Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems.

Global risk dynamics of Borrelia miyamotoi in the context of climate change.

The impact of Borrelia miyamotoi on human health, facilitated by the expanding geographical distribution and increasing population of Ixodes ticks, remains obscure in the context of global climate change. We employed multiple models to evaluate the effect of global climate change on the risk of B. miyamotoi worldwide across various scenarios. The habitat suitability index of four primary vector tick species for B. miyamotoi, including Ixodes persulcatus, Ixodes ricinus, Ixodes pacificus and Ixodes scapularis, was projected using a boosted regression tree model, considering multiple shared socio-economic pathway scenarios over various time periods. The modelling analysis reveals that, apart from I. scapularis, future global warming will result in a northward shift in the other three vector tick species and a gradual reduction in suitable habitats. Random forest models indicate consistent changes in B. miyamotoi and its primary tick species, with potential risk areas shrinking and shifting northward, particularly in the eastern USA, northeastern and northern Europe and northeast Asia. These findings highlight the urgent need for enhanced active surveillance of B. miyamotoi infection in primary vector tick species across projected potential risk areas. The effect of climate change on B. miyamotoi distribution might have significant implications for public health decision-making regarding tick-borne pathogens.

The complex hexaploid oil-Camellia genome traces back its phylogenomic history and multi-omics analysis of Camellia oil biosynthesis.

Oil-Camellia (Camellia oleifera), belonging to the Theaceae family Camellia, is an important woody edible oil tree species. The Camellia oil in its mature seed kernels, mainly consists of more than 90% unsaturated fatty acids, tea polyphenols, flavonoids, squalene and other active substances, which is one of the best quality edible vegetable oils in the world. However, genetic research and molecular breeding on oil-Camellia are challenging due to its complex genetic background. Here, we successfully report a chromosome-scale genome assembly for a hexaploid oil-Camellia cultivar Changlin40. This assembly contains 8.80 Gb genomic sequences with scaffold N50 of 180.0 Mb and 45 pseudochromosomes comprising 15 homologous groups with three members each, which contain 135 868 genes with an average length of 3936 bp. Referring to the diploid genome, intragenomic and intergenomic comparisons of synteny indicate homologous chromosomal similarity and changes. Moreover, comparative and evolutionary analyses reveal three rounds of whole-genome duplication (WGD) events, as well as the possible diversification of hexaploid Changlin40 with diploid occurred approximately 9.06 million years ago (MYA). Furthermore, through the combination of genomics, transcriptomics and metabolomics approaches, a complex regulatory network was constructed and allows to identify potential key structural genes (SAD, FAD2 and FAD3) and transcription factors (AP2 and C2H2) that regulate the metabolism of Camellia oil, especially for unsaturated fatty acids biosynthesis. Overall, the genomic resource generated from this study has great potential to accelerate the research for the molecular biology and genetic improvement of hexaploid oil-Camellia, as well as to understand polyploid genome evolution.

Continuation of same programmed death-1 inhibitor regime beyond progression is a novel option for advanced gastric cancer.

BACKGROUND: Gastric cancer is a significant global malignancy with poor prognosis. Although the emergence of immune checkpoint inhibitors (ICIs) prolonged the duration of survival, resistance and progression are inevitable. We aim to evaluate the effectiveness of programmed death-1 (PD-1) inhibitors in immunotherapy beyond progression (IBP). METHOD: We divided the advanced gastric cancer patients who received two lines immunotherapy into same regimen group (with same PD-1 inhibitor regime after IBP) and different regimen group (with different PD-1 inhibitor regime after IBP). Statistical analysis conducted to compare patient characteristics and evaluate survival differences between groups. RESULT: The clinical outcome analysis showed that the same PD-1 inhibitor regime seemed to exhibit a higher disease control rate (DCR) (51.8% vs. 29.2%, P = 0.062), significantly prolonged progression-free survival 2 (PFS2) (162 vs. 75 days, P = 0.001) and overall survival (OS) (312 vs. 166 days, P = 0.022) when compared with those of cross line. In the multivariate analysis, when using different regimen group as reference, the same regimen group was found to be independently associated with improved PFS2 [hazard ratio (HR) = 0.467, 95% confidence interval (CI): 0.267-0.816, P = 0.008] and OS (HR = 0.508, 95%CI: 0.278-0.927, P = 0.027). CONCLUSION: Continuation of the same type of PD-1 inhibitor regime in IBP shows clinical benefits and represents a promising therapeutic approach.

A systematic review of environmental covariates and methods for spatial or temporal scrub typhus distribution prediction.

BACKGROUND: Scrub typhus is underdiagnosed and underreported but emerging as a global public health problem. To inform future burden and prediction studies we examined through a systematic review the potential effect of environmental covariates on scrub typhus occurrence and the methods which have been used for its prediction. METHODS: In this systematic review, we searched PubMed, Scopus, Web of Science, China National Knowledge Infrastructure and other databases, with no language and publication time restrictions, for studies that investigated environmental covariates or utilized methods to predict the spatial or temporal human. Data were manually extracted following a set of queries and systematic analysis was conducted. RESULTS: We included 68 articles published in 1978-2024 with relevant data from 7 countries/regions. Significant environmental risk factors for scrub typhus include temperature (showing positive or inverted-U relationships), precipitation (with positive or inverted-U patterns), humidity (exhibiting complex positive, inverted-U, or W-shaped associations), sunshine duration (with positive, inverted-U associations), elevation, the normalized difference vegetation index (NDVI), and the proportion of cropland. Socioeconomic and biological factors were rarely explored. Autoregressive Integrated Moving Average (ARIMA) (n = 8) and ecological niche modelling (ENM) approach (n = 11) were the most popular methods for predicting temporal trends and spatial distribution of scrub typhus, respectively. CONCLUSIONS: Our findings summarized the evidence on environmental covariates affecting scrub typhus occurrence and the methodologies used for predictive modelling. We review the existing knowledge gaps and outline recommendations for future studies modelling disease prediction and burden. TRIAL REGISTRATION: PROSPERO CRD42022315209.

Characteristics of the time processing of adults' strongest sustained attentional bias toward neutral infant faces.

Previous studies have shown that adults exhibit the strongest attentional bias toward neutral infant faces when viewing faces with different expressions at different attentional processing stages due to different stimulus presentation times. However, it is not clear how the characteristics of the temporal processing associated with the strongest effect change over time. Thus, we combined a free-viewing task with eye-tracking technology to measure adults' attentional bias toward infant and adult faces with happy, neutral, and sad expressions of the same face. The results of the analysis of the total time course indicated that the strongest effect occurred during the strategic processing stage. However, the results of the analysis of the split time course revealed that sad infant faces first elicited adults' attentional bias at 0 to 500 ms, whereas the strongest effect of attentional bias toward neutral infant faces was observed at 1000 to 3000 ms, peaking at 1500 to 2000 ms. In addition, women and men had no differences in their responses to different expressions. In summary, this study provides further evidence that adults' attentional bias toward infant faces across stages of attention processing is modulated by expressions. Specifically, during automatic processing adults' attentional bias was directed toward sad infant faces, followed by a shift to the processing of neutral infant faces during strategic processing, which ultimately resulted in the strongest effect. These findings highlight that this strongest effect is dynamic and associated with a specific time window in the strategic process.

Associations between exposure to various air pollutants and risk of metabolic syndrome: a systematic review and meta-analysis.

BACKGROUND: Metabolic Syndrome (MetS) is a widely observed metabolic disorder that is increasingly prevalent worldwide, leading to substantial societal consequences. Previous studies have conducted two separate meta-analyses to investigate the relationship between MetS and air pollutants. However, these studies yielded conflicting results, necessitating a thorough systematic review and meta-analysis to reassess the link between different air pollutants and the risk of developing MetS. METHODS: We conducted a comprehensive search of relevant literature in databases including PubMed, Embase, Cochrane Library, and Web of Science up to October 9, 2023. The search was specifically restricted to publications in the English language. Following the screening of studies investigating the correlation between air pollution and MetS, we utilized random-effects models to calculate pooled effect sizes along with their respective 95% confidence intervals (CIs). We would like to highlight that this study has been registered with PROSPERO, and it can be identified by the registration number CRD42023484421. RESULTS: The study included twenty-four eligible studies. The results revealed that an increase of 10 µg/m3 in annual concentrations of PM1, PM2.5, PM10, NO2, SO2, and O3 was associated with a 29% increase in metabolic syndrome (MetS) risk for PM1 (OR = 1.29 [CI 1.07-1.54]), an 8% increase for PM2.5 (OR = 1.08 [CI 1.06-1.10]), a 17% increase for PM10 (OR = 1.17 [CI 1.08-1.27]), a 24% increase for NO2 (OR = 1.24 [CI 1.01-1.51]), a 19% increase for SO2 (OR = 1.19 [CI 1.04-1.36]), and a 10% increase for O3 (OR = 1.10 [CI 1.07-1.13]). CONCLUSION: The findings of this study demonstrate a significant association between exposure to fine particulate matter (PM1, PM2.5, PM10), nitrogen dioxide (NO2), sulfur dioxide (SO2), ozone (O3), and the incidence of metabolic syndrome (MetS). Moreover, the results suggest that air pollution exposure could potentially contribute to the development of MetS in humans.

The Application of Health Management and Drug Self-management Education in the Control of Chronic Diseases in the Elderly: A Retrospective Study.

Objective: The objective of this study was to analyze the application of health management and medication self-management education in the control of chronic diseases in the elderly, specifically focusing on patients with diabetes, hypertension, cardiovascular diseases, and chronic obstructive pulmonary disease (COPD). The study aimed to assess the impact of these interventions on patients> self-management abilities, quality of life, medication adherence, intervention satisfaction, and the occurrence of adverse events. The findings aimed to provide a scientific basis for improving elderly chronic disease management and enhancing patients> health and quality of life. Methods: A total of 106 elderly chronic disease patients admitted to our hospital from July 2021 to April 2023 were selected as the research subjects. All patients met the complete inclusion criteria. They were divided into two groups based on the type of health management intervention received. The control group (n=53) received conventional health management intervention. In contrast, the observation group (n=53) received health management from the medical examination center based on the PDCA model and medication self-management education intervention. The self-management ability, quality of life, medication adherence, occurrence of adverse events, and intervention satisfaction of the two groups of patients were compared. The PDCA (Plan-Do-Check-Act) model was chosen as the framework for this study due to its systematic approach to management and its potential to address the specific needs and complexities associated with chronic diseases in the elderly. The PDCA model emphasizes a continuous cycle of improvement, involving planning, implementation, evaluation, and adjustment of interventions. Results: Before the intervention, there was no significant difference in self-concept, self-management responsibility, self-management knowledge, and self-management skills between the two groups (P > .05). After the intervention, the observation group's self-concept, self-management responsibility, self-management knowledge, and self-management skills were significantly higher than those of the control group (P < .05). Before the intervention, there was no significant difference in SF-36 scores between the two groups (P > .05). After the intervention, the SF-36 scores of the observation group were significantly higher than those of the control group (P < .05). The medication adherence score in the control group was (5.73±0.92), and the incidence of adverse events was 32.08%. In the observation group, the medication adherence score was (7.42±0.81), and the incidence of adverse events was 11.32%. The medication adherence score in the observation group was significantly higher than that in the control group, and the incidence of adverse events was significantly lower than that in the control group (P < .05). The intervention satisfaction in the control group was 73.58%. In comparison, the intervention satisfaction in the observation group was 96.23%, indicating that the intervention satisfaction in the observation group was significantly higher than that in the control group (P < .05). These results suggest that the implementation of the PDCA model in health management and medication self-management education can enhance patients' self-management abilities, improve medication adherence, and ultimately lead to better quality of life and reduced risk of adverse events for elderly chronic disease patients. Conclusion: The application of health management and medication self-management education based on the PDCA model in the control of elderly chronic diseases is ideal. Compared to conventional health management interventions, the former can enhance patients' self-management abilities and improve medication adherence, thereby further improving patients' quality of life, satisfaction, and the risk of adverse events. Therefore, this approach is worthy of clinical promotion and application.

The chromosome-scale reference genome of mirid bugs (Adelphocoris suturalis) genome provides insights into omnivory, insecticide resistance, and survival adaptation.

BACKGROUND: Adelphocoris suturalis (Hemiptera: Miridae) is a notorious agricultural pest, which causes serious economic losses to a diverse range of agricultural crops around the world. The poor understanding of its genomic characteristics has seriously hindered the establishment of sustainable and environment-friendly agricultural pest management through biotechnology and biological insecticides. RESULTS: Here, we report a chromosome-level assembled genome of A. suturalis by integrating Illumina short reads, PacBio, 10x Chromium, and Hi-C mapping technologies. The resulting 1.29 Gb assembly contains twelve chromosomal pseudomolecules with an N50 of 1.4 and 120.6 Mb for the contigs and scaffolds, respectively, and carries 20,010 protein-coding genes. The considerable size of the A. suturalis genome is predominantly attributed to a high amount of retrotransposons, especially long interspersed nuclear elements (LINEs). Transcriptomic and phylogenetic analyses suggest that A. suturalis-specific candidate effectors, and expansion and expression of gene families associated with omnivory, insecticide resistance and reproductive characteristics, such as digestion, detoxification, chemosensory receptors and long-distance migration likely contribute to its strong environmental adaptability and ability to damage crops. Additionally, 19 highly credible effector candidates were identified and transiently overexpressed in Nicotiana benthamiana for functional assays and potential targeting for insect resistance genetic engineering. CONCLUSIONS: The high-quality genome of A. suturalis provides an important genomic landscape for further investigations into the mechanisms of omnivory, insecticide resistance and survival adaptation, and for the development of integrated management strategies.

Classification and characterisation of extracellular vesicles-related tuberculosis subgroups and immune cell profiles.

Around the world, tuberculosis (TB) remains one of the most common causes of morbidity and mortality. The molecular mechanism of Mycobacterium tuberculosis (Mtb) infection is still unclear. Extracellular vesicles (EVs) play a key role in the onset and progression of many disease states and can serve as effective biomarkers or therapeutic targets for the identification and treatment of TB patients. We analysed the expression profile to better clarify the EVs characteristics of TB and explored potential diagnostic markers to distinguish TB from healthy control (HC). Twenty EVs-related differentially expressed genes (DEGs) were identified, and 17 EVs-related DEGs were up-regulated and three DEGs were down-regulated in TB samples, which were related to immune cells. Using machine learning, a nine EVs-related gene signature was identified and two EVs-related subclusters were defined. The single-cell RNA sequence (scRNA-seq) analysis further confirmed that these hub genes might play important roles in TB pathogenesis. The nine EVs-related hub genes had excellent diagnostic values and accurately estimated TB progression. TB's high-risk group had significantly enriched immune-related pathways, and there were substantial variations in immunity across different groups. Furthermore, five potential drugs were predicted for TB using CMap database. Based on the EVs-related gene signature, the TB risk model was established through a comprehensive analysis of different EV patterns, which can accurately predict TB. These genes could be used as novel biomarkers to distinguish TB from HC. These findings lay the foundation for further research and design of new therapeutic interventions aimed at treating this deadly infectious disease.

Molecular signatures between citrus and Candidatus Liberibacter asiaticus.

Citrus Huanglongbing (HLB), also known as citrus greening, is one of the most devastating citrus diseases worldwide. Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain associated with HLB, which is yet to be cultured in vitro. None of the commercial citrus cultivars are resistant to HLB. The pathosystem of Ca. Liberibacter is complex and remains a mystery. In this review, we focus on the recent progress in genomic research on the pathogen, the interaction of host and CLas, and the influence of CLas infection on the transcripts, proteins, and metabolism of the host. We have also focused on the identification of candidate genes for CLas pathogenicity or the improvements of HLB tolerance in citrus. In the end, we propose potentially promising areas for mechanistic studies of CLas pathogenicity, defense regulators, and genetic improvement for HLB tolerance/resistance in the future.

Nomogram to Predict Recurrence and Guide a Pragmatic Surveillance Strategy After Resection of Hepatoid Adenocarcinoma of the Stomach: A Retrospective Multicenter Study.

BACKGROUND: An accurate recurrence risk assessment system and surveillance strategy for hepatoid adenocarcinoma of the stomach (HAS) remain poorly defined. This study aimed to develop a nomogram to predict postoperative recurrence of HAS and guide individually tailored surveillance strategies. METHODS: The study enrolled all patients with primary HAS who had undergone curative-intent resection at 14 institutions from 2004 to 2019. Clinicopathologic variables with statistical significance in the multivariate Cox regression were incorporated into a nomogram to build a recurrence predictive model. RESULTS: The nomogram of recurrence-free survival (RFS) based on independent prognostic factors, including age, preoperative carcinoembryonic antigen, number of examined lymph nodes, perineural invasion, and lymph node ratio, achieved a C-index of 0.723 (95% confidence interval [CI], 0.674-0.772) in the whole cohort, which was significantly higher than those of the eighth American Joint Committed on Cancer (AJCC) staging system (C-index, 0.629; 95% CI, 0.573-0.685; P < 0.001). The nomogram accurately stratified patients into low-, middle-, and high-risk groups of postoperative recurrence. The postoperative recurrence risk rates for patients in the middle- and high-risk groups were respectively 3 and 10 times higher than for the low-risk group. The patients in the middle- and high-risk groups showed more recurrence and metastasis, particularly multiple site metastasis, within 36 months after the operation than those in the low-risk group (low, 2.2%; middle, 8.6%; high, 24.0%; P = 0.003). CONCLUSIONS: The nomogram achieved good prediction of postoperative recurrence for the patients with HAS after radical resection. For the middle- and high-risk patients, more active surveillance and targeted examination methods should be adopted within 36 months after the operation, particularly for liver and multiple metastases.

Projecting spatiotemporal dynamics of severe fever with thrombocytopenia syndrome in the mainland of China.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with increasing incidence and geographic extent. The extent to which global climate change affects the incidence of SFTS disease remains obscure. We use an integrated multi-model, multi-scenario framework to assess the impact of global climate change on SFTS disease in China. The spatial distribution of habitat suitability for the tick Haemaphysalis longicornis was predicted by applying a boosted regression tree model under four alternative climate change scenarios (RCP2.6, RCP4.5, RCP6.0, and RCP8.5) for the periods 2030-2039, 2050-2059, and 2080-2089. We incorporate the SFTS cases in the mainland of China from 2010 to 2019 with environmental variables and the projected distribution of H. longicornis into a generalized additive model to explore the current and future spatiotemporal dynamics of SFTS. Our results demonstrate an expanded geographic distribution of H. longicornis toward Northern and Northwestern China, showing a more pronounced change under the RCP8.5 scenario. In contrast, the environmental suitability of H. longicornis is predicted to be reduced in Central and Eastern China. The SFTS incidence in three time periods (2030-2039, 2050-2059, and 2080-2089) is predicted to be increased as compared to the 2010s in the context of various RCPs. A heterogeneous trend across provinces, however, was observed, when an increased incidence in Liaoning and Shandong provinces, while decreased incidence in Henan province is predicted. Notably, we predict possible outbreaks in Xinjiang and Yunnan in the future, where only sporadic cases have been reported previously. These findings highlight the need for tick control and population awareness of SFTS in endemic regions, and enhanced monitoring in potential risk areas.

A novel mitovirus isolated from the filamentous fungus Hypoxylon fendleri.

Members of the fungal genus Hypoxylon of the family Xylariaceae are known to produce secondary metabolites with significant chemical diversity. There are more than 200 species in the genus, including the filamentous fungus Hypoxylon fendleri. To the best of our knowledge, there have been no reports of mycoviruses in H. fendleri. In this study, a novel mycovirus, designated "Hypoxylon fendleri mitovirus 1" (HfMV1), was isolated from this fungus. The genome of HfMV1 is 2850 nt in length with a G + C content of 36% and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). BLASTp analysis revealed that the RdRp domain of HfMV1 had 28.30-50.90% sequence identity to those of members of the genus Duamitovirus and had the highest identity (50.90%) to Fusarium graminearum mitovirus 2-2 (FgMV2-2). Phylogenetic analysis further indicated that HfMV1 is a member of the genus Duamitovirus of the family Mitoviridae. This is the first report of a mycovirus in H. fendleri.

A Novel ypTLM Staging System Based on LODDS for Gastric Cancer After Neoadjuvant Therapy: Multicenter and Large-Sample Retrospective Study.

BACKGROUND: The accuracy of the eighth AJCC ypTNM staging system on the prognosis of gastric cancer (GC) patients after neoadjuvant therapy (NAT) is controversial. This study aimed to develop and validate a novel staging system using the log odds of positive lymph nodes scheme (LODDS). METHODS: A retrospective analysis of 606 GC patients who underwent radical gastrectomy after neoadjuvant therapy was conducted as the development cohort. (Fujian Medical University Affiliated Union Hospital (n = 183), Qinghai University Affiliated Hospital (n = 169), Mayo Clinic (n = 236), Lanzhou University First Hospital (n = 18)). The validation cohort came from the SEER database (n = 1701). A novel ypTLoddsS (ypTLM) staging system was established using the 3-year overall survival. The predictive performance of two systems was compared. RESULTS: Two-step multivariate Cox regression analysis in both cohorts showed that ypTLM was an independent predictor of overall survival of GC patients after neoadjuvant therapy (HR: 1.57, 95% CI: 1.30-1.88, p < 0.001). In the development cohort, ypTLM had better discrimination ability than ypTNM (C-index: 0.663 vs 0.633, p < 0.001), better prediction homogeneity (LR: 97.7 vs. 70.9), and better prediction accuracy (BIC: 3067.01 vs 3093.82; NRI: 0.36). In the validation cohort, ypTLM had a better prognostic predictive ability (C-index: 0.614 vs 0.588, p < 0.001; LR: 11,909.05 vs. 11,975.75; BIC: 13,263.71 vs 13,328.24; NRI: 0.22). The time-dependent ROC curve shows that the predictive performance of ypTLM is better than ypTNM, and the analysis of the decision curve shows that ypTLM achieved better net benefits. CONCLUSION: A LODDS-based ypTLM staging system based on multicenter data was established and validated. The predictive performance was superior to the eighth AJCC ypTNM staging system.

Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.

Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 µM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.

CCL2 Promotes Novel Coronavirus-Mediated Inflammatory Responses in Macrophages.

PURPOSE: The hyperinflammatory response is one of the main complications associated with novel coronavirus disease 2019 (COVID-19), and there is no effective treatment for cytokine storm. Therefore, it is important to investigate the key genes associated with severity of the disease. METHODS: In this study, we used a microarray data set to analyze the key genes associated with severe illness in patients with COVID-19. The proportion of immune cells was determined using the CIBERSORT algorithm. The key genes were further verified by detecting the levels of cytokines and chemokines in the serum of patients. Additionally, macrophages were stimulated with SARS-CoV-2 spike protein and chemokine ligand (CCL) 2. The expression of cytokines, ERK1/2, and NF-κB in macrophages was detected. RESULTS: Four hub genes were identified. Among them, C-C motif chemokine receptor 2 (CCR2) was an upregulated hub gene, while killer cell lectin-like receptor subfamily K member 1 (KLRK1), macrophage colony-stimulating factor receptor (CSF1R), and CD3D human recombinant protein (CD3D) were downregulated genes. Immune cell type identification found that the proportion of monocytes was higher in patients with severe COVID-19 than that in controls. Moreover, levels of CCL2 were significantly higher in patients with COVID-19. When stimulated with SARS-CoV-2 S protein and CCL2, macrophages secreted more inflammatory cytokines. The expression level of ERK1/2 was elevated. CONCLUSIONS: These results suggested that S protein and CCL2 may mediate macrophage inflammatory responses through the ERK1/2 signaling pathway. This study provides a basis for clinical treatment and improves the prognosis of critically ill patients with COVID-19.

Delta computed tomography radiomics features-based nomogram predicts long-term efficacy after neoadjuvant chemotherapy in advanced gastric cancer.

BACKGROUND AND OBJECTIVE: No effective preoperative tool is available for predicting the prognosis of advanced gastric cancer (AGC) treated by neoadjuvant chemotherapy (NAC). We aimed to explore the association between change values ("delta") in the radiomic signatures of computed tomography (CT) (delCT-RS) before and after NAC for AGC and overall survival(OS). METHODS AND DESIGN: A total of 132 AGC patients with AGC were studied as a training cohort in our center, and 45 patients from another center were used as an external validation set. A radiomic signatures-clinical-nomogram(RS-CN) was established using delCT-RS and preoperative clinical variables. The prediction performance of RS-CN was evaluated using the area under the receiver operating characteristic (ROC)curve (AUC values), time-dependent ROC, decision curve analysis(DCA) and C-index. RESULTS: Multivariable Cox regression analyses showed that delCT-RS, cT-stage, cN-stage, Lauren-type and the value of variation of carcinoma embryonic antigen (CEA) between NAC were independent risk factors for 3-year OS of AGC. In the training cohort, RS-CN had a good prediction performance for OS (C-Index 0.73) and AUC values were significantly better than those of delCT-RS, ypTNM-stage and tumor regression grade(TRG) (0.827 vs 0.704 vs 0.749 vs 0.571, p < 0.001). DCA and time-dependent ROC of RS-CN were better than those of ypTNM stage, TRG grade and delCT-RS. The prediction performance of the validation set was equivalent to that of the training set. The cut-off (177.2) of RS-CN score was obtained from X-Tile software, a score of > 177.2 was defined as high-risk group(HRG), and scores of ≤ 177.2 were defined as the low-risk group(LRG). The 3-year OS and disease free survival(DFS) of patients in the LRG were significantly better than those in the HRG. Adjuvant chemotherapy(AC) can only significantly improve the 3-year OS and DFS of the LRG. (p < 0.05). CONCLUSIONS: Our nomogram based on delCT-RS has good prediction of prognosis before surgery and helps identify patients that are most likely to benefit from AC. It works well in precise and individualised NAC in AGC.

Bacteria-induced amino acid metabolism involved in appearance characteristics of high-temperature Daqu.

BACKGROUND: Significant changes occurd in Daqu bricks on the 15th day of incubation, and brick color (yellow, brown, or dark) is generally used as a standard for quality evaluation by experienced workers. This study aimed to explore the basis behind the phenomenon through multi-omics studies. The physicochemical properties of different high-temperature Daqu were compared. Furthermore, PacBio sequencing and the ultra-high-performance liquid chromatographic-Q-exactive-mass spectrometric approach were employed to analyze the differences in the microbiome and metabolome among different Daqu samples. RESULTS: Bacillus was the biomarker of yellow Daqu, Thermoactinomyces and Thermoascus were the key genera in brown Daqu, and Burkholderiales, Sphingomonas, and Ralstonia were biomarkers in dark Daqu. The physicochemical characteristics (especially the color values) of different high-temperature Daqu showed strong correlations with the bacterial alpha diversity and the relative abundance of dominant bacterial genera. Amino acid metabolism pathways including tryptophan metabolism, ß-alanine metabolism, and arginine biosynthesis were the key factors resulting in the characteristic differences where Bacillus, Burkholderia, Ralstonia, and Sphingomonas were pivotal bacterial genera. The relative abundance of Bacillus had a positive correlation with the content of 3-hydroxykynurenamine, l-glutamic acid, and pantothenic acid, while it showed a negative correlation with indoleacetic acid, l-tryptophan, N-acetylserotonin, l-histidine, l-aspartic acid, phosphatidylserine, 5-methoxyindoleacetate, and L-serine. Burkholderia, Ralstonia, and Sphingomonas had the opposite effects. CONCLUSION: Microbes play different roles in amino acid metabolism pathways, producing different metabolites, contributing to the differences in Daqu appearance and quality. © 2022 Society of Chemical Industry.

Dynamic functional connectivity in modular organization of the hippocampal network marks memory phenotypes in temporal lobe epilepsy.

Temporal lobe epilepsy (TLE) is a network disorder with a high incidence of memory impairment. Memory processing ability highly depends on the dynamic coordination between distinct modules within the hippocampal network. Here, we investigate the relationship between memory phenotypes and modular alterations of dynamic functional connectivity (FC) in the hippocampal network in TLE patients. Then, 31 healthy controls and 66 TLE patients with hippocampal sclerosis were recruited. The patients were classified into memory-intact (MI, 35 cases) group and memory-deficit (MD, 31 cases) group, each based on individual's Wechsler Memory Scale-Revised score. The sliding-windows approach and graph theory analysis were used to analyze the hippocampal network based on resting state functional magnetic resonance imaging. Temporal properties and modular metrics were calculated. Two discrete and switchable states were revealed: a high modularized state (State I) and a low modularized state (State II), which corresponded to either anterior or posterior hippocampal network dominated pattern. TLE was prone to drive less State I but more State II, and the tendency was more obvious in TLE-MD. Additionally, TLE-MD showed more widespread alterations of modular properties compared with TLE-MI across two states. Furthermore, the dynamic modularity features had unique superiority in discriminating TLE-MD from TLE-MI. These findings demonstrated that state transitions and modular function of dissociable hippocampal networks were altered in TLE and more importantly, they could reflect different memory phenotypes. The trend revealed potential values of dynamic FC in elucidating the mechanism underlying memory impairments in TLE.