LVPT: Lazy Velocity Pseudotime Inference Method

The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the probability and direction of cell differentiation. LVPT shows better and comparable performance of pseudotime inference compared with other existing methods on both simulated datasets with different structures and real datasets. The validation results were consistent with prior knowledge, indicating that LVPT is an accurate and efficient method for pseudotime inference.

[Efficacy of CT-guided partial radiofrequency ablation of bilateral responsible cranial nerves in the treatment of Meige syndrome]

Objective: To evaluate the efficacy of CT-guided partial radiofrequency ablation of bilateral responsible cranial nerves in the treatment of Meige syndrome. Methods: The Clinical data of 56 patients with Meige syndrome in the Department of Pain Medicine, Affiliated Hospital of Jiaxing University from June 2019 to January 2023 were retrospectively analyzed [19 males and 37 females, aged 42-76 (58.6±8.3) years], including 51 cases of blepharospasm, 3 cases of oromandibular dystonia and 2 cases of blepharospasm concomitant with oromandibular dystonia. CT-guided partial radiofrequency ablation of bilateral responsible cranial nerves was performed on different types of Meige syndrome. And the efficacy and complications of the technique were observed. Results: Fifty-one patients with blepharospasm Meige syndrome underwent CT-guided radiofrequency of facial nerve through bilateral stylomastoid foramen punctures, the symptoms of blepharospasm disappeared completely, leaving bilateral mild and moderate facial paralysis symptoms. Three patients with oral-mandibular dystonia underwent CT-guided radiofrequency therapy by bilateral foramen ovale puncture of mandibular branches of trigeminal nerve, masticatory muscle spasm disappeared, the patients had no difficulty opening the mouth, and the skin numbness in bilateral mandibular nerve innervation area was left. Two cases of Meige syndrome with blepharospasm concomitant with oromandibular dystonia were treated by radiofrequency of facial nerve and mandibular branch of trigeminal nerve, and all symptoms disappeared. The patients were followed up for 1-44 months after the operation, and the symptoms of mild and moderate facial paralysis disappeared at (3.2±0.8) months after the operation, but the numbness did not disappear. Three patients with blepharospasm recurred at the 14, 18 and 22 months after the operation, respectively, while the rest cases did not recur. Conclusions: According to different types of Meige syndrome, CT-guided partial radiofrequency ablation of responsible cranial nerves can effectively treat the corresponding type of Meige syndrome. The complications are only mild and moderate facial paralysis which can be recovered, and/or skin numbness in the mandibular region.

"Double-edged sword" effect of reactive oxygen species (ROS) in tumor development and carcinogenesis

Reactive oxygen species (ROS) are small reactive molecules produced by cellular metabolism and regulate various physiological and pathological functions. Many studies have shown that ROS plays an essential role in the proliferation and inhibition of tumor cells. Different concentrations of ROS can have a "double-edged sword" effect on the occurrence and development of tumors. A certain concentration of ROS can activate growth-promoting signals, enhance the proliferation and invasion of tumor cells, and cause damage to biomacromolecules such as proteins and nucleic acids. However, ROS can enhance the body's antitumor signal at higher levels by initiating oxidative stress-induced apoptosis and autophagy in tumor cells. This review analyzes ROS's unique bidirectional regulation mechanism on tumor cells, focusing on the key signaling pathways and regulatory factors that ROS affect the occurrence and development of tumors and providing ideas for an in-depth understanding of the mechanism of ROS action and its clinical application.

COVIDanno, COVID-19 annotation in human

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim of this resource is to provide a reference resource of intensive functional annotations of differentially expressed genes (DEGs) among different time points of COVID-19 infection in human in vitro models. To do this, we performed differential expression analysis for 136 individual datasets across 13 tissue types. In total, we identified 4,935 DEGs. We performed multiple bioinformatics/computational biology studies for these DEGs. Furthermore, we developed a novel tool to help users predict the status of SARS-CoV-2 infection for a given sample. COVIDanno will be a valuable resource for identifying SARS-CoV-2-related genes and understanding their potential functional roles in different time points and multiple tissue types.

[Dermatophagoides farinae induces conjunctival epithelial cell damage to promote neutrophil migration and neutrophil extracellular traps formation]

OBJECTIVE

To investigate the mechanisms underlying allergic conjunctivitis caused by conjunctival epithelial cell damage, neutrophil migration and neutrophil extracellular traps (NETs) formation induced by crude extracts of Dermatophagoides farinae mite (CDM).

METHODS

Human conjunctival epithelial cells were stimulated with 500, 1 000, 2 000, 4 000 ng/mL, and the expression levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ) and IL-8 were detected using quantitative real-time PCR (qPCR) assay and enzyme-linked immunosorbent assay (ELISA). The culture supernatant of human conjunctival epithelial cells was collected and co-cultured with neutrophils. Neutrophil migration was measured using Transwell migration assay, and the expression of NETs markers myeloperoxidase (MPO) and citrullinated histone H3 (CitH3) was quantified using immunofluorescence staining. Neutrophils were stimulated with phorbol 12-myristate 13-acetate (PMA), and then NETs were collected for treatment of human conjunctival epithelial cells. Cell apoptosis was detected using flow cytometry, and the levels of IL-6, TNF-α, IFN-γ and IL-8 were measured in the cell culture supernatant using ELISA.

RESULTS

Treatment with CDM at concentrations of 2 000 ng/mL and 4 000 ng/mL up-regulated IL-6, TNF-α, IFN-γ and IL-8 expression in human conjunctival epithelial cells. Following treatment with CDM at concentrations of 2 000 ng/mL and 4 000 ng/mL, the culture supernatant of human conjunctival epithelial cells promoted neutrophil migration and induced increases in the staining intensity of MPO and CitH3. In addition, increased NETs triggered the apoptosis of human conjunctival epithelial cells and IL-6, TNF-α, IFN-γ and IL-8 secretion in the culture supernatant of human conjunctival epithelial cells.

CONCLUSIONS

CDM induces human conjunctival epithelial cell damages, thereby promoting neutrophil migration and NETs formation, while the release of NETs further aggravates human conjunctival epithelial cell damages.

[Determination of misoprostol in workplace air by high performance liquid chromatography]

Objective: To establish a high performance liquid chromatography method for the determination of misoprostol in workplace air. Methods: From February to August 2021, the misoprostol in the workplace air was collected by glass fiber filter membrane, and theeluent was separated by C18 liquid chromatography column, determined by UV detector, and quantified by external standard method. Results: The quantitative lower limit of misoprostol determination method was 0.05 μg/ml, and the lowest quantitative concentration was 1.4 μg/m(3) (calculated by collecting 75 L air sample). The concentration of misoprostol has a good linear relationship between 0.05 to 10.00 μg/ml. The relative coefficient was 0.9998. The regression equation of the standard working curve was y=495759x-45257. The range of average recovery rates were from 95.5% to 102.8%. The intra-assay precision of the method was 1.2%-4.6%, and the inter-assay precision was 2.0%-5.9%. The samples could be stored stably for 7 days at 4 ℃. Conclusion: The high performance liquid chromatography method for the determination of misoprostol has high sensitivity, good specificity and simple procedure of sample pretreatment. It is suitable for the detection of misoprostol in the workplace air.

[Population structure of food-borne Staphylococcus aureus in China]

Objective: To understand the population structure of food-borne Staphylococcus (S.) aureus in China. Methods: Whole genome sequencing was used to analyze 763 food-borne S. aureus strains from 16 provinces in China from 2006 to 2020. Multilocus sequence typing (MLST), staphylococcal protein A gene (spa) typing, and staphylococcal chromosome cassettemec (SCCmec) typing were conducted, and minimum spanning tree based on ST types (STs) was constructed by BioNumerics 7.5 software. Thirty-one S. aureus strains isolated from imported food products were also included in constructing the genome phylogenetic tree. Results: A total of 90 STs (20 novel types) and 160 spa types were detected in the 763 S. aureus isolates. The 72 STs (72/90, 80.0%) were related to 22 clone complexes. The predominant clone complexes were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, accounting for 82.44% (629/763) of the total. The STs and spa types in the predominant clone complexes changed over the years. The methicillin-resistant S. aureus (MRSA) detection rate was 7.60%, and 7 SCCmec types were identified. The ST59-t437-Ⅳa (17.24%, 10/58), ST239-t030-Ⅲ (12.07%, 7/58), ST59-t437-Ⅴb (8.62%, 5/58), ST338-t437-Ⅴb (6.90%, 4/58) and ST338-t441-Ⅴb (6.90%, 4/58) were the main types in MRSA strains. The genome phylogenetic tree had two clades, and the strains with the same CC, ST, and spa types clustered together. All CC7 methicillin sensitive S. aureus strains were included in Clade1, while 21 clone complexes and all MRSA strains were in Clade2. The MRSA strains clustered according to the SCCmec and STs. The strains from imported food products in CC398, CC7, CC30, CC12, and CC188 had far distances from Chinese strains in the tree. Conclusions: In this study, the predominant clone complexes of food-borne strains were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, which overlapped with the previously reported clone complexes of hospital and community-associated strains in China, suggesting that close attention needs to be paid to food, a vehicle of pathogen transmission in community and food poisoning.

[Quantitative study of supraspinatus tendon injury grading based on synthetic magnetic resonance imaging]

Objective: To investigate the diagnostic value of quantitative parameters of synthetic magnetic resonance imaging (SyMRI) in the grade of supraspinatus tendon injury. Methods: Ninety-seven patients with clinical definite of supraspinatus tendon injury from July 2021 to July 2022 in General Hospital of Ningxia Medical University were prospectively collected (case group), including 54 males and 43 females, with an age of 29 to 56 (37.4±9.6) years. According to the results of shoulder arthroscopy, the case group were divided into three subgroups included tendinopathy group (37 cases, grade Ⅱ), partial tear group (34 cases, grade Ⅲ) and complete tear group (26 cases, grade Ⅳ). During the same period, 28 normal rotator cuff volunteers without supraspinatus tendon injury were recruited (control group), including 16 males and 12 females, aged 23 to 49 (36.1±7.2) years, and marked as grade Ⅰ. All the subjects underwent MRI scan of articulatio humeri included T₁-weighted imaging(T₁WI) fast spin echo(FSE) sequences in axial view, T₂-weighted imaging(T₂WI) fat suppression(FS) sequences in axial view, T₂WI FS sequences in oblique coronal view, proton density-weighted (PDW) imaging in oblique sagittal view and SyMRI in oblique coronal view. The supraspinatus tendon was divided into lateral, medial and middle subregions according to its shape in oblique coronal T₂WI view, two radiologists measured the T₁, T₂ and PD values of the supraspinatus tendon. The interclass correlation coefficient (ICC) were used to compare the consistency between and within observers. One-way analysis of variance or Kruskal-Wallis H test were used to compare the differences of quantitative parameters in different grades, the multivariate logistic regression model was used to analyze the risk factors of supraspinatus tendon injury grade, and the receiver operating characteristic (ROC) curves and area under curve (AUC) was drawn and calculated to evaluate the diagnostic efficacy. The Spearman correlation was used to analyze the correlation between the quantitative values and grades of supraspinatus tendon injury. Results: The ICC values of T₁, T₂ and PD values for the three subregions of the supraspinatus tendon were greater than 0. 700. The differences of T₁ values in the lateral subregion, T₂ values in the lateral and middle subregions were statistically significant in the overall comparison across different grades (all P<0. 001).The differences of T₁ values in the middle and medial subregions, T₂ values in the medial subregion and PD values in the lateral, middle and medial subregions were not statistically significant in the overall comparison of different grades (all P>0. 05). Multiple logistic regression model analysis showed that T₂ values in the lateral and middle subregions were related factors for the grade of supraspinatus tendon injury[ OR (95%CI):1.123 (1.037-1.216), 0.122 (1.151-1.197);all P<0.001 ]. The AUC of the T₂ values in lateral subregion diagnosing grade Ⅰ vs grade Ⅳ, grade Ⅱ vs grade Ⅳ and grade Ⅲ vs grade Ⅳ were 0.891(95%CI: 0.801-0.981), 0.797(95%CI: 0.680-0.914), 0.723(95%CI: 0.594-0.853) (all P<0.001), and the AUC of the T₂ values in middle subregion diagnosing grade Ⅰ vs Ⅳ, grade Ⅱ vs Ⅳ, grade Ⅱ vs Ⅲ, and grade Ⅰ vs Ⅲ were 0.946 (95%CI: 0.849-0.989), 0.886 (95%CI: 0.809-0.962), 0.746 (95%CI: 0.631-0.861), 0.843 (95%CI: 0.745-0.941)(all P<0.001). The T₂ values in the lateral and middle subregions were positively correlated with the grade of supraspinatus tendon injury (r=0.542, 0.615; both P<0.001), while T₁ values and T₂ values in the medial subregions were not significantly correlated with the grade of supraspinatus tendon injury (both P>0.05). Conclusion: SyMRI has high clinical application value in the grading of supraspinatus tendon injury, especially T₂ value can be used as an effective quantitative parameter for the grading of supraspinatus tendon injury.

A novel integrated approach to predicting cancer immunotherapy efficacy

Immunotherapies have revolutionized cancer treatment modalities; however, predicting clinical response accurately and reliably remains challenging. Neoantigen load is considered as a fundamental genetic determinant of therapeutic response. However, only a few predicted neoantigens are highly immunogenic, with little focus on intratumor heterogeneity (ITH) in the neoantigen landscape and its link with different features in the tumor microenvironment. To address this issue, we comprehensively characterized neoantigens arising from nonsynonymous mutations and gene fusions in lung cancer and melanoma. We developed a composite NEO2IS to characterize interplays between cancer and CD8+ T-cell populations. NEO2IS improved prediction accuracy of patient responses to immune-checkpoint blockades (ICBs). We found that TCR repertoire diversity was consistent with the neoantigen heterogeneity under evolutionary selections. Our defined neoantigen ITH score (NEOITHS) reflected infiltration degree of CD8+ T lymphocytes with different differentiation states and manifested the impact of negative selection pressure on CD8+ T-cell lineage heterogeneity or tumor ecosystem plasticity. We classified tumors into distinct immune subtypes and examined how neoantigen-T cells interactions affected disease progression and treatment response. Overall, our integrated framework helps profile neoantigen patterns that elicit T-cell immunoreactivity, enhance the understanding of evolving tumor-immune interplays and improve prediction of ICBs efficacy.

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression

Lung adenocarcinoma (LUAD) is a deadly tumor with dynamic evolutionary process. Although much endeavors have been made in identifying the temporal patterns of cancer progression, it remains challenging to infer and interpret the molecular alterations associated with cancer development and progression. To this end, we developed a computational approach to infer the progression trajectory based on cross-sectional transcriptomic data. Analysis of the LUAD data using our approach revealed a linear trajectory with three different branches for malignant progression, and the results showed consistency in three independent cohorts. We used the progression model to elucidate the potential molecular events in LUAD progression. Further analysis showed that overexpression of BUB1B, BUB1 and BUB3 promoted tumor cell proliferation and metastases by disturbing the spindle assembly checkpoint (SAC) in the mitosis. Aberrant mitotic spindle checkpoint signaling appeared to be one of the key factors promoting LUAD progression. We found the inferred cancer trajectory allows to identify LUAD susceptibility genetic variations using genome-wide association analysis. This result shows the opportunity for combining analysis of candidate genetic factors with disease progression. Furthermore, the trajectory showed clear evident mutation accumulation and clonal expansion along with the LUAD progression. Understanding how tumors evolve and identifying mutated genes will help guide cancer management. We investigated the clonal architectures and identified distinct clones and subclones in different LUAD branches. Validation of the model in multiple independent data sets and correlation analysis with clinical results demonstrate that our method is effective and unbiased.

[Development and validation of prognostic nomogram for malignant pleural mesothelioma]

Objective: To development the prognostic nomogram for malignant pleural mesothelioma (MPM). Methods: Two hundred and ten patients pathologically confirmed as MPM were enrolled in this retrospective study from 2007 to 2020 in the People's Hospital of Chuxiong Yi Autonomous Prefecture, the First and Third Affiliated Hospital of Kunming Medical University, and divided into training (n=112) and test (n=98) sets according to the admission time. The observation factors included demography, symptoms, history, clinical score and stage, blood cell and biochemistry, tumor markers, pathology and treatment. The Cox proportional risk model was used to analyze the prognostic factors of 112 patients in the training set. According to the results of multivariate Cox regression analysis, the prognostic prediction nomogram was established. C-Index and calibration curve were used to evaluate the model's discrimination and consistency in raining and test sets, respectively. Patients were stratified according to the median risk score of nomogram in the training set. Log rank test was performed to compare the survival differences between the high and low risk groups in the two sets. Results: The median overall survival (OS) of 210 MPM patients was 384 days (IQR=472 days), and the 6-month, 1-year, 2-year, and 3-year survival rates were 75.7%, 52.6%, 19.7%, and 13.0%, respectively. Cox multivariate regression analysis showed that residence (HR=2.127, 95% CI: 1.154-3.920), serum albumin (HR=1.583, 95% CI: 1.017-2.464), clinical stage (stage Ⅳ: HR=3.073, 95% CI: 1.366-6.910) and the chemotherapy (HR=0.476, 95% CI: 0.292-0.777) were independent prognostic factors for MPM patients. The C-index of the nomogram established based on the results of Cox multivariate regression analysis in the training and test sets were 0.662 and 0.613, respectively. Calibration curves for both the training and test sets showed moderate consistency between the predicted and actual survival probabilities of MPM patients at 6 months, 1 year, and 2 years. The low-risk group had better outcomes than the high-risk group in both training (P=0.001) and test (P=0.003) sets. Conclusion: The survival prediction nomogram established based on routine clinical indicators of MPM patients provides a reliable tool for prognostic prediction and risk stratification.

[Association between vitamin D level and blood eosinophil count in healthy population and patients with chronic obstructive pulmonary disease]

OBJECTIVE

To investigate the prevalence of vitamin D deficiency and its association with blood eosinophil count in healthy population and patients with chronic obstructive pulmonary disease (COPD).

METHODS

We analyzed the data of a total 6163 healthy individuals undergoing routine physical examination in our hospital between October, 2017 and December, 2021, who were divided according to their serum 25(OH)D level into severe vitamin D deficiency group (< 10 ng/mL), deficiency group (< 20 ng/mL), insufficient group (< 30 ng/mL) and normal group (≥30 ng/mL). We also retrospectively collected the data of 67 COPD patients admitted in our department from April and June, 2021, with 67 healthy individuals undergoing physical examination in the same period as the control group. Routine blood test results, body mass index (BMI) and other parameters were obtained from all the subjects, and logistic regression models were used to investigate the association between 25(OH)D levels and eosinophil count.

RESULTS

The overall abnormal rate of 25(OH)D level (< 30 ng/mL) in the healthy individuals was 85.31%, and the rate was significantly higher in women (89.29%) than in men. Serum 25(OH)D levels in June, July, and August were significantly higher than those in December, January, and February. In the healthy individuals, blood eosinophil counts were the lowest in severe 25(OH)D deficiency group, followed by the deficiency group and insufficient group, and were the highest in the normal group (P < 0.05). Multivariable regression analysis showed that an older age, a higher BMI, and elevated vitamin D levels were all risk factors for elevated blood eosinophils in the healthy individuals. The patients with COPD had lower serum 25(OH)D levels than the healthy individuals (19.66±7.87 vs 26.39±9.28 ng/mL) and a significantly higher abnormal rate of serum 25(OH)D (91% vs 71%; P < 0.05). A reduced serum 25(OH)D level was a risk factor for COPD. Blood eosinophils, sex and BMI were not significantly correlated with serum 25(OH)D level in patients with COPD.

CONCLUSION

Vitamin D deficiency is common in both healthy individuals and COPD patients, and the correlations of vitamin D level with sex, BMI and blood eosinophils differ obviously between healthy individuals and COPD patients.

[S100A10 promotes proliferation and invasion of lung adenocarcinoma cells by activating the Akt-mTOR signaling pathway]

OBJECTIVE

To investigate the effects of expression levels of S100 calcium-binding protein A10 (S100A10) in lung adenocarcinoma (LUAD) on patient prognosis and the regulatory role of S100A10 in lung cancer cell proliferation and metastasis.

METHODS

Immunohistochemistry was used to detect the expression levels of S100A10 in LUAD and adjacent tissues, and the relationship between S100A10 expression and clinicopathological parameters and prognosis of the patients was statistically analyzed. The lung adenocarcinoma expression dataset in TCGA database was analyzed using gene enrichment analysis (GSEA) to predict the possible regulatory pathways of S100A10 in the development of lung adenocarcinoma. Lactate production and glucose consumption of lung cancer cells with S100A10 knockdown or overexpression were analyzed to assess the level of glycolysis. Western blotting, CCK-8 assay, EdU-594 assay, and Transwell assays were performed to determine the expression level of S100A10 protein, proliferation and invasion ability of lung cancer cells. A549 cells with S100A10 knockdown and H1299 cells with S100A10 overexpression were injected subcutaneously in nude mice, and tumor growth was observed.

RESULTS

The expression level of S100A10 was significantly upregulated in LUAD tissues as compared with the adjacent tissues, and an elevated S100A10 expression level was associated with lymph node metastasis, advanced tumor stage and distant organ metastasis (P < 0.05), but not with tumor differentiation or the patients' age or gender (P > 0.05). Survival analysis showed that elevated S100A10 expressions in the tumor tissue was associated with a poor outcome of the patients (P < 0.001). In the lung cancer cells, S100A10 overexpression significantly promoted cell proliferation and invasion in vitro (P < 0.001). GSEA showed that the gene sets of glucose metabolism, glycolysis and mTOR signaling pathway were significantly enriched in high expressions of S100A10. In the tumor-bearing nude mice, S100A10 overexpression significantly promoted tumor growth, while S100A10 knockdown obviously suppressed tumor cell proliferation (P < 0.001).

CONCLUSION

S100A10 overexpression promotes glycolysis by activating the Akt-mTOR signaling pathway to promote proliferation and invasion of lung adenocarcinoma cells.

[Prevalence and trends of anemia among pregnant women in eight provinces of China from 2016 to 2020]

This study analyzed the anemia status and change trend of 219 835 pregnant women in eight provinces from 2016 to 2020 in the Maternal and Newborn Health Monitoring Program(MNHMP). The results showed that from 2016 to 2020, the anemia rate of pregnant women in eight provinces was 41.27%, and the rates of mild, moderate and severe anemia were 28.56%, 12.59% and 0.12% respectively; the anemia rates in eastern, central and western regions were 41.87%, 36.09% and 44.63% respectively, and the anemia rates in urban and rural areas were 39.87% and 42.23%. From 2016 to 2020, the anemia rate of pregnant women decreased from 44.93% to 38.22%, with an average annual decline of 3.86% (95%CI:-5.84%, -1.85%). The anemia rate among pregnant women of the eastern region (AAPC=-6.16%, 95%CI:-9.79%, -2.38%) fell faster than that among pregnant women of the central region (AAPC=0.71%, 95%CI:-6.59%, 8.57%) and western region (AAPC=-1.53%, 95%CI:-5.19%, 2.28%). From 2016 to 2020, the moderate anemia rate in pregnant women decreased from 14.98% to 10.74%, with an average annual decline of 8.72% (95%CI:-12.90%, -4.34%), with a statistically significant difference (P<0.05); AAPC for mild and severe anemia in pregnant women was 1.56% (95%CI: 3.44%, 0.36%) and 18.86% (95%CI: 39.88%, 9.52%), respectively, without statistically significant difference (P>0.05).

CVAM: CNA Profile Inference of the Spatial Transcriptome Based on the VGAE and HMM

Tumors are often polyclonal due to copy number alteration (CNA) events. Through the CNA profile, we can understand the tumor heterogeneity and consistency. CNA information is usually obtained through DNA sequencing. However, many existing studies have shown a positive correlation between the gene expression and gene copy number identified from DNA sequencing. With the development of spatial transcriptome technologies, it is urgent to develop new tools to identify genomic variation from the spatial transcriptome. Therefore, in this study, we developed CVAM, a tool to infer the CNA profile from spatial transcriptome data. Compared with existing tools, CVAM integrates the spatial information with the spot's gene expression information together and the spatial information is indirectly introduced into the CNA inference. By applying CVAM to simulated and real spatial transcriptome data, we found that CVAM performed better in identifying CNA events. In addition, we analyzed the potential co-occurrence and mutual exclusion between CNA events in tumor clusters, which is helpful to analyze the potential interaction between genes in mutation. Last but not least, Ripley's K-function is also applied to CNA multi-distance spatial pattern analysis so that we can figure out the differences of different gene CNA events in spatial distribution, which is helpful for tumor analysis and implementing more effective treatment measures based on spatial characteristics of genes.

The transcription factor CSL homolog in Penaeus vannamei positively regulates the transcription of the hemocyanin small subunit gene

Hemocyanin, a copper-containing respiratory protein, is abundantly present in hemolymph of arthropods and mollusks and performs a variety of immunological functions. However, the regulatory mechanisms of hemocyanin gene transcription remain largely unclear. Our previous work showed that knockdown of the transcription factor CSL, a component of the Notch signaling pathway, downregulated the expression of Penaeus vannamei hemocyanin small subunit gene (PvHMCs), indicating the involvement of CSL in regulating the PvHMCs transcription. In this study, we identified a CSL binding motif ("GAATCCCAGA", +1675/+1684 bp) in the core promoter of PvHMCs (designated as HsP3). Dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA) demonstrated that the CSL homolog in P. vannamei (PvCSL) could directly bind and activate the HsP3 promoter. Moreover, in vivo silencing of PvCSL significantly attenuated the mRNA and protein expression of PvHMCs. Finally, in response to Vibrio parahaemolyticus, Streptococcus iniae and white spot syndrome virus (WSSV) challenge, the transcript of PvCSL and PvHMCs showed a positive correlation, suggesting that PvCSL could also modulate the expression of PvHMCs upon pathogen stimulation. Taken together, our present finding is the first to demonstrate that PvCSL is a crucial factor in transcriptional control of PvHMCs.

[Analysis of typing conversion and perinatal outcomes in twins with selective intrauterine growth restriction of different subtypes]

Objective: To retrospectively analyze the clinical data of different types of selective intrauterine growth restriction (sIUGR) pregnant women under expectant management, including the natural evolution, typing conversion and perinatal outcomes. Methods: The clinical data of 153 pregnant women with sIUGR under expected treatment in Women's Hospital, Zhejiang University School of Medicine from January 2014 to December 2018 were collected. Maternal characteristics including maternal age, gravidity, parity, method of conception, pregnancy complication, gestational age at delivery, indication for delivery, birth weight, the rate of intrauterine and neonatal death and neonatal outcomes were recorded. Pregnant women with sIUGR were divided into three types according to end-diastolic umbilical artery flow Doppler ultrasonography, and the differences of typing conversion and perinatal outcomes of sIUGR pregnant women based on the first diagnosis were compared. Results: (1) Clinical characteristics and pregnancy outcomes: among 153 pregnant women with sIUGR, 100 cases (65.3%) were diagnosed with type Ⅰ, 35 cases (22.9%) with type Ⅱ, and 18 cases (11.8%) with type Ⅲ. There were no significant differences in age, conception mode, pregnancy complications, first diagnosis gestational age, characteristics of umbilical cord insertion, delivery indications, fetal intrauterine mortality and neonatal mortality among three types of sIUGR pregnant women (all P>0.05). The average gestational age at delivery of type Ⅰ sIUGR was (33.5±1.9) weeks, which was significantly later than those of type Ⅱ and Ⅲ [(31.3±1.8), (31.2±1.1) weeks, P<0.001]. The percentage disordance in estimated fetal weight (EFW) of type Ⅰ sIUGR was significantly lower than those of type Ⅱ and type Ⅲ (P<0.001). The incidence rate of neonatal intensive care unit (NICU) admission, cerebral leukomalacia and respiratory complications of both fetus and necrotizing enterocolitis of large fetus in type Ⅰ were significantly lower than those in type Ⅱ and type Ⅲ (all P<0.05). (2) Typing conversion: in 100 cases of type Ⅰ sIUGR, 18 cases progressed to type Ⅱ and 10 cases progressed to type Ⅲ. Compared with 72 stable type Ⅰ sIUGR, those with progressed type Ⅰ sIUGR had higher incidence of NICU admission and lung disease in both fetuses, and cerebral leukomalacia and necrotizing enterocolitis in large fetus (all P<0.05). The proportion of inconsistent cord insertion was significantly higher in those type Ⅰ progressed to type Ⅲ (6/10) than in those with stable type Ⅰ (19.4%, 14/72) and type Ⅰ progressed to type Ⅱ sIUGR [0 (0/18), P=0.001]. Four cases of type Ⅱ sIUGR reversed to type Ⅰ and 6 cases reversed to type Ⅲ. Compared with type Ⅱ reversed to type Ⅰ sIUGR, those stable type Ⅱ and type Ⅱ reversed to type Ⅲ sIUGR had a higher incidence of NICU admission in large fetus (P<0.05). Two cases of type Ⅲ sIUGR reversed to type Ⅰ and 6 cases progressed to type Ⅱ. There were no significant differences in fetal serious complications in type Ⅲ sIUGR with or without doppler changes (all P>0.05). Conclusions: The different types of sIUGR could convert to each other. The frequency of ultrasound examinations should be increased for patients with the type Ⅰ sIUGR, especially when the percentage discordance in EFW is substantial or with discordant cord insersion.

EVALUATION OF PRE-ABLATION NLR AND LMR AS PREDICTORS OF DISTANT METASTASES IN PATIENTS WITH DIFFERENTIATED THYROID CANCER

Objective

This research aim was to evaluates the role of the pre-ablation neutrophil-to-lymphocyte ratio (NLR) and lymphocyte-to-monocyte ratio (LMR) as predictors of distant metastases in patients with differentiated thyroid cancer (DTC).

Methods

A retrospective analysis was given to 140 patients with DTC who received 131I remnant ablation after surgery. The patients were divided into two groups based on the existence of distant metastasis.

Results

The two groups showed no significant difference in age, gender, WBCs, neutrophils, monocytes, eosinophils, basophils and whether the tumor was multifocal. In the univariate analysis, significant differences were found in tumor size (p=0.021), lymphocyte (p=0.012), NLR (p=0.027), and LMR (p=0.007). According to the ROC curves, NLR had an AUC of 0.612 ± 0.097 with a cut-off value of 1.845, sensitivity of 60.0%, and specificity of 66.2% (p=0.027). LMR had an AUC of 0.638 ± 0.095 with a cut-off value of 4.630, sensitivity of 84.6%, and specificity of 35.4% (p=0.007). In the multivariate analysis, larger tumor size (OR=5.246, 95% CI 1.269-10.907, p=0.009) and higher NLR (OR=2.087, 95% CI 0.977-4.459, p=0.034) were statistically significant for distant metastases.

Conclusion

This research reveals that pre-ablation NLR and tumor size are significantly statistically correlated with distant metastases in patients with DTC.

Genetic impact on the association of sleep patterns and chronic kidney disease: A prospective cohort study of 157,175 UK Biobank participants

OBJECTIVES

The association between sleep pattern and chronic kidney disease (CKD) incidence, and whether the association is dependent on the genetic backgrounds has not been addressed. We sought to investigate the association of multidimensional sleep pattern with CKD in consideration of genetic polymorphisms.

METHODS

In this prospective cohort study of 157,175 participants from the UK Biobank, sleep patterns were derived by multiple correspondence analysis (MCA) and k-means clustering of individual sleep traits (sleep duration, insomnia, chronotype, daytime sleepiness, snoring, and night shift status). Cox proportional hazard regression was used to estimate the association between sleep patterns and CKD incidence. Gene-environment-wide interaction study (GEWIS) was performed to detect whether gene polymorphisms were modifiers on this association.

RESULTS

Compared with "healthy sleep" pattern, increased CKD incidence was observed in the clusters with "long sleep duration" (hazard ratios (HR) 1.42, 95% confidence intervals (CI), 1.18-1.72) and "night shift" (HR 1.23, 95% CI, 1.05-1.45) patterns, but not with the "short sleep duration" pattern. By GEWIS, we identified 167 SNPs as suggestive effect modifiers that interacted with unhealthy sleep patterns and affected the risk of CKD.

CONCLUSIONS

Unhealthy sleep patterns, with features of long sleep duration and night shift, may increase the risk of CKD. The study highlights the interaction of sleep and individual genetic risk to affect health outcomes.

[Morphology of the esophagus of ferrets and expression profile of molecular markers]

OBJECTIVE

To examine the morphological characteristics and the expression profile of molecular markers of ferret esophagus and assess the feasibility of using ferrets as animal models for studying human esophageal diseases.

METHODS

Frozen sections and paraffin- embedded specimens of the esophageal tissues were obtained from adult ferrets (aged 6 to 8 months) and ferrets aged 1 day, 3 days, 5 days, 1 week and 2 weeks. HE staining and periodic acid-Schiff (PAS) staining were used for morphological analysis of the esophageal submucosal glands (SMGs) of adult ferrets, and the expressions of MUC5B and MUC5AC were tested using Mucin staining; The expressions of cytokeratins (CK4, CK5, CK7, CK8, CK14, CK17, CK18, CK19, and CK20) in adult ferret esophagus were examined using HE staining and immunofluorescence assay. The expressions of LEF1 in the esophageal epithelium and SMGs were detected with immunofluorescence assay.

RESULTS

In adult ferrets, the esophageal SMGs were connective tissues below the muscularis mucosa of the esophagus with secretory functions. Cytokeratins were expressed differentially in different esophageal cells: CK4, CK8 and CK20 were expressed mainly in the mucous cells, ductal cells and epithelial cells, respectively, while the mucous cells expressed the largest variety of cytokeratins. Mucin staining showed positive MUC5B and MUC5AC expression in the cytoplasm and lumen of adult ferret esophageal glands. Lectin from DBA, ECL, GSLI, GSL Ⅱ, SBA, Tacalin bioylated, ULEX, WGA, GSL Ⅰ and GSL Ⅱ were expressed on ductal cell membrane, and ECL, PNA and WGA were detected on epithelial cell membrane. Lectin with ConA, PHA-E and PHA-L were expressed on serous cell membrane. Immunofluorescence assay showed that LEF1 in the developing glands were visible from 3 days to 1 week of age and then disappeared as the glands matured. The intensity of LEF1 expression in the esophageal glands differed significantly between ferrets aged 1 to 7 days and those aged two weeks.

CONCLUSION

Ferrets and human share similar esophageal tissue structures and some common molecular markers, suggesting the possibility of using ferrets as animal models of human esophageal diseases.

Development of [18F]F-5-OMe-Tryptophans through Photoredox Radiofluorination: A New Method to Access Tryptophan-Based PET Agents

Although various radiolabeled tryptophan analogs have been developed to monitor tryptophan metabolism using positron emission tomography (PET) for various human diseases including melanoma and other cancers, their application can be limited due to the complicated synthesis process. In this study, we demonstrated that photoredox radiofluorination represents a simple method to access novel tryptophan-based PET agents. In brief, 4-F-5-OMe-tryptophans (l/d-T13) and 6-F-5-OMe-tryptophans (l/d-T18) were easily synthesized. The 18F-labeled analogs were produced by photoredox radiofluorination with radiochemical yields ranging from 2.6 ± 0.5% to 32.4 ± 4.1% (3 ≤ n ≤ 5, enantiomeric excess ≥ 99.0%) and over 98.0% radiochemical purity. Small animal imaging showed that l-[18F]T13 achieved 9.58 ± 0.26%ID/g tumor uptake and good contrast in B16F10 tumor-bearing mice (n = 3). Clearly, l-[18F]T13 exhibited prominent tumor uptake, warranting future evaluations of its potential usage in precise immunotherapy monitoring.

All-fiber-device-coupled compact, transportable ultra-stable laser

In response to the demand for operation in non-laboratory environments, there has been a trend toward the development of compact, transportable ultra-stable lasers. This paper reports on this sort of laser system assembled in a cabinet. The whole optical part utilizes fiber-coupled devices to simplify the integration. In addition, spatial beam collimation and alignment into the high-finesse cavity are realized by a five-axis positioner and a focus-adjustable fiber collimator, which significantly relax the alignment and adjustment. A theoretical analysis is performed on how the collimator adjusts the beam profile and coupling efficiency. The support structure of the system is specially designed as well so that it features robustness and transportation without performance degradation. The observed linewidth is 1.4 Hz within a duration of 1 s. After subtracting the linear drift of 70 mHz/s, the fractional frequency instability is better than 4 × 10^-15, for the averaging time ranging from 1 to 100 s, which is close to the thermal noise limit of the high-finesse cavity.

Real-time prediction of organ failures in patients with acute pancreatitis using longitudinal irregular data

It is extremely important to identify patients with acute pancreatitis who are at high risk for developing persistent organ failures early in the course of the disease. Due to the irregularity of longitudinal data and the poor interpretability of complex models, many models used to identify acute pancreatitis patients with a high risk of organ failure tended to rely on simple statistical models and limited their application to the early stages of patient admission. With the success of recurrent neural networks in modeling longitudinal medical data and the development of interpretable algorithms, these problems can be well addressed. In this study, we developed a novel model named Multi-task and Time-aware Gated Recurrent Unit RNN (MT-GRU) to directly predict organ failure in patients with acute pancreatitis based on irregular medical EMR data. Our proposed end-to-end multi-task model achieved significantly better performance compared to two-stage models. In addition, our model not only provided an accurate early warning of organ failure for patients throughout their hospital stay, but also demonstrated individual and population-level important variables, allowing physicians to understand the scientific basis of the model for decision-making. By providing early warning of the risk of organ failure, our proposed model is expected to assist physicians in improving outcomes for patients with acute pancreatitis.

Automated CT Pancreas Segmentation for Acute Pancreatitis Patients by combining a Novel Object Detection Approach and U-Net

Acute pancreatitis is an inflammatory disorder of the pancreas. Medical imaging, such as computed tomography (CT), has been widely used to detect volume changes in the pancreas for acute pancreatitis diagnosis. Many pancreas segmentation methods have been proposed but no methods for pancreas segmentation from acute pancreatitis patients. The segmentation of an inflamed pancreas is more challenging than the normal pancreas due to the following two reasons. 1) The inflamed pancreas invades surrounding organs and causes blurry boundaries. 2) The inflamed pancreas has higher shape, size, and location variability than the normal pancreas. To overcome these challenges, we propose an automated CT pancreas segmentation approach for acute pancreatitis patients by combining a novel object detection approach and U-Net. Our approach includes a detector and a segmenter. Specifically, we develop an FCN-guided region proposal network (RPN) detector to localize the pancreatitis regions. The detector first uses a fully convolutional network (FCN) to reduce the background interference of medical images and generates a fixed feature map containing the acute pancreatitis regions. Then the RPN is employed on the feature map to precisely localize the acute pancreatitis regions. After obtaining the location of pancreatitis, the U-Net segmenter is used on the cropped image according to the bounding box. The proposed approach is validated using a collected clinical dataset with 89 abdominal contrast-enhanced 3D CT scans from acute pancreatitis patients. Compared with other start-of-the-art approaches for normal pancreas segmentation, our method achieves better performance on both localization and segmentation in acute pancreatitis patients.

The role of interferon-stimulated gene 15 in the occurence and progression of cervical squamous cell carcinoma

To identify molecular markers for early diagnosis and new targets for treatment of cervical squamous cell carcinoma. Our study involved 52 carcinoma tissues that were confirmed pathologically as cervical squamous cell carcinoma (CSCC) at the Fourth Hospital of Hebei Medical University in 2021. We obtained 36 control specimens from patients who had undergone hysterectomy for benign uterine diseases in 2021, with no cervical lesions as confirmed by pathology. Total RNA was extracted from all the samples. Reverse transcription and quantitative real-time PCR were performed. Immunohistochemical staining for interferon-stimulated gene 15 (ISG15) protein was performed. Descriptive analyses including mean and standard deviation were used to compare different groups. For data that do not conform to normal distribution, we use Wilcox rank sum test to make statistics to compare different groups with the median and interquartile. Mann Whitney U test was used to compare non-parametric continuous data, and categorical variables were analyzed using chi-square test. Receiver operating characteristic (ROC) curve was used to evaluate the possibility of using ISG15 as a new biomarker for cervical squamous cell carcinoma. Compared with normal cervical tissues, mRNA expression of ISG15 in cervical cancer tissues was significantly lower (P<0.01); mRNA expression was significantly lower in patients with nerve invasion (P<0.05). Difference in ISG15 protein expression was statistically significant (no expression/low expression) in the cancer samples compared to normal tissues (P<0.01). The area under ROC curve was 0.810 (P<0.001) and the sensitivity and specificity were 75% and 54%, respectively. Spearman's correlation analysis showed that ISG15 mRNA was positively correlated with protein expression (r=0.358, P=0.001). Deficiency of ISG15 may be associated with the occurrence and progression of CSCC. It could be used as a potential tumor marker in research and treatment of CSCC.