The association between polymorphism of LDL-R gene and ischemic stroke risk in Chinese population: A meta-analysis

Objective

Low-density lipoprotein receptor (LDL-R) gene polymorphisms have been indicated to be correlated with ischemic cerebrovascular disease including ischemic stroke susceptibility. However, the results from each published study are inconsistent.

Methods

All eligible case-control studies that met the search terms were retrieved in PubMed, Embase, Wanfang Med Online and Chinese National Knowledge Infrastructure (CNKI) databases. We identified seven independent case-control studies with a total of 10,355 subjects from Chinese population up to May 2023. Summary odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the susceptibility of ischemic stroke.

Results

Meta-analysis results indicated that rs1122608 polymorphism of LDL-R gene significantly decreased ischemic stroke risk under dominant model (OR = 0.69, 95% CI = 0.54-0.87), heterozygote comparison (OR = 0.69, 95% CI = 0.53-0.92) and allele comparison (OR = 0.74, 95% CI = 0.65-0.84) in overall analysis. Furthermore, pooled analysis showed that significant associations were observed between rs688 polymorphism and ischemic stroke risk in heterozygote carriers (OR = 1.71, 95% CI = 1.07-2.71) and dominant model (OR = 1.67, 95% CI = 1.04-2.68) in Chinese population.

Conclusions

Our comprehensive meta-analysis on the role of LDL-R gene rs1122608 and rs688 polymorphisms in the risk of ischemic stroke revealed that the rs1122608 polymorphism was associated with a decreased risk, while the rs688 polymorphism was associated with an increased risk of ischemic stroke in Chinese population. Further multicenter studies were needed to confirm the effect on the susceptibility of ischemic stroke.

Prevalence and influencing factors of depressive and anxiety symptoms among hospital-based healthcare workers during the surge period of the COVID-19 pandemic in the Chinese mainland: a multicenter cross-sectional study

BACKGROUND

From November 2022 to February 2023, the Chinese mainland experienced a surge in COVID-19 infection and hospitalization, and the hospital-based healthcare workers (HCWs) might suffer serious psychological crisis during this period. This study aims to assess the depressive and anxiety symptoms among HCWs during the surge of COVID-19 pandemic and to provide possible reference on protecting mental health of HCWs in future infectious disease outbreaks.

METHODS

A multicenter cross-sectional study was carried out among hospital-based HCWs in the Chinese mainland from 5 January to 9 February 2023. The PHQ-9 (nine-item Patient Health Questionnaire) and GAD-7 (seven-item Generalized Anxiety Disorder Questionnaire) were used to measure depressive and anxiety symptoms. Ordinal logistic regression analysis was performed to identify influencing factors.

RESULTS

A total of 6522 hospital-based HCWs in the Chinse mainland were included in this survey. The prevalence of depressive symptoms among the HCWs was 70.75%, and anxiety symptoms was 47.87%. The HCWs who perceived higher risk of COVID-19 infection and those who had higher work intensity were more likely to experience depressive and anxiety symptoms. Additionally, higher levels of mindfulness, resilience and perceived social support were negatively associated with depressive and anxiety symptoms.

CONCLUSION

This study revealed that a high proportion of HCWs in the Chinese mainland suffered from mental health disturbances during the surge of the COVID-19 pandemic. Resilience, mindfulness and perceived social support are important protective factors of HCWs' mental health. Tailored interventions, such as mindfulness practice, should be implemented to alleviate psychological symptoms of HCWs during the COVID-19 pandemic or other similar events in the future.

Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering

Single-cell Hi-C (scHi-C) technology enables the investigation of 3D chromatin structure variability across individual cells. However, the analysis of scHi-C data is challenged by a large number of missing values. Here, we present a scHi-C data imputation model HiC-SGL, based on Subgraph extraction and graph representation learning. HiC-SGL can also learn informative low-dimensional embeddings of cells. We demonstrate that our method surpasses existing methods in terms of imputation accuracy and clustering performance by various metrics.

The axial and sagittal CT values of the 7th thoracic vertebrae in screening for osteoporosis and osteopenia

AIM

To evaluate the difference in computed tomography (CT) attenuation value of different planes of the 7th thoracic vertebra and investigate the efficacy of axial and sagittal vertebral CT measurements in predicting osteoporosis.

MATERIALS AND METHODS

Patients who underwent routine chest CT and dual-energy X-ray absorptiometry (DXA) within 1 month were included in this retrospective study. The CT attenuation values of different planes were compared. Logistic regression and receiver operating characteristic (ROC) were used to analyse the difference of each plane in the diagnosis of osteoporosis.

RESULTS

The study included 1,338 patients (mean age of 61.9±11.9; 54% female). The CT attenuation values decreased successively in the normal group, osteopenia group, and osteoporosis group. The paired t-test results showed that the mid-axial measurements were greater than mid-sagittal measurements, with a mean difference of 9 HU, the difference was statistically significant (p<0.001, 95% confidence interval [CI] = 7.8-10.1). For each one-unit reduction in mid-sagittal CT attenuation value, the risk of osteopenia or osteoporosis increased by 3.6%. To distinguish osteoporosis from non-osteoporosis (osteopenia + normal), the sensitivity was 90% and the specificity was 52.4% at the mid-sagittal threshold of 113.7 HU.

CONCLUSIONS

The CT attenuation values of mid-sagittal plane have higher diagnostic efficacy than axial planes in predicting osteoporosis. For patients with a sagittal CT attenuation value of <113.7 HU in the T7, further DXA examination is warranted.

Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities

In silico design of single guide RNA (sgRNA) plays a critical role in clustered regularly interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. Continuous efforts are aimed at improving sgRNA design with efficient on-target activity and reduced off-target mutations. In the last 5 years, an increasing number of deep learning-based methods have achieved breakthrough performance in predicting sgRNA on- and off-target activities. Nevertheless, it is worthwhile to systematically evaluate these methods for their predictive abilities. In this review, we conducted a systematic survey on the progress in prediction of on- and off-target editing. We investigated the performances of 10 mainstream deep learning-based on-target predictors using nine public datasets with different sample sizes. We found that in most scenarios, these methods showed superior predictive power on large- and medium-scale datasets than on small-scale datasets. In addition, we performed unbiased experiments to provide in-depth comparison of eight representative approaches for off-target prediction on 12 publicly available datasets with various imbalanced ratios of positive/negative samples. Most methods showed excellent performance on balanced datasets but have much room for improvement on moderate- and severe-imbalanced datasets. This study provides comprehensive perspectives on CRISPR/Cas9 sgRNA on- and off-target activity prediction and improvement for method development.

Gene based message passing for drug repurposing

The medicinal effect of a drug acts through a series of genes, and the pathological mechanism of a disease is also related to genes with certain biological functions. However, the complex information between drug or disease and a series of genes is neglected by traditional message passing methods. In this study, we proposed a new framework using two different strategies for gene-drug/disease and drug-disease networks, respectively. We employ long short-term memory (LSTM) network to extract the flow of message from series of genes (gene path) to drug/disease. Incorporating the resulting information of gene paths into drug-disease network, we utilize graph convolutional network (GCN) to predict drug-disease associations. Experimental results showed that our method GeneDR (gene-based drug repurposing) makes better use of the information in gene paths, and performs better in predicting drug-disease associations.

HMGB1 acts as an agent of host defense at the gut mucosal barrier

Mucosal barriers provide the first line of defense between internal body surfaces and microbial threats from the outside world. ¹ In the colon, the barrier consists of two layers of mucus and a single layer of tightly interconnected epithelial cells supported by connective tissue and immune cells. ² Microbes colonize the loose, outer layer of colonic mucus, but are essentially excluded from the tight, epithelial-associated layer by host defenses. ³ The amount and composition of the mucus is calibrated based on microbial signals and loss of even a single component of this mixture can destabilize microbial biogeography and increase the risk of disease. ^4-7 However, the specific components of mucus, their molecular microbial targets, and how they work to contain the gut microbiota are still largely unknown. Here we show that high mobility group box 1 (HMGB1), the prototypical damage-associated molecular pattern molecule (DAMP), acts as an agent of host mucosal defense in the colon. HMGB1 in colonic mucus targets an evolutionarily conserved amino acid sequence found in bacterial adhesins, including the well-characterized Enterobacteriaceae adhesin FimH. HMGB1 aggregates bacteria and blocks adhesin-carbohydrate interactions, inhibiting invasion through colonic mucus and adhesion to host cells. Exposure to HMGB1 also suppresses bacterial expression of FimH. In ulcerative colitis, HMGB1 mucosal defense is compromised, leading to tissue-adherent bacteria expressing FimH. Our results demonstrate a new, physiologic role for extracellular HMGB1 that refines its functions as a DAMP to include direct, virulence limiting effects on bacteria. The amino acid sequence targeted by HMGB1 appears to be broadly utilized by bacterial adhesins, critical for virulence, and differentially expressed by bacteria in commensal versus pathogenic states. These characteristics suggest that this amino acid sequence is a novel microbial virulence determinant and could be used to develop new approaches to diagnosis and treatment of bacterial disease that precisely identify and target virulent microbes.

The air temperature change effect on water quality in the Kvarken Archipelago area

The Kvarken Archipelago is Finland's World Heritage site designated by UNESCO. How climate change has affected the Kvaken Archipelago remains unclear. This study was conducted to investigate this issue by analyzing air temperature and water quality in this area. Here we use long-term historical data sets of 61 years from several monitoring stations. Water quality parameters included chlorophyll-a; total phosphorus; total nitrogen; coliform bacteria thermos tolerant; temperature; nitrate as nitrogen; nitrite-nitrate as nitrogen, and Secchi depth and correlations analysis was conducted to identify the most relevant parameters. Based on the correlation analysis of weather data and water quality parameters, air temperature showed a significant correlation with water temperature (Pearson's correlations = 0.89691, P < 0.0001). The air temperature increased in April (R² (goodness-of-fit) = 0.2109 &P = 0.0009) and July (R² = 0.1207 &P = 0.0155) which has indirectly increased the chlorophyll-a level (e.g. in June increasing slope = 0.39101, R² = 0.4685, P < 0.0001) an indicator of phytoplankton growth and abundance in the water systems. The study concludes that there might be indirect effects of the likely increase in air temperature on water quality in the Kvarken Archipelago, in particular causing water temperature and chlorophyll-a concentration to increase at least in some months.

Difference in general practice telehealth utilisation associated with birth country during COVID-19 from two Australian states

Objective

Telehealth has been an integral part of ensuring continued general practice access during the COVID-19 pandemic. Whether telehealth was similarly adopted across different ethnic, cultural, and linguistic groups in Australia is unknown. In this study, we assessed how telehealth utilisation differed by birth country.

Methods

In this retrospective observational study, electronic health record data from 799 general practices across Victoria and New South Wales, Australia between March 2020 to November 2021 were extracted (12,403,592 encounters from 1,307,192 patients). Multivariate generalised estimating equation models were used to assess the likelihood of a telehealth consultation (against face-to-face consultation) by birth country (relative to Australia or New Zealand born patients), education index, and native language (English versus others).

Results

Patients born in Southeastern Asia (aOR: 0.54; 95% CI: 0.52-0.55), Eastern Asia (aOR: 0.63; 95% CI: 0.60-0.66), and India (aOR: 0.64; 95% CI: 0.63-0.66) had a lower likelihood of having a telehealth consultation compared to those born in Australia or New Zealand. Northern America, British Isles, and most European countries did not present with a statistically significant difference. Additionally, higher education levels (aOR: 1.34; 95% CI: 1.26-1.42) was associated with an increase in the likelihood of a telehealth consultation, while being from a non-English-speaking country was associated with a reduced likelihood (aOR: 0.83; 95% CI: 0.81-0.84).

Conclusions

This study provides evidence showing differences in telehealth use associated with birth country. Strategies to ensure continued healthcare access for patients, whose native language is not English, such as providing interpreter services for telehealth consultations, would be beneficial.

Perspectives

Understanding cultural and linguistic differences may reduce health disparities in telehealth access in Australia and could present an opportunity to promote healthcare access in diverse communities.

M-E-AWA: A Novel Task Scheduling Approach Based on Weight Vector Adaptive Updating for Fog Computing

Task offloading and real-time scheduling are hot topics in fog computing. This paper aims to address the challenges of complex modeling and solving multi-objective task scheduling in fog computing environments caused by widely distributed resources and strong load uncertainties. Firstly, a task unloading model based on dynamic priority adjustment is proposed. Secondly, a multi-objective optimization model is constructed for task scheduling based on the task unloading model, which optimizes time delay and energy consumption. The experimental results show that M-E-AWA (MOEA/D with adaptive weight adjustment based on external archives) can effectively handle multi-objective optimization problems with complex Pareto fronts and reduce the response time and energy consumption costs of task scheduling.

Comparative clinical outcomes and predictive biomarkers of sintilimab combinations vs. single therapy in cancer: a systematic review and meta-analysis of randomized controlled trials

OBJECTIVE

This study aimed to compare the efficacy and safety between sintilimab combinations and single treatment in cancer patients, as well as identify biomarkers for selection of patients who might benefit from the combination treatments.

MATERIALS AND METHODS

A search of randomized clinical trials (RCTs) comparing sintilimab combinations vs. single treatment in different tumors according to the PRISMA guidelines was performed. Selected endpoints included completion response rate (CR), objective response rate (ORR), disease control rate (DCR), overall survival (OS), progression-free survival (PFS), major adverse effects (AEs), immune-related adverse events (irAEs). Subgroup analyses based on different combination regimens, tumor type and basic biomarkers were included.

RESULTS

Results reported from 11 RCTs involving 2,248 patients were included in this analysis. Pooled results indicated that both sintilimab plus chemotherapy and sintilimab plus targeted therapy significantly improved CR [RR=2.44, 95% CI (1.14, 5.20), p=0.021; RR=2.91, 95% CI (1.29, 6.57), p=0.010], ORR [RR=1.34, 95% CI (1.13, 1.59), p=0.001; RR=1.70, 95% CI (1.13, 2.56), p=0.011], PFS [HR=0.56, 95% CI (0.43, 0.69), p<0.001; HR=0.56, 95% CI (0.49, 0.64), p<0.001] and OS [HR=0.59, 95% CI (0.48, 0.70), p<0.001]. Subgroup analyses suggested that the sintilimab-chemotherapy group exhibited a superior PFS benefit than the chemotherapy alone group regardless of age, gender, EGOS PS, PD-L1 expression, smoking status, and clinical stage. There were no significant statistical differences in the incidence of any grade and grade 3 or worse AEs between the two groups [RR=1.00, 95% CI (0.91, 1.10), p=0.991; RR=1.06, 95% CI (0.94, 1.20), p=0.352]. While the incidence of any grade irAEs was higher with sintilimab plus chemotherapy as compared to chemotherapy alone (RR=1.24, 95% CI (1.01, 1.54), p=0.044), but no significant difference was found for grade 3 or worse irAEs (RR=1.11, 95% CI (0.60, 2.03), p=0.741).

CONCLUSIONS

Sintilimab combinations brought benefits to a greater number of patients at the cost of a mild increase of irAEs. PD-L1 expression may not be used as a predictive biomarker, composite biomarkers consisting of PD-L1 and MHC class II expression are worth to be explored to enlarge the patient population that benefits from sintilimab combinations.

Enhancing gosling growth and secretion of somatotrophic and thyrotrophic axis hormones through egg turning during incubation

1. Growth performance of Yangzhou geese hatched from eggs with turning angles of 50° or 70° was evaluated in association with serum hormones and somatotrophic gene mRNA expression.2. Egg turning at 70° significantly (P< 0.05) increased hatchability, gosling quality and hatching weight. Gosling post-hatch body weight, leg and breast muscle weight in the 70° turning group was significantly heavier until 50 d of age.3. Serum concentrations of GH were significantly higher until 30 d of age in the 70° turning group goslings, and those of IGF-I and T3 were higher from hatching to 50 d of age.4. The mRNA expression of GHRH, pituitary GH, liver and leg muscle IGF-I were all significantly higher at 1 and 30 d of age after hatch, but not at 70 d after hatch, in the 70° turning group.5. Egg turning at 70° during incubation improves embryo and gosling quality and growth performance through up-regulation of gene expression and secretion of somatotrophic axis hormones, GHRH, GH and IGF-I, as well as T3.

Preclinical Evaluation of a Lead Specific Chelator (PSC) Conjugated to Radiopeptides for 203Pb and 212Pb-Based Theranostics

203Pb and 212Pb have emerged as promising theranostic isotopes for image-guided α-particle radionuclide therapy for cancers. Here, we report a cyclen-based Pb specific chelator (PSC) that is conjugated to tyr3-octreotide via a PEG2 linker (PSC-PEG-T) targeting somatostatin receptor subtype 2 (SSTR2). PSC-PEG-T could be labeled efficiently to purified 212Pb at 25 °C and also to 212Bi at 80 °C. Efficient radiolabeling of mixed 212Pb and 212Bi in PSC-PEG-T was also observed at 80 °C. Post radiolabeling, stable Pb(II) and Bi(III) radiometal complexes in saline were observed after incubating [203Pb]Pb-PSC-PEG-T for 72 h and [212Bi]Bi-PSC-PEG-T for 5 h. Stable [212Pb]Pb-PSC-PEG-T and progeny [212Bi]Bi-PSC-PEG-T were identified after storage in saline for 24 h. In serum, stable radiometal/radiopeptide were observed after incubating [203Pb]Pb-PSC-PEG-T for 55 h and [212Pb]Pb-PSC-PEG-T for 24 h. In vivo biodistribution of [212Pb]Pb-PSC-PEG-T in tumor-free CD-1 Elite mice and athymic mice bearing AR42J xenografts revealed rapid tumor accumulation, excellent tumor retention and fast renal clearance of both 212Pb and 212Bi, with no in vivo redistribution of progeny 212Bi. Single-photon emission computed tomography (SPECT) imaging of [203Pb]Pb-PSC-PEG-T and [212Pb]Pb-PSC-PEG-T in mice also demonstrated comparable accumulation in AR42J xenografts and renal clearance, confirming the theranostic potential of the elementally identical 203Pb/212Pb radionuclide pair.

Magnetic-Property Assessment on Dy-Nd-Fe-B Permanent Magnet by Thermodynamic Calculation and Micromagnetic Simulation

Heavy rare-earth (HRE) elements are important for the preparation of high-coercivity permanent magnets. A further understanding of the thermodynamic properties of HRE phases, and the magnetization reversal mechanism of magnets are still critical issues to obtain magnets that can achieve better performance. In this work, the Nd−Dy−Fe−B multicomponent system is investigated via the calculation of the phase diagram (CALPHAD) method and micromagnetic simulation. The phase composition of magnets with various ratios of Nd and Dy is assessed using critically optimized thermodynamic data. γ-Fe and Nd2Fe17 phases are suppressed when partial Nd is substituted with Dy (<9.3%), which, in turn, renders the formation of Nd2Fe14B phase favorable. The influence of the magnetic properties of grain boundaries (GBs) on magnetization reversal is detected by the micromagnetic simulations with the 3D polyhedral grains model. Coercivity was enhanced with both 3 nm nonmagnetic and the hard-magnetic GBs for the pinning effect besides the GBs. Moreover, the nucleation and propagation of reversed domains in core-shell grains are investigated, which suggests that the magnetic structure of grains can also influence the magnetization reversal of magnets. This study provides a theoretical route for a high-efficiency application of the Dy element, realizing a deterministic enhancement of the coercivity in Nd−Fe−B-based magnets.

Alkylresorcinol, a biomarker for whole grain intake, and its association with osteoarthritis: the MOST study

INTRODUCTION

Higher intake of fiber has been associated with lower risk of incident symptomatic osteoarthritis (OA). We examined whether levels of alkylresorcinol (AR), a marker of whole grain intake, were associated with OA in subjects in The Multicenter Osteoarthritis (MOST) Study.

METHOD

Knee x-rays and knee pain were assessed at baseline and through 60-months. Stored baseline fasting plasma samples were analyzed for AR homologues (C17:0, C19:0, C21:0, C23:0, C25:0) and total AR levels (AR sum). Two nested case-control studies, one for incident radiographic OA and one for incident symptomatic OA were performed with participants re-assessed at 15, 30 and 60 months. Multivariable conditional logistic regression with baseline covariates including age, sex, BMI, physical activity, quadriceps strength, race, smoking, depressive symptoms, diabetes and knee injury tested the association of log transformed AR levels with OA outcomes.

RESULTS

Seven hundred seventy-seven subjects were, on average, in their 60's, and most were women. For 60-month cumulative incidence, there was no significant association between quartiles of AR concentration and incident radiographic (e.g., for incident radiographic OA, highest vs lowest quartile of AR sum showed RR = 0.93 (95% CI 0.59, 1.47), and for symptomatic OA RR was 1.22 (95% CI 0.76, 1.94). In secondary analyses examining 30-month incidence, high AR levels were associated with a reduced risk of X-ray OA (RR = 0.31 (95% CI 0.15, 0.64).

CONCLUSION

In primary analyses, AR levels were not associated with risk of OA, but secondary analyses left open the possibility that high AR levels may protect against OA.

[Progress and policy considerations on the pilot program of standardized training for public health physicians in China]

The standardized training for public health physicians plays an important role in exploring the cultivation public health professionals and strengthening the construction of public health service providers. In 2018, the National Health Commission of China launched a pilot program of standardized training for public health physicians in 10 provinces. This paper clarifies the definition of the standardized training for public health physicians, systematically analyzes the status quo of the training in China and other countries, articulates the design and progress of the training in the perspective of Centers for Disease Control and Prevention, and makes some suggestions for the priorities of the pilot training program, so as to provide reference and basis for the better development of the standardized training for public health physicians in China in the future.

[Interference of P2X4 receptor expression in tumor-associated macrophages suppresses migration and invasion of glioma cells]

OBJECTIVE

To investigate the effect of interference of P2X4 receptor expression in tumor-associated macrophages (TAMs) on invasion and migration of glioma cells.

METHODS

C57BL/6 mouse models bearing gliomas in the caudate nucleus were examined for glioma pathology with HE staining and expressions of Iba-1 and P2X4 receptor with immunofluorescence assay. RAW264.7 cells were induced into TAMs using conditioned medium from GL261 cells, and the changes in mRNA expressions of macrophage polarization-related markers and the mRNA and protein expressions of P2X4 receptor were detected with RT-qPCR and Western blotting. The effect of siRNA-mediated P2X4 interference on IL-1β and IL-18 mRNA and protein expressions in the TAMs was detected with RT-qPCR and Western blotting. GL261 cells were cultured in the conditioned medium from the transfected TAMs, and the invasion and migration abilities of the cells were assessed with Transwell invasion and migration experiment.

RESULTS

The glioma tissues from the tumor-bearing mice showed a significantly greater number of Iba-1-positive cells, where an obviously increased P2X4 receptor expression was detected (P=0.001), than the brain tissues of the control mice (P < 0.001). The M2 macrophage markers (Arg-1 and IL-10) and M1 macrophage markers (iNOS and TNF-α) were both significantly up-regulated in the TAMs derived from RAW264.7 cells (all P < 0.01), but the up-regulation of the M2 macrophage markers was more prominent; the expression levels of P2X4 receptor protein and mRNA were both increased in the TAMs (P < 0.05). Interference of P2X4 receptor expression significantly lowered the mRNA(P < 0.01)and protein (P < 0.01, P < 0.05)expression levels of IL-1β and IL-18 in the TAMs and obviously inhibited the ability of the TAMs to promote invasion and migration of the glioma cells (P < 0.05).

CONCLUSION

Interference of P2X4 receptor in the TAMs suppresses the migration and invasion of glioma cells possibly by lowering the expressions of IL-1β and IL-18.

Field cancerization profile-based prognosis signatures lead to more robust risk evaluation in hepatocellular carcinoma

The development of reliable biomarkers has been an urgent issue as well as a hot spot of research on the diagnosis, treatment, and prognostic evaluation of hepatocellular carcinoma (HCC). Here, we established and validated two field cancerization profile-based prognostic signatures (gene expression score [GES] and immune score [IS]) for HCC. Our study confirmed that field cancerization profile-based models outperform conventional models on risk evaluation, offering insights for further studies on prognostic model construction. The nomogram constructed by combining GES, IS, and TNM stage was proved effective in improving the individualized prediction of the overall risk of patients. Distinct peritumoral characteristics were observed in several immune cells (e.g., CD8 T cells and dendritic cells), which might explain the diversified prognosis and clinical benefit of immunotherapy. Moreover, a series of drug targets, prognosis-associated genes, and pathways were identified, which may contribute to molecular mechanism studies as well as therapeutic target development of HCC.

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Two field cancerization feature-based prognostic signatures for HCC were developed

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Joint nomogram is effective in improving individualized risk prediction

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Different peritumor signatures were observed in several immune cells

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Several peritumoral drug targets, prognostic genes, and pathways were identified

REIA: A database for cancer A-to-I RNA editing with interactive analysis

Epitranscriptomic changes caused by adenosine-to-inosine (A-to-I) RNA editing contribute to the pathogenesis of human cancers; however, only a small fraction of the millions editing sites detected so far has clear functionality. To facilitate more in-depth studies on the editing, this paper offers REIA (http://bioinfo-sysu.com/reia), an interactive web server that analyses and visualizes the association between human cancers and A-to-I RNA editing sites (RESs). As a comprehensive database, REIA curates not only 8,447,588 RESs from 9,895 patients across 34 cancers, where 33 are from TCGA and 1 from GEO, but also 13 different types of multi-omic data for the cancers. As an interactive server, REIA provides various options for the user to specify the interested sites, to browse their annotation/editing level/profile in cancer, and to compare the difference in multi-omic features between editing and non-editing groups. From the editing profiles, REIA further detects 658 peptides that are supported by mass spectrum data but not yet covered in any prior works.

[Emergency training need and effect evaluation analysis of novel coronavirus pneumonia in centers of disease control and prevention]

A questionnaire was used to investigate the emergency training needs of novel coronavirus pneumonia of disease prevention and control institutions in provinces, deputy provincial level regions and cities specifically designated in the state plan, and the effect evaluation of emergency training activities conducted by Chinese Center for Disease Control and Prevention (China CDC). The results showed that 67.4% of 47 disease prevention and control institutions (31/46) believed that the emergency training at the initial stage of the epidemic should be conducted as soon as possible, and the form of network training should be given priority. The training should focus on the urgently needed technologies such as epidemiological investigation, formulation and response of prevention and control strategies, laboratory testing, etc. The teaching materials should highlight pertinence and practicability and be presented in the form of electronic video. The average satisfaction score of the video training conducted by China CDC was (8.81±1.125) and the score of audio-video courseware was (8.97±0.893). The needs analysis and evaluation of novel coronavirus pneumonia prevention and control in disease prevention and control institutions could provide reference for the follow-up training and improve the emergency training management.

[Current situation and suggestions of public health personnel training in disease control and prevention institutions]

Under the background that the national health has become the national priority development strategy, it is essential to speed up public health ability among talents. Based on the consulting project of the Chinese Academy of Engineering, "Research on the training strategy of medical and health personnel in China", this paper analyzes the current situation and existing problems of public health personnel training in disease control and prevention institutions. Based on three stages of public health education, this paper puts forward that the public health personnel training should first solve the problem of public health personnel team construction and create programs on college education-post graduate education-continuing education. Through the personnel training system, different training modes are designed for other groups of people to improve the ability of public health personnel in an all-around way.

[The Museum of Western Studies on Chinese Medicine:Chinese medicine in the western societies]

The historical artifacts displayed in the Museum of Western study on Chinese Medicine at Yunnan University of Chinese Medicine came from a variety of Chinese medical schools in America and European countries. They are in the memorial galleries for some well-known figures, such as George Soulié de Morant (Su Lie), Jacques-André Lavier (La Wei Ai), Felix Mann (Man Fu Li) and Manfred Porkert (Man Xi Bo), representing the development and status of respective Chinese medical schools in America and European countries. The displayed artifacts are nearly 3,000 photos, manuscripts, documents and more than 500 hours of audiovisual materials, including instruments for acupuncture and moxibustion, books, passports, letters and even supplies for their life. The displayed artifacts demonstrate the process and the access of people in the western societies to know, learn and take use of Chinese medicine.

Copper stimulates neonicotinoid insecticide thiacloprid degradation by Ensifer adhaerens TMX-23

AIMS

Aims of this study are to elucidate the molecular mechanism of copper-improved thiacloprid (THI) degradation by Ensifer adhaerens TMX-23 and characterize copper resistance of this strain.

METHODS AND RESULTS

Resting cells of E. adhaerens TMX-23 were used to degrade THI, with formation of THI amide and 98·31% of 0·59 mmol l^-1 THI was degraded in 100 min. The addition of copper improved the degradation of THI and showed little inhibitory effects on the growth of E. adhaerens TMX-23. E. adhaerens TMX-23 degraded THI to THI amide by nitrile hydratases (NhcA and NhpA). QPCR analysis indicated that the expression of nhpA was up-regulated in the presence of copper. E. adhaerens TMX-23 nitrile hydratases were purified, and enzyme assay of NhpA exhibited the highest NHase activity toward THI. The addition of copper activated the activity of NhcA. Soil degradation experiment indicated that E. adhaerens TMX-23 could quickly eliminate THI residual in copper-added soil.

CONCLUSIONS

Copper improved THI degradation by E. adhaerens TMX-23 was attributed to the induced expression of nhpA and activated NhcA.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study broadens the investigation of regulatory mechanism of NHase expression and provided theoretical basis for using metal-resistant microbes to degrade pesticide in heavy metal co-contaminated environments.

[Survey on provincial disease prevention and control professionals' attitudes and cognition to public health physician standardized training in China]

Objective: To understand the attitudes and cognition of disease control and prevention professionals at provincial level on public health physician standardized training and provide evidence for the improvement of the standardized training and exploration of more effective training mode in China. Methods: By cluster sampling, 2 193 professionals at provincial centers for disease control and prevention (CDC) in 6 provinces, including Jiangsu and Guangdong, Shanxi and Hubei,Sichuan and Xinjiang were selected as the study subjects, the sample size was estimated to be 1 933 persons. Results: A total of 1 716 provincial-level CDC professionals were surveyed, the support rate to the standardized training was 70.7%(1 213/1 716). The level of support was negatively associated with the educational level of professionals and their specialty of public health and preventive medicine. Of 875 public health and preventive medicine professionals, 61.6%(318/516) of those with master's degree or above supported the standard training for public health physicians, which was lower than 73.1%(225/308) of those with bachelor's degree and 86.3%(44/51) of those with college degree or below. There were 14.9%(232/1 555) of the respondents suggested a two year training, and 60.4%(933/1 544) suggesting a field training mode. In terms of training content, 86.6%(1 355/1 564) suggesting "epidemiological survey and public health practice", and 76.7%(1 199/1 564) suggesting "basic theories and methodology". Conclusions: In general, the professionals of provincial CDC showed a relatively low interest in the standardized training for public health physicians and failed to reach a consensus. Besides, they were ill-informed about current training duration, method and content. Thas, the professionals at provincial CDC are suggested to be the key target-population whom should be mobilized during the training pilot period, especially the highly educated ones with relevant specialties of public health. It is suggested that public health physician standardized training should to be implemented in whole CDC system to reach full consensus based on its practical achievements and effects. It is also suggested to establish public health graduate medical education system in China.

Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks

CRISPR/Cas9 is a preferred genome editing tool and has been widely adapted to ranges of disciplines, from molecular biology to gene therapy. A key prerequisite for the success of CRISPR/Cas9 is its capacity to distinguish between single guide RNAs (sgRNAs) on target and homologous off-target sites. Thus, optimized design of sgRNAs by maximizing their on-target activity and minimizing their potential off-target mutations are crucial concerns for this system. Several deep learning models have been developed for comprehensive understanding of sgRNA cleavage efficacy and specificity. Although the proposed methods yield the performance results by automatically learning a suitable representation from the input data, there is still room for the improvement of accuracy and interpretability. Here, we propose novel interpretable attention-based convolutional neural networks, namely CRISPR-ONT and CRISPR-OFFT, for the prediction of CRISPR/Cas9 sgRNA on- and off-target activities, respectively. Experimental tests on public datasets demonstrate that our models significantly yield satisfactory results in terms of accuracy and interpretability. Our findings contribute to the understanding of how RNA-guide Cas9 nucleases scan the mammalian genome. Data and source codes are available at https://github.com/Peppags/CRISPRont-CRISPRofft.

Metabolomic evaluation of serum metabolites of geese reared at different stocking densities

1. Stocking density is an issue for poultry production. High stocking density can impact biochemical parameters, production, and reproductive performance; however, information regarding the effects of stocking density on serum metabolites in geese is limited.2. Twenty-day-old, Sanhua male geese (n = 240) were allocated to one of two experimental groups for 50 days. One group was housed under a low stocking density (LSD; two birds per m²) and one under a high stocking density (HSD; five birds per m²). Body weight and feed intake were recorded every 10 d. Eight serum samples per group were used for metabonomic analysis by liquid chromatography-mass spectrometry.3. Stocking density did not affect the spleen, liver, thymus, or bursa of Fabricius weights after 50 d. Feed intake and body weight was significantly lower in geese from the HSD group versus the LSD group (P < 0.05). Thirty-six differential serum metabolites were identified (P < 0.05), indicating altered amino acid, carbohydrate, lipid and vitamin cofactor metabolism.4. The results demonstrated that high-density stocking impacts geese, and provides insights into the mechanisms underlying the adverse health effects associated with HSD.

The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers

The majority of the human genome encodes long noncoding RNA (lncRNA) genes, critical regulators of various cellular processes, which largely outnumber protein-coding genes. However, lncRNA-involved fusions have not been surveyed and characterized yet. Here, we present a systematic study of the lncRNA fusion landscape across cancer types and identify >30 000 high-confidence tumor-specific lncRNA fusions (using 8284 tumor and 6946 normal samples). Fusions positively correlated with DNA damage and cancer stemness and were specifically low in microsatellite instable (MSI)-High or virus-infected tumors. Moreover, fusions distribute differently among cancer molecular subtypes, but with shared enrichment in tumors that are microsatellite stable (MSS), with high somatic copy number alterations (SCNA), and with poor survival. Importantly, we find a potentially new mechanism, mediated by enhancer RNAs (eRNA), which generates secondary fusions that form densely connected fusion networks with many fusion hubs targeted by FDA-approved drugs. Finally, we experimentally validate functions of two tumor-promoting chimeric proteins derived from mRNA-lncRNA fusions, KDM4B-G039927 and EPS15L1-lncOR7C2-1. The EPS15L1 fusion protein may regulate (Gasdermin E) GSDME, critical in pyroptosis and anti-tumor immunity. Our study completes the fusion landscape in cancers, sheds light on fusion mechanisms, and enriches lncRNA functions in tumorigenesis and cancer progression.

Percutaneous transluminal septal myocardial ablation markedly reduces energy loss in hypertrophic obstructive cardiomyopathy: a four-dimensional flow magnetic resonance imaging study

Background

Functional follow-up modalities of hypertrophic obstructive cardiomyopathy (HOCM) subjected to percutaneous transluminal septal myocardial ablation (PTSMA) are limited mainly to echocardiography and catheterization. Recent advancements in four-dimensional (4D) flow magnetic resonance imaging (MRI) have enabled us to assess patients from the perspective of fluid dynamics by visualising blood flow and calculating quantitative parameters such as wall shear stress and energy loss within cardiac chambers or blood vessels. Several reports have demonstrated that the intra-cardiac energy loss decreased along with improvement of cardiac function achieved by treatment of cardiac diseases. Whether changes in energy loss occur along with PTSMA in HOCM patients and the underlying mechanism remain unknown.

Purpose

This study sought to investigate the influence of PTSMA in patients with HOCM on energy loss in the left ventricle (LV) and aortic root measured by 4D flow MRI.

Methods

We retrospectively recruited HOCM patients who underwent PTSMA at a referral centre from May to November 2019. Patients who underwent 4D flow MRI both before and after PTSMA were included. We collected demographic and clinical data from electronic health records. MRI scans implemented two-dimensional phase-contrast imaging of the three-chamber plane with three-directional velocity, using a 1.5 T scanner. Furthermore, 4D blood flow analysis was performed on off-line saved data, using iTFlow version 1.9. We assessed energy loss in one cardiac cycle within the three-chamber plane of the LV and aortic root (area surrounded by the LV endocardium, sinotubular junction, and mitral annulus).

Results

This study finally included 12 patients, whose mean age was 66±12 years, and 5 (42%) of whom were men. The pressure gradient between the LV apex and ascending aorta was 81±32 mmHg before and 20±22 mmHg immediately after PTSMA (P&lt;0.005, paired). Before PTSMA, 6 patients were in New York Heart Association functional class III and the other 6 in class II. However, after PTSMA, 10 patients improved to class I and 2 to class II. PTSMA reduced energy loss in one cardiac cycle within the three-chamber plane of the LV and aortic root, from 79±36 mJ/m to 55±19 mJ/m (P=0.001, paired).

Conclusions

PTSMA in patients with HOCM reduced energy loss within the LV and aortic root, indicating significant decrease with cardiac workload. Four-dimensional flow MRI of the three-chamber plane to assess energy loss within the LV and aortic root is a time-efficient and reproducible quantitative method to evaluate the effects of PTSMA. Given its non-invasive nature, it also enables to sequentially follow-up HOCM patients who underwent PTSMA.

Periprocedural changes of energy loss

Funding Acknowledgement

Type of funding source: None

SANPolyA: a deep learning method for identifying Poly(A) signals

MOTIVATION

Polyadenylation plays a regulatory role in transcription. The recognition of polyadenylation signal (PAS) motif sequence is an important step in polyadenylation. In the past few years, some statistical machine learning-based and deep learning-based methods have been proposed for PAS identification. Although these methods predict PAS with success, there is room for their improvement on PAS identification.

RESULTS

In this study, we proposed a deep neural network-based computational method, called SANPolyA, for identifying PAS in human and mouse genomes. SANPolyA requires no manually crafted sequence features. We compared our method SANPolyA with several previous PAS identification methods on several PAS benchmark datasets. Our results showed that SANPolyA outperforms the state-of-art methods. SANPolyA also showed good performance on leave-one-motif-out evaluation.

AVAILABILITY AND IMPLEMENTATION

https://github.com/yuht4/SANPolyA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning

Circular RNA (circRNA) is a closed long non-coding RNA (lncRNA) formed by covalently closed loops through back-splicing. Emerging evidence indicates that circRNA can influence cellular physiology through various molecular mechanisms. Thus, accurate circRNA identification and prediction of its regulatory information are critical for understanding its biogenesis. Although several computational tools based on machine learning have been proposed for circRNA identification, the prediction accuracy remains to be improved. Here, first we present circLGB, a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing adenosine to inosine (A-to-I) deamination, A-to-I density and the internal ribosome entry site. circLGB categorizes circRNAs by utilizing a LightGBM classifier with feature selection. Second, we introduce circMRT, an ensemble machine learning framework to systematically predict the regulatory information for circRNA, including their interactions with microRNA, the RNA binding protein, and transcriptional regulation. Feature sets including sequence-based features, graph features, genome context, and regulatory information features were modeled in circMRT. Experiments on public and our constructed datasets show that the proposed algorithms outperform the available state-of-the-art methods. circLGB is available at http://www.circlgb.com. Source codes are available at https://github.com/Peppags/circLGB-circMRT.

SRHiC: A Deep Learning Model to Enhance the Resolution of Hi-C Data

Hi-C data is important for studying chromatin three-dimensional structure. However, the resolution of most existing Hi-C data is generally coarse due to sequencing cost. Therefore, it will be helpful if we can predict high-resolution Hi-C data from low-coverage sequencing data. Here we developed a novel and simple computational method based on deep learning named super-resolution Hi-C (SRHiC) to enhance the resolution of Hi-C data. We verified SRHiC on Hi-C data in human cell line. We also evaluated the generalization power of SRHiC by enhancing Hi-C data resolution in other human and mouse cell types. Results showed that SRHiC outperforms the state-of-the-art methods in accuracy of prediction.

Overexpression of miR-146a inhibits the apoptosis of hippocampal neurons of rats with cerebral hemorrhage by regulating autophagy

In this study, to investigate the effect of overexpression of miR-146a on autophagy of hippocampal neurons in rats with intracerebral hemorrhage (ICH), 72 Sprague-Dawley rats were randomly divided into the sham, ICH, miR-146a agomir, and miR-146a agomir control groups. The ICH model was constructed by injection of collagenase VII. The apoptosis of hippocampal neurons was measured by TUNEL assay. The levels of LC3 and Beclin 1 were analyzed by immunohistochemistry. Mitochondrial autophagy was examined by transmission electron microscopy. The levels of LC3A, LC3B, Beclin 1, Bax, Bcl-2, and cleaved caspase 3 were examined by Western blot. Western blot was also used to evaluate the expression of nuclear factor κB signaling pathway-related factors. To examine the effect of autophagy inhibitor (3-methyladenine (3-MA)) on miR-146a-regulated apoptotic protein expression, 30 rats were further divided into the sham, ICH, miR-146a agomir, 3-MA, and miR-146a + 3-MA groups. The levels of Bax, Bcl-2, and cleaved caspase 3 were examined by Western blot. Compared with the sham group, the nerve function scores, brain water content, the percentage of apoptotic cells, and the expression levels of LC3, Beclin 1, Bax, cleaved caspase 3, and p-P65 in the hippocampus of rats in the ICH group were all significantly increased (p < 0.05), whereas the expression levels of miR-146a, Bcl-2, and p-IκBα were markedly decreased (p < 0.05). Mitochondrial autophagy was also evident. Furthermore, compared with the ICH group, the results of the abovementioned tests in the miR-146a agomir group were reversed. The overexpression of miR-146a inhibited the autophagy of hippocampal neurons in rats with ICH.

C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

CRISPR/Cas9 is a hot genomic editing tool, but its success is limited by the widely varying target efficiencies among different single guide RNAs (sgRNAs). In this study, we proposed C-RNNCrispr, a hybrid convolutional neural networks (CNNs) and bidirectional gate recurrent unit network (BGRU) framework, to predict CRISPR/Cas9 sgRNA on-target activity. C-RNNCrispr consists of two branches: sgRNA branch and epigenetic branch. The network receives the encoded binary matrix of sgRNA sequence and four epigenetic features as inputs, and produces a regression score. We introduced a transfer learning approach by using small-size datasets to fine-tune C-RNNCrispr model that were pre-trained from benchmark dataset, leading to substantially improved predictive performance. Experiments on commonly used datasets showed C-RNNCrispr outperforms the state-of-the-art methods in terms of prediction accuracy and generalization. Source codes are available at https://github.com/Peppags/C_RNNCrispr.

A Novel Hybrid CNN-SVR for CRISPR/Cas9 Guide RNA Activity Prediction

Accurate prediction of guide RNA (gRNA) on-target efficacy is critical for effective application of CRISPR/Cas9 system. Although some machine learning-based and convolutional neural network (CNN)-based methods have been proposed, prediction accuracy remains to be improved. Here, firstly we improved architectures of current CNNs for predicting gRNA on-target efficacy. Secondly, we proposed a novel hybrid system which combines our improved CNN with support vector regression (SVR). This CNN-SVR system is composed of two major components: a merged CNN as the front-end for extracting gRNA feature and an SVR as the back-end for regression and predicting gRNA cleavage efficiency. We demonstrate that CNN-SVR can effectively exploit features interactions from feed-forward directions to learn deeper features of gRNAs and their corresponding epigenetic features. Experiments on commonly used datasets show that our CNN-SVR system outperforms available state-of-the-art methods in terms of prediction accuracy, generalization, and robustness. Source codes are available at https://github.com/Peppags/CNN-SVR.

[Reflections on the orientation of public health physicians]

Public health physician is one of the four statutory types of physicians in China, but there is no consensus on their connotation. The main problems are that public health physician is confused with those who perform public health tasks, the relationship between public health physician and clinician and the connotation of prescription right is not clear, and there is limitation in public health education and relevant laws and regulations. Public health physician is positioned as professionals who monitor, investigate, evaluate, and intervene in population health-related issues. It is suggested to retain the practicing qualification of public health physicians and highlight the attribute of public health physicians' prescribing the prescriptions for community health. Encourage public health physicians to obtain qualification for clinicians to individual prescription, Encourage clinicians to access to public health physician qualification. Improve public health school education, take the pilot of public health physician standardization training, cultivate "prevention and treatment combined" physician.