/Th17 cell ratio was found in the PM_2.5 group of PE-like rats. The mRNA expression of Foxp3 was downregulated, while the mRNA expression of RORα and RORγτ was upregulated after PM_2.5 exposure. Furthermore, we observed that both the mRNA and protein levels of TNF-a, CCL2, CCL3 and CCR1 increased in the PM_2.5 groups. Our study suggested that systemic inflammation may contribute to the development of FGR associated with PM_2.5 exposure throughout pregnancy.

Red blood cell transfusions post diagnosis of necrotizing enterocolitis and the deterioration of necrotizing enterocolitis in full-term and near-term infants: a propensity score adjustment retrospective cohort study

Background

Necrotizing enterocolitis (NEC) is one of serious gastrointestinal inflammatory diseases in newborn infants, with a high morbidity and mortality. Red blood cell transfusion (RBCT) plays a controversial and doubtful role in the treatment of NEC. In present study, we aim to analyze the association between RBCT and the deterioration of NEC.

Methods

This was a retrospective cohort study of near-term and full-term infants with a confirmed diagnosis of Bell’s stage II NEC between Jan 1, 2010 and Jan 31, 2020. The maternal and infant baseline characteristics, treatment information and laboratory test for each case were collected. The eligible subjects were divided into two groups based on receiving RBCT post NEC diagnosis or not. The propensity score was used to eliminate potential bias and baseline differences. A multivariate logistic regression model was used to adjust the propensity score and calculate the odds ratio (OR) and 95% confidential interval (CI) of RBCT for the deterioration of NEC.

Results

A total of 242 infants were included in this study, 60 infants had a history of RBCT post NEC diagnosis, and 40 infants deteriorated from Bell’s stage II to stage III. By adjusting the propensity score, RBCT post NEC diagnosis was associated with an increased risk for NEC deteriorating from stage II to III (adjusted OR 6.06, 95%CI 2.94–12.50, P = 0.000).

Conclusions

NEC infants who required RBCT post NEC diagnosis were more likely to deteriorate from stage II to III in full-term and near-term infants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03276-4.

Genetic, Pharmacogenomic and Immune landscapes of enhancer RNAs across human cancers

Enhancer RNAs (eRNA) regulate gene expression and play critical roles in cancer. Using large-scale omics data from The Cancer Genome Atlas (TCGA), we systematically investigated the impact of genetic variants on eRNA expression and identified ~1 million eRNA quantitative trait loci (eRNA-QTL) as cis- and trans-acting. Over 16,000 eRNA-QTLs were associated with patient overall survival. Assessing the impact of eRNAs on >1,000 imputed anti-cancer drug responses across ~10,000 cancer patients revealed > 7 million significant associations. Furthermore, ~240,000 significant associations were identified between eRNA expression and immune cell abundance deconvoluted by TIMER, CIBERSORT, ImmuCellAI, and ImmuneCellGSVA. Finally, a user-friendly data portal was generated: Genetic, Pharmacogenomic, and Immune landscapes of eRNAs (GPIeR, https://hanlab.tamhsc.edu/GPIeR/). GPIeR is a large-scale multi-dimensional data portal that can be used to explore eRNA-associated genetic variants, drug responses, and immune infiltration with the purpose of facilitating functional and clinical investigations of eRNAs in cancer.

ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction

MOTIVATION

Immune cells are important components of the immune system and are crucial for disease initiation, progression, prognosis and survival. Although several computational methods have been designed for predicting the abundance of immune cells, very few tools are applicable to mouse. Given that, mouse is the most widely used animal model in biomedical research, there is an urgent need to develop a precise algorithm for predicting mouse immune cells.

RESULTS

We developed a tool named Immune Cell Abundance Identifier for mouse (ImmuCellAI-mouse), for estimating the abundance of 36 immune cell (sub)types from gene expression data in a hierarchical strategy of three layers. Reference expression profiles and robust marker gene sets of immune cell types were curated. The abundance of cells in three layers was predicted separately by calculating the ssGSEA enrichment score of the expression deviation profile per cell type. Benchmark results showed high accuracy of ImmuCellAI-mouse in predicting most immune cell types, with correlation coefficients between predicted value and real cell proportion of most cell types being larger than 0.8. We applied ImmuCellAI-mouse to a mouse breast tumor dataset and revealed the dynamic change of immune cell infiltration during treatment, which is consistent with the findings of the original study but with more details. We also constructed an online server for ImmuCellAI-mouse, on which users can upload expression matrices for analysis. ImmuCellAI-mouse will be a useful tool for studying the immune microenvironment, cancer immunology and immunotherapy in mouse models, providing an indispensable supplement for human disease studies.

AVAILABILITY AND IMPLEMENTATION

Software is available at http://bioinfo.life.hust.edu.cn/ImmuCellAI-mouse/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.

[Analysis on characteristics and influencing factors of COVID-19 confirmed cases with viral nucleic acid re-positive after discharge in Guangdong Province]

Objective: To analyze the epidemiological characteristics and influencing factors of COVID-19 confirmed cases with viral nucleic acid re-positive in anal and/or throat swabs after discharge during the domestic imported epidemic stage in Guangdong Province in early 2020. Methods: The COVID-19 confirmed cases with the onset time before March 1, 2020 in Guangdong Province were collected to analyze the demographic data, epidemiological characteristics, and specimen collection and testing data after discharge. Logistic regression model was used for influencing factors analysis of re-positive cases. Results: A total of 1 286 COVID-19 confirmed cases were included, the M(Q₁,Q₃) of age was 44(32,58)years, 617 cases were male, 224 cases were re-positive in anal and/or throat swabs with the re-positive rate 17.42%. The M(Q₁,Q₃) of age of re-positive cases was 35(23, 50) years, which was younger than that of re-negative cases age was those 46(33, 59) years (P<0.001). With the increase of age, re-positive rate decreased (χ²_trend=52.73, P<0.001). 85.27% (191/224) of re-positive cases were found in 14 d after discharge, the duration time of re-positive status was 13(7, 24) d, and 81.69% (183/224) of re-positive cases were re-tested negative in 28 d after re-positive date. No fever and other symptoms had been observed among re-positive cases during the whole follow-up. No secondary infectious cases had been found among close contacts after 14 d of centralized isolation and sampling screening. Univariate logistic regression model analysis revealed that the influencing factors of the re-positive cases included age, occupation, clusters, clinical types, and admission time. Multivariate logistic regression model analysis revealed that age was an independent risk factor. Conclusions: SARS-CoV-2 viral nucleic acid re-positive is found in COVID-19 confirmed cases after discharge in Guangdong Province. Most re-positive cases are confirmed among 14 d after discharge and re-test to negative among 28 d after re-positive date. Age is an risk factor for re-positive cases after discharge.