Subcutaneous injection granulocyte colony-stimulating factor (G-CSF) is superior to intrauterine infusion on patients with recurrent implantation failure: A systematic review and network meta-analysis

Although both subcutaneous injection and intrauterine infusion of granulocyte colony-stimulating factor (G-CSF) have been reported to improve pregnancy outcomes in patients with recurrent implantation failure (RIF), how to administer it is still no consensus. The study aimed to investigate which administration route is optimal. We searched PubMed, Embase, the Cochrane Library (CENTRAL), Web of Science, and China National Knowledge Internet (CNKI) from inception to April 10, 2023, with language in both English and Chinese. The randomized controlled trials (RCTs) compared the effectiveness of G-CSF to treat patients with RIF were included in this network meta-analysis (NMA). The odds ratio (OR) and 95% confidence interval (CI) in pregnancy outcomes (implantation rate, IR; clinical pregnancy rate, CPR; live birth rate, LBR; miscarriage rate, MR; ectopic pregnancy rate, EPR) were summarized by NMA with a random-effects model. A total of 1360 RIF patients from 14 RCTs were included in this NMA, with no publication bias and small sample effects. No direct evidence compared the effectiveness of different administration routes of G-CSF on IR, LBR and MR. Both subcutaneous injection and intrauterine infusion of G-CSF increased the IR (OR = 2.81, 95% CI: 1.10-7.24; OR = 2.15, 95% CI: 1.50-3.07, respectively) and CPR (OR = 2.79, 95% CI: 1.86-4.17; OR = 1.74, 95% CI: 1.30-2.33, respectively) in patients with RIF. According to SUCRA, subcutaneous injection is more likely to be the optimal medication administration route. However, more high-quality studies were also needed to support these, especially IR and LBR.

Investigating human-derived lactic acid bacteria for alcohol resistance

BACKGROUND

Excessive alcohol consumption has been consistently linked to serious adverse health effects, particularly affecting the liver. One natural defense against the detrimental impacts of alcohol is provided by alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase (ALDH), which detoxify harmful alcohol metabolites. Recent studies have shown that certain probiotic strains, notably Lactobacillus spp., possess alcohol resistance and can produce these critical enzymes. Incorporating these probiotics into alcoholic beverages represents a pioneering approach that can potentially mitigate the negative health effects of alcohol while meeting evolving consumer preferences for functional and health-centric products.

RESULTS

Five lactic acid bacteria (LAB) isolates were identified: Lactobacillus paracasei Alc1, Lacticaseibacillus rhamnosus AA, Pediococcus acidilactici Alc3, Lactobacillus paracasei Alc4, and Pediococcus acidilactici Alc5. Assessment of their alcohol tolerance, safety, adhesion ability, and immunomodulatory effects identified L. rhamnosus AA as the most promising alcohol-tolerant probiotic strain. This strain also showed high production of ADH and ALDH. Whole genome sequencing analysis revealed that the L. rhamnosus AA genome contained both the adh (encoding for ADH) and the adhE (encoding for ALDH) genes.

CONCLUSIONS

L. rhamnosus AA, a novel probiotic candidate, showed notable alcohol resistance and the capability to produce enzymes essential for alcohol metabolism. This strain is a highly promising candidate for integration into commercial alcoholic beverages upon completion of comprehensive safety and functionality evaluations.

MiR-135a-5p regulates window of implantation by suppressing pinopodes development and decidualization of endometrial stromal cells

PURPOSE

The window of implantation (WOI) is a brief period during which the endometrium is receptive to embryo implantation. This study investigated the relationship between miR-135a-5p and endometrial receptivity.

METHODS

Peripheral blood was collected on the day of ovulation and the 5th day after ovulation for high-throughput sequencing from women who achieved clinical pregnancy through natural cycle frozen embryo transfer. RT-qPCR assessed miR-135a-5p expression in the endometrium tissue or cells during the mouse implantation window or decidualization. Scanning electron microscopy was utilized to observe pinopode morphology and quantity in mice overexpressing miR-135a-5p during the WOI. Human endometrial stromal cells (HESC) and artificial induction of mouse uterine decidualization were used to explore whether miR-135a-5p overexpression inhibits decidualization by regulating HOXA10 and BMPR2. Furthermore, the impact of miR-135a-5p on HESC proliferation and HTR8/SVneo invasion was explored.

RESULTS

A total of 54 women were enrolled in the study. bioinformatics analysis and animal models demonstrated that miR-135a-5p was significantly downregulated during the WOI, and its high expression can lead to abnormal pregnancy outcomes. Overexpression of miR-135a-5p resulted in the absence of pinopode in mouse endometrial tissue during the WOI. High miR-135a-5p levels were found to potentially inhibit endometrial tissue decidualization by downregulating HOXA10 and BMPR2 expression. Finally, CEBPD was identified as a potential regulator of miR-135a-5p, which would explain the decreased miR-135a-5p expression during the WOI.

CONCLUSION

MiR-135a-5p expression is significantly downregulated during the WOI. High miR-135a-5p levels suppress pinopode development and endometrial tissue decidualization through HOXA10 and BMPR2, contributing to inadequate endometrial receptivity.

Higenamine inhibits acute and chronic inflammatory pain through modulation of TRPV4 channels

Pain is the cardinal symptom of many debilitating diseases and results in heavy health and economic burdens worldwide. Asarum (Asarum sieboldii Miq.) is a commonly used analgesic in Chinese medicine. However, the analgesic components and mechanisms of asarum in acute and chronic pain mice model remain unknown. In this study, we first generated asarum water extract and confirmed strong analgesic properties in mice in both the acute thermal and mechanical pain models, as well as in the complete Freund's adjuvant (CFA) induced chronic inflammatory pain model. Second, we identified higenamine as a major component of asarum and found that higenamine significantly inhibited thermal and mechanical induced acute pain and CFA induced chronic inflammatory pain. Then, using Trpv4-/- mice, we found that TRPV4 is necessary for CFA induced thermal and mechanical allodynia, and demonstrated that higenamine analgesia in the CFA model is partly through TRPV4 channel inhibition. Finally, we found that GSK1016790A, a TRPV4 agonist, induced calcium response was significantly inhibited by higenamine in both cultured DRG neurons and TRPV4 transfected HEK293 cells. Consistent with calcium imaging results, higenamine pretreatment also dose-dependently inhibited GSK1016790A induced acute pain. Taken together, our behavior and calcium imaging results demonstrate that the asarum component higenamine inhibits acute and chronic inflammatory pain by modulation of TRPV4 channels.

Mechanism of action and treatment of type I interferon in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) caused by HBV, HCV infection, and other factors is one of the most common malignancies in the world. Although, percutaneous treatments such as surgery, ethanol injection, radiofrequency ablation, and transcatheter treatments such as arterial chemoembolization are useful for local tumor control, they are not sufficient to improve the prognosis of patients with HCC. External interferon agents that induce interferon-related genes or type I interferon in combination with other drugs can reduce the recurrence rate and improve survival in HCC patients after surgery. Therefore, in this review, we focus on recent advances in the mechanism of action of type I interferons, emerging therapies, and potential therapeutic strategies for the treatment of HCC using IFNs.

GPC3 and PEG10 peptides associated with placental gp96 elicit specific T cell immunity against hepatocellular carcinoma

The placenta and tumors can exhibit a shared expression profile of proto-oncogenes. The basis of placenta-derived heat shock protein gp96, which induces prophylactic and therapeutic T cell responses against cancer including hepatocellular carcinoma (HCC), remains unknown. Here, we identified the associated long peptides from human placental gp96 using matrix-assisted laser desorption/ionization-time-of-flight and mass spectrometry and analyzed the achieved proteins through disease enrichment analysis. We found that placental gp96 binds to numerous peptides derived from 73 proteins that could be enriched in multiple cancer types. Epitope-harboring peptides from glypican 3 (GPC3) and paternally expressed gene 10 (PEG10) were the major antigens mediating anti-HCC T cell immunity. Molecular docking analysis showed that the GPC3- and PEG10-derived peptides, mainly obtained from the cytotrophoblast layer of the mature placenta, bind to the lumenal channel and client-bound domain of the gp96 dimer. Immunization with bone marrow-derived dendritic cells pulsed with recombinant gp96-GPC3 or recombinant gp96-PEG10 peptide complex induced specific T cell responses, and T cell transfusion led to pronounced growth inhibition of HCC tumors in nude mice. We demonstrated that the chaperone gp96 can capture antigenic peptides as an efficient approach for defining tumor rejection oncoantigens in the placenta and provide a basis for developing GPC3 and PEG10 peptide-based vaccines against HCC. This study provides insight into the underlying mechanism of the antitumor response mediated by embryonic antigens from fetal tissues, and this will incite more studies to identify potential tumor rejection antigens from placenta.

Treatments for cesarean scar pregnancy: 11-year experience at a medical center

BACKGROUND

Cesarean scar pregnancy (CSP) is a long-term complication after cesarean section that can cause severe maternal morbidity and mortality. Although a variety of treatments have been described, there is no consensus as to the optimal management approach. Many grading systems for CSP have been proposed, among which the classification made by the consensus of Chinese experts in 2016 was shown to provide improved treatment guidance for clinical practice. The purpose of the present study was to analyze the success rate of different treatments for each type of CSP as classified according to the Chinese Expert's Consensus (2016), and to develop a management strategy for CSP.

METHODS

A retrospective study was performed among patients diagnosed with CSP at Shandong Provincial Hospital between January 2009 and December 2019. We reviewed clinical characteristics, treatment methods, and subsequent outcomes; and analyzed these endpoints using the statistical software package SPSS 22.0 (SPSS, Inc., Chicago, IL).

RESULTS

For type I CSP, systemic methotrexate (MTX) administration exhibited a success rate of 79.2% for type Ia and 14.3% for type Ib. Local and systemic MTX administration success rates were 88.9% for type Ia and 66.7% for type Ib. Dilation and curettage (D&C), curettage after uterine artery embolization (UAE + C), and hysteroscopic curettage (H + C) were 100% successful. For type II, UAE + C, H + C, and laparoscopy combined with hysteroscopic curettage (L + H+C) were 100% successful. D&C had a success rate of 97.0% for type IIa and 88.9% for type IIb. The success rate of systemic MTX administration was 52.0% for type IIa and 62.5% for type IIb. Both UAE + C and L + H+C had 100% success rates for type IIIa CSPs, while for type IIIb, the success rate was 87.9% for UAE + C vs. 96.6% for L + H+C.

CONCLUSIONS

For type I CSPs, D&C was quick, easy, and safe; for type II, H + C was more suitable. For type III and some type II patients who wished to undergo simultaneous repair of the cesarean defect, L + H+C was the optimal method. UAE can be used as a complementary option instead of a prophylactic measure, and when difficulties with endoscopic surgeries were encountered, conversion to laparotomy was the ultimate treatment.

Relationship of retinal capillary plexus and ganglion cell complex with mild cognitive impairment and dementia

OBJECTIVE

To investigate relationship of the retinal capillary plexus (RCP) and ganglion cell complex (GCC) with mild cognitive impairment (MCI) and dementia in a community-based study1.

METHODS

This cross-sectional study incorporated the participants of the Jidong Eye Cohort Study. Optical coherence tomography angiography was performed to obtain RCP vessel density and GCC thickness with detailed segments. The Mini-mental State Examination and Montreal Cognitive Assessment were used to assess cognitive status by professional neuropsychologists. Participants were thus divided into three groups: normal, mild cognitive impairment, and dementia. Multivariable analysis was used to measure relationship of ocular parameters with cognitive impairment.

RESULTS

Of the 2678 participants, the mean age was 44.1 ± 11.7 years. MCI and dementia occurred in 197 (7.4%) and 80 (3%) participants, respectively. Compared to the normal group, the adjusted odds ratio (OR) with the 95% confidence interval was 0.76 (0.65-0.90) for the correlation of lower deep RCP with MCI. We found the following items significantly associated with dementia compared with the normal group: a superficial (OR, 0.68 [0.54-0.86]) and deep (OR, 0.75 [0.57-0.99]) RCP, as well as the GCC (OR, 0.68 [0.54-0.85]). Compared to the MCI group, those with dementia had decreased GCC (OR, 0.75 [0.58-0.97]).

CONCLUSIONS

Decreased deep RCP density was associated with MCI. Decreased superficial and deep RCP and the thin GCC were correlated with dementia. These implied that the retinal microvasculature may develop into a promising non-invasive imaging marker to predict severity of cognitive impairment.

Cellular gp96 upregulates AFP expression by blocking NR5A2 SUMOylation and ubiquitination in hepatocellular carcinoma

Alpha-fetoprotein (AFP) is the most widely used biomarker for the diagnosis of hepatocellular carcinoma (HCC). However, a substantial proportion of HCC patients have either normal or marginally increased AFP levels in serum, and the underlying mechanisms are not fully understood. In the present study, we provided in vitro and in vivo evidence that heat shock protein gp96 promoted AFP expression at the transcriptional level in HCC. NR5A2 was identified as a key transcription factor for the AFP gene, and its stability was enhanced by gp96. A further mechanistic study by co-immunoprecipitation, GST pull-down, and molecular docking showed gp96 and the SUMO E3 ligase RanBP2 competitively binding to NR5A2 at the sites spanning from aa 507 to aa 539. The binding of gp96 inhibited SUMOylation, ubiquitination, and subsequent degradation of NR5A2. In addition, clinical analysis of HCC patients indicated that gp96 expression in tumors was positively correlated with serum AFP levels. Therefore, our study uncovered a novel mechanism that gp96 regulates the stability of its client proteins by directly affecting their SUMOylation and ubiquitination. These findings will help in designing more accurate AFP-based HCC diagnosis and progression monitoring approaches.

Machine learning-based antioxidant protein identification model: Progress and evaluation

Efficient and accurate identification of antioxidant proteins is of great significance. In recent years, many models for identifying antioxidant proteins have been proposed, but the low sensitivity and high dimensionality of the models are common problems. The generalization ability of the model needs to be improved. Researchers have tried different feature extraction algorithms and feature selection algorithms to obtain the most effective feature combination and have chosen more appropriate classification algorithms and tools to improve model performance. In this article, we systematically reviewed the data set of the most frequently used antioxidant proteins and the method selection for each step of model establishment and discussed the characteristics of each method. We have conducted a detailed analysis of recent research and believe that the practical ability and efficiency of model application can be improved by reducing model dimensions. The key to improving the performance of antioxidant protein recognition models in the future may lie in feature selection, so this paper also focuses on the combination of feature extraction and selection steps in the analysis of the model building process.

Evaluation of renal function in chronic kidney disease (CKD) by mDIXON-Quant and Amide Proton Transfer weighted (APTw) imaging

BACKGROUND

Chronic kidney disease (CKD) is a long-term condition that affects >10% of the adult population worldwide. Noninvasive assessment of renal function has important clinical significance for disease diagnosis and prognosis evaluation.

OBJECTIVE

To explore the value of mDIXON-Quant combined with amide proton transfer weighted (APTw) imaging for accessing renal function in chronic kidney disease (CKD).

MATERIALS AND METHODS

Twenty-two healthy volunteers (HVs) and 30 CKD patients were included in this study, and the CKD patients were divided into the mild CKD (mCKD) group (14 cases) and moderate-to-severe CKD (msCKD) group (16 cases) according to glomerular filtration rate (eGFR). The cortex APT (cAPT), medulla APT (mAPT), cortex R2⁎ (cR2⁎), medulla R2⁎ (mR2⁎), cortex FF (cFF) and medulla FF (mFF) values of the right renal were independently measured by two radiologists. Intra-group correlation coefficient (ICC) test was used to test the inter-observer consistency. The analysis of variance (ANOVA) was used to compare the difference among three groups. Mann-Whitney U test was used to analyze the differences of R2⁎, FF and APT values among the patient and HV groups. Area under the receiver operating characteristic (ROC) curve (AUC) was used to analyze the diagnostic efficiency. The corresponding threshold, sensitivity, and specificity were obtained according to the maximum approximate index. The combined diagnostic efficacy of R2⁎, FF, and APT values was analyzed by binary Logistic regression, and the AUC of combined diagnosis was compared with the AUC of the single parameter by the Delong test.

RESULTS

The cAPT value of the HV, mCKD and msCKD groups increased gradually. The mAPT value and cR2⁎ values of the mCKD and msCKD groups were higher than those of the HV group, while the mFF value of the mCKD group was lower than HV group (all P < 0.05). The cAPT and mAPT values showed good diagnostic efficacy in evaluating different degrees of renal damage, while cR2⁎ and mFF values showed moderate diagnostic efficacy. When combining the APT, R2⁎, and FF values, the diagnostic efficiency was significantly improved.

CONCLUSION

mDIXON-Quant combined APTw imaging can be used for improved diagnosis of CKD.

[Clinical characteristics of sudden sensorineural hearing loss with acute cerebral infarction]

Objective: To analyze the clinical and imaging features of patients with sudden sensorineural deafness and acute cerebral infarction in order to provide evidence for early recognition of such diseases. Methods: This was a case series reporting study. A retrospective analysis was performed on the clinical and imaging data of 29 patients with sudden hearing loss (SHL) who admitted to the Otolaryngology Head and Neck Surgery Department of Beijing Tiantan Hospital from January 2017 to December 2021 and diagnosed with acute cerebral infarction using MRI-DWI. Results: The patients were aged 31-71 years, with an average age of 56±12 years, and 82.8% (24/29) were men. In total, 82.8% (24/29) of the patients had three or more atherosclerotic risk factors, and 24.1% (7/29) had a history of SHL. The hearing types were flat and total deafness: 86.2% (25/29) of the patients had severe hearing loss, 27.6% (8/29) had bilateral SHL, 17.2% (5/29) had further hearing loss during hospitalization, and 82.8% (24/29) had dizziness or vertigo at the onset. The signs of central nervous system involvement mainly included speech impairment, diplopia, dysphagia, central facial paralysis, facial and limb hypoesthesia, ataxia, and decreased muscle strength. Imaging evaluation showed that 21 cases were located in the posterior circulation supply area and 8 cases in the anterior circulation supply area. Additionally, 82.8% (24/29) patients had vertebrobasilar artery stenosis, and 58.6% (17/29) patients had severe vertebrobasilar artery stenosis or occlusion. Conclusions: Patients with SHL who progress to cerebral infarction often have multiple atherosclerotic risk factors and SHL. Most of the patients are middle-aged and older men who often complain of dizziness or dizziness accompanied by severe flat and total deafness with unilateral or bilateral SHL. Imaging findings suggest that most patients have posterior circulation infarction, often accompanied by severe stenosis or occlusion of the vertebrobasilar artery.

Dynamic peripheral blood microRNA expression landscape during the peri-implantation stage in women with successful pregnancy achieved by single frozen-thawed blastocyst transfer

STUDY QUESTION

What are the dynamic expression features of plasma microRNAs (miRNAs) during the peri-implantation period in women with successful pregnancy via single frozen-thawed blastocyst transfer?

SUMMARY ANSWER

There is a significant change in the plasma miRNA expression profile before and after blastocyst transfer, during the window of implantation.

WHAT IS KNOWN ALREADY

The expression of miRNAs in peripheral blood has indicative functions during the peri-implantation period. Nevertheless, the dynamic expression profile of circulating miRNAs during the peri-implantation stage in women with a successful pregnancy has not been studied.

STUDY DESIGN SIZE DURATION

Seventy-six women treated for infertility with a single frozen-thawed blastocyst transfer in a natural cycle were included in this study. Among them, 57 women had implantation success and a live birth, while 19 patients experienced implantation failure. Peripheral blood samples were collected at five different time points throughout the peri-implantation period, including D0 (ovulation day), D3, D5, D7, and D9 in this cycle of embryo transfer. The plasma miRNAs in women with blastocyst transfer were isolated, sequenced, and analyzed.

PARTICIPANTS/MATERIALS SETTING METHODS

Peripheral blood samples were collected in EDTA tubes and stored at -80°C until further use. miRNAs were isolated from blood, cDNA libraries were constructed, and the resulting sequences were mapped to the human genome. The plasma miRNAs were initially analyzed in a screening cohort (n = 34) with successful pregnancy. Trajectory analysis, including a global test and pairwise comparisons, was performed to detect dynamic differentially expressed (DE) miRNAs. Fuzzy c-means clustering was conducted for all dynamic DE miRNAs. The correlation between DE miRNAs and clinical characteristics of patients was investigated using a linear mixed model. Target genes of the miRNAs were predicted, and functional annotation analysis was performed. The expression of DE miRNAs was also identified in a validation set consisting of women with successful (n = 23) and unsuccessful (n = 19) pregnancies.

MAIN RESULTS AND THE ROLE OF CHANCE

Following small RNA sequencing, a total of 2656 miRNAs were determined as valid read values. After trajectory analysis, 26 DE miRNAs (false discovery rate < 0.05) were identified by the global test, while pairwise comparisons in addition identified 20 DE miRNAs. A total of seven distinct clusters representing different temporal patterns of miRNA expression were discovered. Nineteen DE miRNAs were further identified to be associated with at least one clinical trait. Endometrium thickness and progesterone level showed a correlation with multiple DE miRNAs (including two of the same miRNAs, hsa-miR-1-3p and hsa-miR-6741-3p). Moreover, the 19 DE miRNAs were predicted to have 403 gene targets, and there were 51 (12.7%) predicted genes likely involved in both decidualization and embryo implantation. Functional annotation for predicted targets of those clinically related DE miRNAs suggested the involvement of vascular endothelial growth factor and Wnt signaling pathways, as well as responses to hormones, immune responses, and cell adhesion-related signaling pathways during the peri-implantation stage.

LARGE SCALE DATA

The raw miRNA sequence data reported in this article have been deposited in the Genome Sequence Archive (GSA-Human: HRA005227) and are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human/browse/HRA005227.

LIMITATIONS REASONS FOR CAUTION

Although the RNA sequencing results revealed the global dynamic changes of miRNA expression, further experiments examining the clinical significance of the identified DE miRNAs in embryo implantation outcome and the relevant regulatory mechanisms involved are warranted.

WIDER IMPLICATIONS OF THE FINDINGS

Understanding the dynamic landscape of the miRNA transcriptome could shed light on the physiological mechanisms involved from ovulation to the post-implantation stage, as well as identifying biomarkers that characterize stage-related biological process.

STUDY FUNDING/COMPETING INTERESTS

The study was funded by the Major clinical research project of Tangdu Hospital (2021LCYJ004) and the Discipline Platform Improvement Plan of Tangdu Hospital (2020XKPT003). The funders had no influence on the study design, data collection, and analysis, decision to publish, or preparation of the article. There are no conflicts of interest to declare.

[Hemophagocytic syndrome secondary to COVID-19: a case report and literature review]

Objective: To improve the awareness of hemophagocytic syndrome(HPS) secondary to COVID-19 (COVID-sHPS). Methods: We reported an adult case of COVID-sHPS, including clinical presentation, laboratory examinations, histopathological findings, treatment strategy, and outcome. We also conducted literature research in PubMed database and Wanfang database using the keywords "COVID-19" and "hemophagocytic syndrome" and subsequently summarized relevant literature. Results: A 49-year-old man was admitted to our hospital after 4 weeks of recurrent fever. Prior to this hospitalization, he had received an empiric combination therapy with antibiotics and antiviral drugs against SARS-CoV-2. His vital signs were within the normal range and no abnormalities were found on physical examination on admission. After admission, throat swab nucleic acid tests were weakly positive for SARS-CoV-2, and negative for influenza and respiratory syncytial virus. Blood nucleic acid tests for cytomegalovirus and EB virus were negative, as was blood mNGS. Laboratory tests showed a series of abnormalities, including leukopenia, thrombocytopenia, low fibrinogen, elevated serum ferritin, elevated transaminase, decreased NK cell activity, and hemophagocytosis in bone marrow. According to the HPS-2004 diagnostic criteria, he was diagnosed with hemophagocytic syndrome, which was high likely to be caused by COVID-19 infection due to the lack of evidence of genetic risk factors and other clear triggers. He was initially treated with dexamethasone at a dose of 10 mg·m-2·d-1 and his condition improved rapidly. The literature search identified twenty-three articles on COVID-sHPS, 22 of which were in English. A total of 89 patients had COVID-sHPS and 55 (61.7%) were male. COVID-sHPS could occur at any age, but mainly in adults (86/89, 96%). Fever was reported in the literature with a clear description of the course of the disease. Most HPS occurred during the acute phase of COVID-19, but 3 patients developed HPS during the convalescent phase. Almost all reported cases presented with increased ferritin, elevated transaminases, elevated triglycerides, and cytopenia, mainly anemia and thrombocytopenia. In the retrieved literature, HS-score≥169 was frequently used to diagnose COVID-sHPS, and glucocorticoid in combination with immunoglobulin was the most common treatment strategy. COVID-sHPS had a poor prognosis and a high mortality rate (84.2%, 75/89). Conclusions: The prognosis of COVID-sHPS is poor, so clinicians should raise their awareness of the disease, identify high-risk suspected populations, and arrange reasonable relevant examinations for definite diagnosis and early initial treatment to improve their outcome.

Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin

Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.

[A comparative analysis of the clinical symptoms of benign paroxysmal positional vertigo between older and young and middle-aged patients]

Objective: To compare the differences in clinical symptoms and the time required for diagnosis of benign paroxysmal positional vertigo (BPPV) between older patients and young and middle-aged patients in the structured inquiry of dizziness history. Methods: The medical records of 6 807 patients diagnosed with BPPV from the Vertigo Database of Vertigo Clinical Diagnosis, Treatment, and Research Center of Beijing Tiantan Hospital, Capital Medical University, between January 2019 and October 2021 were retrospectively analyzed. The data included basic demographic information, clinical symptoms in a structured medical history questionnaire, and the time interval from the appearance of BPPV symptoms to diagnosis consultation. The patients were divided into the young and middle-aged group (<65 years old) and the older group (≥65 years old). The differences in clinical symptoms and consultation time were compared between these two groups. Categorical variables were represented by numbers (%), and compared using Chi-squared tests or Fisher's exact probability test for analysis; whereas, continuous variables conforming to normal distribution were represented by mean±standard deviation. Both data groups were compared and analyzed by Student's t-test. Results: The mean age of the older group was 65-92 (71±5) years, while the mean age of the middle-aged group was 18-64 (49±12) years. The incidence of vertigo (42.5% vs. 49.1%, χ²=23.69, P<0.001); vertigo triggered by changes in position of the head or body (52.4% vs. 58.7%, χ²=22.31, P<0.001); and autonomic symptoms (10.1% vs. 12.4%, χ²=7.09, P=0.008) were lower, but hearing loss (11.8% vs. 7.8%, χ²=27.36, P<0.001) and sleep disorders (18.5% vs. 15.2%, χ²=11.13, P=0.001) were higher in the older group than in the young and middle-aged group. The time from the appearance of dizziness to diagnosis was commonly longer in the older patient group than the other group (55.0% vs. 38.5%, χ²=55.95, P<0.001). Conclusions: Older patients with BPPV have more atypical symptoms and complex concomitant symptoms than young and middle-aged patients. For older patients with dizziness, positional testing is needed to confirm the possibility of BPPV even if the clinical symptoms are atypical.

Bacterial antibiotic resistance among cancer inpatients in China: 2016-20

BACKGROUND

The incidence of infections among cancer patients is as high as 23.2-33.2% in China. However, the lack of information and data on the number of antibiotics used by cancer patients is an obstacle to implementing antibiotic management plans.

AIM

This study aimed to investigate bacterial infections and antibiotic resistance in Chinese cancer patients to provide a reference for the rational use of antibiotics.

DESIGN

This was a 5-year retrospective study on the antibiotic resistance of cancer patients.

METHODS

In this 5-year surveillance study, we collected bacterial and antibiotic resistance data from 20 provincial cancer diagnosis and treatment centers and three specialized cancer hospitals in China. We analyzed the resistance of common bacteria to antibiotics, compared to common clinical drug-resistant bacteria, evaluated the evolution of critical drug-resistant bacteria and conducted data analysis.

FINDINGS

Between 2016 and 2020, 216 219 bacterial strains were clinically isolated. The resistance trend of Escherichia coli and Klebsiella pneumoniae to amikacin, ciprofloxacin, cefotaxime, piperacillin/tazobactam and imipenem was relatively stable and did not significantly increase over time. The resistance of Pseudomonas aeruginosa strains to all antibiotics tested, including imipenem and meropenem, decreased over time. In contrast, the resistance of Acinetobacter baumannii strains to carbapenems increased from 4.7% to 14.7%. Methicillin-resistant Staphylococcus aureus (MRSA) significantly decreased from 65.2% in 2016 to 48.9% in 2020.

CONCLUSIONS

The bacterial prevalence and antibiotic resistance rates of E. coli, K. pneumoniae, P. aeruginosa, A. baumannii, S. aureus and MRSA were significantly lower than the national average.

A comparative study on classification of edible vegetable oils by infrared, near infrared and fluorescence spectroscopy combined with chemometrics

Driven by economic benefits like any other foods, vegetable oil has long been plagued by mislabeling and adulteration. Many studies have addressed the field of classification and identification of vegetable oils by various analysis techniques, especially spectral analysis. A comparative study was performed using Fourier transform infrared spectroscopy (FTIR), visible near-infrared spectroscopy (Vis-NIR) and excitation-emission matrix fluorescence spectroscopy (EEMs) combined with chemometrics to distinguish different types of edible vegetable oils. FTIR, Vis-NIR and EEMs datasets of 147 samples of five vegetable oils from different brands were analyzed. Two types of pattern recognition methods, principal component analysis (PCA)/multi-way principal component analysis (M-PCA) and partial least squares discriminant analysis (PLS-DA)/multilinear partial least squares discriminant analysis (N-PLS-DA), were used to resolve these data and distinguish vegetable oil types, respectively. PCA/M-PCA analysis exhibited that three spectral data of five vegetable oils showed a clustering trend. The total correct recognition rate of the training set and prediction set of FTIR spectra of vegetable oil based on PLS-DA method are 100%. The total recognition rate of Vis-NIR based on PLS-DA are 100% and 97.96%. However, the total correct recognition rate of training set and prediction set of EEMs data based on N-PLS-DA method is 69.39% and 75.51%, respectively. The comparative study showed that FTIR and Vis-NIR combined with chemometrics were more suitable for vegetable oil species identification than EEMs technique. The reason may be concluded that almost all chemical components in vegetable oil can produce FTIR and NIR absorption, while only a small amount of fluorophores can produce fluorescence. That is, FTIR and NIR can provide more spectral information than EEMs. Analysis of EEMs data using self-weighted alternating trilinear decomposition (SWATLD) also showed that fluorophores were a few and irregularly distributed in vegetable oils.

Passion fruit peel and its zymolyte enhance gut function in Sanhuang broilers by improving antioxidation and short-chain fatty acids and decreasing inflammatory cytokines

The passion fruit peel (PFP) is the by-product of juice processing and is rich in phenolic compounds and dietary fibers. As the high ADF content in PFP (34.20%), we proceeded to treat PFP with cellulase. The ADF decreased to 16.70% after enzymatic processing, and we supposed that enzymolytic passion fruit peel (EPF) should have a greater growth performance than PFP to broilers. Two trials were conducted to evaluate the effects of dietary PFP or EPF supplementation on growth performance, serum biochemical indices, meat quality, and cecal short-chain fatty acids, microbiota, and metabolites in broilers. In Exp. 1, 180 1-day-old Sanhuang broilers (male, 36.17 ± 2.47 g) were randomly allocated into 3 treatments, with 6 replicates in each treatment. The 3 experimental diets included 1 basal diet (control) and 2 PFP-added diets supplemented with 1 and 2% PFP, respectively. The trial lasted for 42 d. In Exp. 2, 144 Sanhuang broilers (male, 112-day-old, 1.62 ± 0.21 kg) were randomly allocated to 3 treatments. Each treatment was distributed among 6 pens, and each pen contained 8 broilers. The 3 treatment diets included: a control diet, a positive control diet supplementing 75 mg/kg chlortetracycline, and the experimental diet supplementing 3% EPF. The trial lasted for 56 d. Results showed that dietary 1 and 2% PFP addition did not affect growth performance in Exp. 1, and the 3% EPF supplementation had a negative effect on ADFI (P < 0.05) in Exp. 2. A decreased serum triglyceride (P < 0.05) in broilers was observed in Exp. 1. Broilers fed EPF had a higher glutathione peroxidase (GSH-Px) (P < 0.05), and lower levels of tumor necrosis factor-α (TNF-α) (P < 0.05) and glucose (P < 0.05) in Exp. 2. We also found that broilers from PFP or EPF-treated treatments had an increased butyrate content and higher microbial diversity in the cecum. The effects of antioxidation, anti-inflammatory function, and elevated SCFAs were confirmed after the microbe and untargeted metabolomic analysis. Dietary EPF supplementation significantly increased the SCFA-generating bacteria, anti-inflammatory-related bacteria, the antioxidant-related and anti-inflammatory-related metabolites. Moreover, dietary 3% EPF addition positively affects the biosynthesis of phenylpropanoids, which strongly correlate with the antioxidant and anti-inflammatory properties. In conclusion, the proper addition level did not affect the growth performance, and the PFP and EPF could improve the antioxidation state, anti-inflammatory activity, and intestinal functions of Sanhuang broilers to some extent.

Enhancer-FRL: Improved and Robust Identification of Enhancers and Their Activities Using Feature Representation Learning

Enhancers are crucial for precise regulation of gene expression, while enhancer identification and strength prediction are challenging because of their free distribution and tremendous number of similar fractions in the genome. Although several bioinformatics tools have been developed, shortfalls in these models remain, and their performances need further improvement. In the present study, a two-layer predictor called Enhancer-FRL was proposed for identifying enhancers (enhancers or nonenhancers) and their activities (strong and weak). More specifically, to build an efficient model, the feature representation learning scheme was applied to generate a 50D probabilistic vector based on 10 feature encodings and five machine learning algorithms. Subsequently, the multiview probabilistic features were integrated to construct the final prediction model. Compared with the single feature-based model, Enhancer-FRL showed significant performance improvement and model robustness. Performance assessment on the independent test dataset indicated that the proposed model outperformed state-of-the-art available toolkits. The webserver Enhancer-FRL is freely accessible at http://lab.malab.cn/∼wangchao/softwares/Enhancer-FRL/, The code and datasets can be downloaded at the webserver page or at the Github https://github.com/wangchao-malab/Enhancer-FRL/.

Rapid detection and quality evaluation of Shuang-Huang-Lian injection by ATR-IR and NIR spectroscopy combined with chemometrics

Quality evaluation and consistency evaluation of drugs are the keys to ensure the therapeutic effect and safety of drugs. In this study, attenuated total refraction infrared (ATR-IR) spectroscopy and near-infrared (NIR) spectroscopy combined with chemometrics were used for rapid detection and quality evaluation of active components of Shuang-Huang-Lian injection (SHLI), a traditional Chinese medicine preparation commonly used in China. Taking the chromatographic detection results as a reference, the partial least squares (PLS) model based on ATR-IR and NIR data was constructed by removing the bands with serious noise interference and low signal frequency band. The results showed that the PLS model achieved satisfactory results for the prediction of the three active components (chlorogenic acid, baicalin and phillyrin) in SHLI, indicating that the two spectral techniques combined with the PLS regression method could be successfully used for rapid quantitative analysis of the three active ingredients in SHLI. Relatively, the PLS model based on the ATR-IR spectrum has higher R² and smaller RMSE than it based on the NIR spectrum. Furthermore, based on the rapid quantitative analysis of the three active ingredients in SHLI, the quality of 140 SHLI samples from seven manufacturers was evaluated by TOPSIS (technique for order preference by similarity to the ideal solution) analysis, and the consistency of different batches of SHLI products from the same manufacturer was evaluated. The results showed that there were differences in the quality of SHLI produced by different manufacturers, and the quality of different batches of SHLI produced by the same manufacturer was not completely consistent. In conclusion, ATR-IR and NIR spectroscopy combined with chemometrics can be used for accurate and rapid quantitative analysis and quality evaluation of SHLI. This study provides a good idea for the rapid quantitative analysis and quality evaluation of drugs or food based on spectroscopic technology and chemometrics.

Utilize a few features to classify presynaptic and postsynaptic neurotoxins

Neurotoxins are a class of proteins that have a significant damaging effect on nerve tissue. Neurotoxins are classified into presynaptic neurotoxins and postsynaptic neurotoxins, and accurate identification of neurotoxins plays a key role in drug development. In this study, 90 presynaptic neurotoxins and 165 postsynaptic neurotoxins were classified. The features of the presynaptic and postsynaptic neurotoxin sequences were extracted using the AutoProp feature extraction method and feature selection was performed using the maximum relevance maximum distance (MRMD) program, Finally, only two features were retained to achieve 84.7% classification accuracy. Moreover, it was found that the two retained features were present in the conserved sites and motifs of presynaptic neurotoxins and could represent the critical structures of presynaptic neurotoxins. This method demonstrates that using a few key features to classify proteins can effectively identify critical protein structures.

Ganoderma lingzhi culture enhance growth performance via improvement of antioxidant activity and gut probiotic proliferation in Sanhuang broilers

Introduction

The experiment was conducted to evaluate the effects of Ganoderma lingzhi culture (GLC) as a fermented feed on growth performance, serum biochemical profile, meat quality, and intestinal morphology and microbiota in Sanhuang broilers. In addition, the association between gut bacteria and metabolites was investigated via untargeted metabolomic analysis.

Methods

A total of 192 Sanhuang broilers (112 days old) with an initial body weight of 1.62 ± 0.19 kg were randomly allocated to four treatments, six replicate pens per treatment with 8 broilers per pen. The four treatments contain a control diet (corn-soybean meal basal diet, CON), a positive control diet (basal diet + 75 mg/kg chlortetracycline, PCON), and the experimental diets supplemented with 1.5 and 3% of GLC, respectively. The trial includes phase 1 (day 1-28) and phase 2 (day 29-56).

Results

The results showed that broilers in PCON and GLC-added treatments showed a lower FCR (P < 0.05) in phase 2 and overall period and a higher ADG (P < 0.05) in phase 2. On day 56, the concentrations of serum SOD (P < 0.05), and HDL (P < 0.05) and cecal SCFA contents (P < 0.05) were increased in broilers fed GLC diets. Broilers fed GLC also showed a higher microbiota diversity and an elevated abundance of SCFA-related bacteria in the caecum. The association between intestinal bacteria and metabolites was investigated via correlation analysis. The differential metabolites in the caecum, such as L-beta-aspartyl-L-aspartic acid and nicotinamide riboside, were identified.

Conclusion

In summary, dietary GCL supplementation could increase growth performance to some extent. Moreover, GLC might benefit broilers' health by improving serum HDL content, antioxidant status, SCFAs contents, bacterial diversity, and probiotic proliferation in the caecum.

[Phase Separation of Purified Human LSM4 Protein]

Liquid-liquid phase separation of proteins occur in a number of biological processes, such as regulation of transcription, processing, and RNA maturation. Sm-like protein 4 (LSM4) is involved in multiple processes, including pre-mRNA splicing and P-bodies assembly. Before investigating the involvement of LSM4 in the separation of the two liquid phases during RNA processing or maturation, the separation of the liquid phases in an in vitro preparation of LSM4 protein should be first be detected. The mCherry-LSM4 plasmid was derived from pET30a and used to isolate mCherry-LSM4 protein from prokaryotic cells (Escherichia coli strain BL21). The mCherry LSM4 protein was purified using Ni-NTA resin. The protein was further purified by fast protein liquid chromatography. Delta-Vision wide-field fluorescence microscopy was used to observe the dynamic liquid-liquid phase separation of the LSM4 protein in vitro. Analysis of the LSM4 protein structure using the Predictor of Natural Disordered Regions database revealed that its C-terminus contains a low complexity domain. A purified preparation of full-length human LSM4 protein was obtained from E. coli. Human LSM4 was shown to provide concentration-dependent separation of liquid-liquid phases in vitro in buffer with crowding reagents. Salts in high concentration and 1,6-hexanediol block the LSM4-induced separation of the two liquid phases. In addition, in vitro fusion of LSM4 protein droplets is observed. The results suggest that full-length human LSM4 protein can undergo liquid-liquid phase separation in vitro.

[Effects and mechanism of water-soluble chitosan hydrogel on infected full-thickness skin defect wounds in diabetic mice]

Objective: To explore the effects and mechanism of water-soluble chitosan hydrogel on infected full-thickness skin defect wounds in diabetic mice. Methods: The experimental research method was adopted. The control hydrogel composed of polyvinyl alcohol and gelatin, and the water-soluble chitosan hydrogel composed of the aforementioned two materials and water-soluble chitosan were prepared by the cyclic freeze-thaw method. The fluidity of the two dressings in test tube before and after the first freeze-thawing was generally observed, and the difference in appearance of the final state of two dressings in 12-well plates were compared. According to random number table (the same grouping method below), the cell strains of L929 and HaCaT were both divided into water-soluble chitosan hydrogel group and control hydrogel group, respectively. After adding corresponding dressings and culturing for 24 h, the cell proliferation activity was measured using cell counting kit 8. Rabbit blood erythrocyte suspensions were divided into normal saline group, polyethylene glycol octyl phenyl ether (Triton X-100) group, water-soluble chitosan hydrogel group, and control hydrogel group, which were treated accordingly and incubated for 1 hour, and then the hemolysis degree of erythrocyte was detected by a microplate reader. Twenty-four female db/db mice aged 11-14 weeks were selected, and full-thickness skin defect wounds on their backs were inflicted and inoculated with the methicillin-resistant Staphylococcus aureus (MRSA), 72 h later, the mice were divided into blank control group, sulfadiazine silver hydrogel group, control hydrogel group, and water-soluble chitosan hydrogel group, which were treated accordingly. On post injury day (PID) 0 (immediately), 7, 14, and 21, the healing of the wound was observed. On PID 14 and 21, the wound healing rate was calculated. On PID 14, MRSA concentration in wounds was determined. On PID 21, the wounds were histologically analyzed by hematoxylin and eosin staining; the expression of CD31 in the wounds was detected by immunofluorescence method, and its positive percentage was calculated. Raw264.7 cells were taken and divided into interleukin-4 (IL-4) group, blank control group, control hydrogel group, and water-soluble chitosan hydrogel group, which were treated accordingly. At 48 h of culture, the percentages of CD206 positive cells were detected by flow cytometry. The number of samples was all 3. Data were statistically analyzed with independent sample t test, one-way analysis of variance, analysis of variance for repeated measurement, least significant difference test, and Dunnett T3 test. Results: Two dressings in test tube had certain fluidity before freeze-thawing and formed semi-solid gels after freeze-thawing for once. The final forms of two dressings in 12-well plates were basically stable and translucent sheets, with little difference in transparency. At 24 h of culture, the cell proliferation activities of L929 and HaCaT in water-soluble chitosan hydrogel group were significantly higher than those in control hydrogel group (with t values of 6.37 and 7.50, respectively, P<0.01). At 1 h of incubation, the hemolysis degree of erythrocyte in water-soluble chitosan hydrogel group was significantly lower than that in Triton X-100 group (P<0.01), but similar to that in normal saline group and control hydrogel group (P>0.05). On PID 0, the traumatic conditions of mice in the 4 groups were similar. On PID 7, more yellowish exudates were observed inside the wound in blank control group and control hydrogel group, while a small amount of exudates were observed in the wound in sulfadiazine silver hydrogel group and water-soluble chitosan hydrogel group. On PID 14, the wounds in blank control group and control hydrogel group were dry and crusted without obvious epithelial coverage; in sulfadiazine silver hydrogel group, the scabs fell off and purulent exudate was visible on the wound; in water-soluble chitosan hydrogel group, the base of wound was light red and obvious epithelial coverage could be observed on the wound. On PID 14, the wound healing rate in water-soluble chitosan hydrogel group was significantly higher than that in the other 3 groups (all P<0.01). On PID 21, the wound in water-soluble chitosan hydrogel group was completely closed, while the wounds in the other 3 groups were not completely healed; the wound healing rate in water-soluble chitosan hydrogel group was significantly higher than that in the other 3 groups (all P<0.01). On PID 14, the concentration of MRSA in the wound in water-soluble chitosan hydrogel group was significantly lower than that in blank control group (P<0.01), but similar to that in control hydrogel group and sulfadiazine silver hydrogel group (P>0.05). On PID 21, the new epidermis was severely damaged in blank control group; the epidermis on the wound in control hydrogel group also had a large area of defect; complete new epidermis had not yet being formed on the wound in sulfadiazine silver hydrogel group; the wound in water-soluble chitosan hydrogel group was not only completely covered by the new epidermis, the basal cells of the new epidermis were also regularly aligned. On PID 21, the percentage of CD31 positivity in the wound in water-soluble chitosan hydrogel group was (2.19±0.35)%, which was significantly higher than (0.18±0.05)% in blank control group, (0.23±0.06)% in control hydrogel group, and (0.62±0.25)% in sulfadiazine silver hydrogel group, all P<0.01. At 48 h of culture, the percentage of CD206 positive Raw264.7 cells in water-soluble chitosan hydrogel group was lower than that in IL-4 group (P>0.01) but significantly higher than that in blank control group and control hydrogel group (P<0.05 or P<0.01). Conclusions: The water-soluble chitosan hydrogel has good biosafety and can induce higher level of macrophage M2 polarization than control hydrogel without water-soluble chitosan, so it can enhance the repair effect of MRSA-infected full-thickness skin defect wounds in diabetic mice and promote rapid wound healing.

iPseU-TWSVM: Identification of RNA pseudouridine sites based on TWSVM

Biological sequence analysis is an important basic research work in the field of bioinformatics. With the explosive growth of data, machine learning methods play an increasingly important role in biological sequence analysis. By constructing a classifier for prediction, the input sequence feature vector is predicted and evaluated, and the knowledge of gene structure, function and evolution is obtained from a large amount of sequence information, which lays a foundation for researchers to carry out in-depth research. At present, many machine learning methods have been applied to biological sequence analysis such as RNA gene recognition and protein secondary structure prediction. As a biological sequence, RNA plays an important biological role in the encoding, decoding, regulation and expression of genes. The analysis of RNA data is currently carried out from the aspects of structure and function, including secondary structure prediction, non-coding RNA identification and functional site prediction. Pseudouridine (У) is the most widespread and rich RNA modification and has been discovered in a variety of RNAs. It is highly essential for the study of related functional mechanisms and disease diagnosis to accurately identify У sites in RNA sequences. At present, several computational approaches have been suggested as an alternative to experimental methods to detect У sites, but there is still potential for improvement in their performance. In this study, we present a model based on twin support vector machine (TWSVM) for У site identification. The model combines a variety of feature representation techniques and uses the max-relevance and min-redundancy methods to obtain the optimum feature subset for training. The independent testing accuracy is improved by 3.4% in comparison to current advanced У site predictors. The outcomes demonstrate that our model has better generalization performance and improves the accuracy of У site identification. iPseU-TWSVM can be a helpful tool to identify У sites.

First report of leaf spot on passion fruit in China, caused by Alternaria alternata

Passion fruit (Passiflora edulis Sims), which is native to South America, is an important fruit crop in tropical and subtropical countries. Passion fruit growing areas have increased rapidly in southern China. In 2018 to 2019, circular spots on passion fruit were observed in Shangsi, Guangxi, China (21°15'N, 107°98'E). The disease occurred from June to April of the following year. The disease incidence was generally between 10% to 30%, but could reach up to 50% in purple passion fruit 'Tainong No.1'. The initial lesions on the fruits were small, with a brown center and a greasy margin, and then became sunken and lighter brown with a diameter of about 1 cm in later stages. The spots on the leaves were often surrounded by a yellow halo and turned into larger lesions after coalescence.. Five typical symptomatic fruit and leaves were collected from Shangsi county for the presumed pathogen isolation. Section of the samples were surface sterilized to isolate the fungus on potato dextrose agar (PDA) at 28°C. Five fungal isolates with similar morphology on PDA were obtained by single spore isolation. Colonies at the age of 7 days accompany with flourishing aerial hyphae, showed surface color varying from white to grey. Conidia were ovate or elliptic, light brown to brown, with 2 to 5 diaphragms, 0 to 4 longitudinal-oblique diaphragms, and mostly 8.2 to 36.7 μm × 5.4 to 15.8 μm. The morphology of the fungus resembled Alternaria alternata (Fr.) Keissl (Simmons, 2007). Each of the five isolates (SF-001, SF-002, SF-003, SF-004 and SF-005) was molecularly identified using genomic regions of 18S nrDNA (SSU), 28S nrDNA (LSU), RNA polymerase second largest subunit (RPB2), internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and translation elongation factor 1-alpha (TEF1) (Jayawardena et al., 2019). Nucleotide sequences of SSU (MZ275254, ON055696, ON055697, ON055698 and ON055699), LSU (MZ275253, ON062947, ON062948, ON062949, ON062950), RPB2 (MZ275251, ON055377, ON055378, ON055379 and ON055380), ITS (MW866522, MW866523, ON053451, ON053452 and ON053453), GAPDH (MZ286628, ON055381, ON055382, ON055383 and ON055384) and TEF1 (MZ275255, ON055373, ON055374, ON055375 and ON055376) were deposited in GenBank database. The LSU, GAPDH and TEF1 sequences showed 100% identity with A. alternata in NCBI (KX609773, MK683852 and MK637432, respectively). The SSU, RPB2 and ITS sequences showed 99% identity to A. alternata (U05194, MK605898 and MN856409, respectively). In pathogenicity test (Zhang et al., 2020), 3-month-old grafted 'Tainong No.1' seedlings and mature fruit were used. Five-mm-diameter mycelial plugs taken from 7-day-old PDA colonies of each of 5 isolates were placed on the leaves and fruit that were wounded with a sterilized needle to form 3 pinpricks. Sterile PDA plugs were used as control. Three plants and three fruits were used in each treatment, and the test was repeated twice. The inoculated plants and fruit were kept in plastic bags and grown in a chamber at 28℃. Typical lesions were observed on inoculated plants and fruit after 3 days, but the controls remained healthy. A. alternata was consistently reisolated from these typical lesions. Previously, leaf spot on passion fruit caused by A. alternata has only been recorded in New Zealand (Rheinländer, 2010). To our knowledge, this is the first report of A. alternata (Fr.) Keissl. causing leaf spot on passion fruit in China. The identification of the pathogen may help to take effective management strategies of controlling this disease.

[Influence of gender of reciprocal translocation carriers on the occurrence of embryonic chromosomal abnormalities]

OBJECTIVE

To explore the influence of gender of chromosomal translocation carriers on the occurrence of embryonic chromosomal aberrations.

METHODS

A retrospective study was carried out. Data were collected from 235 couples carrying reciprocal translocations (1163 blastocysts) and 70 couples carrying Robertsonian translocations (351 blastocysts). The preimplantation genetic testing for structural rearrangement (PGT-SR) analysis of 1514 blastocysts were completed through next generation sequencing (NGS).

RESULTS

After adjusting the confounding factors such as female age, AMH, ovarian stimulation regimen, and Gn dosage, the results showed that the risk for blastocyst chromosomal abnormalities was 0.41 [OR(95%CI), 1.41(1.06, 1.87), P < 0.05] times higher in female reciprocal translocation carriers and 1.02 [OR(95%CI), 2.02 (1.20, 3.40), P < 0.01] times higher in female Robertsonian translocation carriers compared with male carriers, respectively. Compared with male carriers, the risk of blastocyst chromosomal abnormalities was increased by 0.67 times [OR(95%CI), 1.67 (1.10, 2.56), P < 0.05] in female reciprocal translocation carriers over 30 years old and 1.06 times [OR(95%CI), 2.06 (1.02, 4.15), P = 0.0434, P < 0.05] in female Robertsonian translocation carriers between 25 and 30 years old.

CONCLUSION

Compared with male carriers, female carriers of reciprocal or Robertsonian translocations have a higher risk for producing embryos with chromosomal abnormalities, and their age may also be a risk factor.

Effects of a new fermented soya bean meal on growth performance, serum biochemistry profile, intestinal immune status and digestive enzyme activities in piglets

BACKGROUND

Fermented soya bean meal (FSBM) is believed to have improved nutritional qualities compared with soya bean meal (SBM) and is also cheaper than soya protein concentration (SPC) and fish meal (FM). Therefore, the present study was conducted to compare the effects of FSBM replacing SBM, SPC and FM in diets on growth performance, serum biochemistry profile, short-chain fatty acid concentrations in digesta, intestinal mucosal enzyme activities, intestinal proinflammatory cytokine concentrations and morphology in weaned piglets. One hundred and twenty 28-day-old piglets (Duroc × Landrace × Yorkshire, body weight: 6.73 ± 1.14 kg) were randomly allocated to four treatment diets (six replicate pens with five piglets per pen) containing SBM, SPC, FM or FSBM as the protein source, respectively.

RESULTS

Dietary FSBM supplementation improved average daily gain (p < 0.05), gain to feed ratio (p < 0.05), and digestibility of dry matter, gross energy, crude protein and organic matter (p < 0.05) in pigs compared with those fed SBM during 0-14 days and reduced diarrhoea rate (p < 0.05) compared with those fed SBM and FM during 0-14 days. Moreover, pigs fed FBSM had greater IgA and IgM contents and antioxidase activities than those provided SBM and SPC on day 14. In addition, the butyrate concentration in the cecum of pigs fed FSBM was greater than those fed the other diets (p < 0.05), and the trypsin activity in duodenum and jejunum of pigs provided FSBM was greater than those fed SBM (p < 0.05). Moreover, higher villus height (p < 0.05) and villus height to crypt depth ratio (p < 0.05) and lower crypt depth (p < 0.05) in the duodenum of pigs fed FSBM were observed, and pigs fed FSBM had a lower (p < 0.05) TNF-α concentration in jejunum compared with those fed SBM.

CONCLUSIONS

In conclusion, dietary FSBM supplementation to replace SBM, SPC and FM could improve piglets' growth performance, intestinal health and immune function.

Association of self-reported snoring with decreased retinal thickness and vessel density

Purpose: Self-reported snoring has been reported to influence nerves and vessels. However, there are few direct evidences of snoring related to nerves and microvessels defects. Therefore, we evaluated the association of self-reported snoring with retinal structure and microcirculation.

Methods: A total of 2,622 participants were recruited from the Jidong eye cohort study (JECS). Physical examinations, laboratory tests, and questionnaires were recorded. We also used optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) to assess the retinal structure and microvascular network. Snoring was defined as “never,” “occasionally,” and “frequently or more severe” according to self-reported frequency.

Results: The prevalence of snoring were 84.6% (n = 983) and 45.0% (n = 657) in males and females, respectively. Compared with never snoring group, the retinal thickness increased in “occasionally” (p &lt; 0.001) and “frequently or more severe” groups (p = 0.001), while no difference was found between snoring groups (p = 0.14). Superficial retinal capillary plexus (RCP) vessel density was lower in “frequently or more severe” group than in “never” (p &lt; 0.001) and “occasionally” snoring groups (p &lt; 0.001). After adjusting for confounders, “frequently or more severe” snoring was significantly associated with thinner total retinal thickness [β = −2.79 (95% CI: −5.27, −0.30)] and lower superficial RCP vessel density [β = −0.71 (95% CI: −1.19, −0.23)].

Conclusion: Our research showed self-reported snoring was associated with thinner retinal thickness and lower superficial RCP vessel density. The findings of our study emphasize the need for self-reported snoring assessments in determining retinal structure and microcirculation impairment.

The effect of ovarian stimulation on aneuploidy of early aborted tissues and preimplantation blastocysts: comparison of the GnRH agonist long protocol with the GnRH antagonist protocol

PURPOSE

To compare aneuploidy rates in early aborted tissues or blastocysts between in vitro fertilization (IVF) cycles after the gonadotropin-releasing hormone (GnRH) antagonist (GnRH-ant) protocol or the GnRH agonist (GnRH-a) long protocol.

METHODS

This was a retrospective cohort study from a university-affiliated fertility center. In total, 550 early miscarriage patients who conceived through IVF/intracytoplasmic sperm injection (ICSI) after receiving the GnRH-ant or GnRH-a long protocol were analyzed to compare aneuploidy rates in early aborted tissues. To compare aneuploidy rates in blastocysts, 404 preimplantation genetic testing for aneuploidy (PGT-A) cycles with the GnRH-ant protocol or GnRH-a long protocol were also analyzed.

RESULTS

For early miscarriage patients who conceived through IVF/ICSI, compared to the GnRH-a long protocol group, the GnRH-ant protocol group had a significantly higher rate of aneuploidy in early aborted tissues (48.51% vs. 64.19%). Regarding PGT-A cycles, the rate of blastocyst aneuploidy was significantly higher in the GnRH-ant protocol group than the GnRH-a long protocol group (39.69% vs. 52.27%). After stratification and multiple linear regression, the GnRH-ant regimen remained significantly associated with an increased risk of aneuploidy in early aborted tissues and blastocysts [OR (95% CI) 1.81 (1.21, 2.71), OR (95% CI) 1.65 (1.13, 2.42)]. Furthermore, the blastocyst aneuploidy rate in the GnRH-ant protocol group was significantly higher but only in young and normal ovarian responders [OR (95% CI) 5.07 (1.99, 12.92)].

CONCLUSION

Compared to the GnRH-a long protocol, the GnRH-ant protocol is associated with a higher aneuploidy rate in early aborted tissues and blastocysts. These results should be confirmed in a multicenter, randomized controlled trial.

[Association of DNA methylation of IFNG gene with no/low response to hepatitis B vaccine in children]

Objective: To explore the association of DNA methylation with immune response to hepatitis B (HepB) vaccine in Han nationality children from Guangxi province. Methods: A total of 263 children aged 8-9 months who had completed HepB immunization program were recruited from three hospitals in Guangxi province by using unmatched case-control method. Children with the HepB surface antibody concentration(Anti-HBs)<100 mIU/ml was set as the case group and ≥100 mIU/ml as the control group. Multiplex PCR and heavy sulfite sequencing were used to treat the samples. Illumina platform was used for high-throughput DNA methylation sequencing of IFNG gene target regions and CpG sites. Unconditional logistic regression was used to analyze the association between cytosine-phospho-guanosine DNA methylation at 18 loci of IFNG gene and HepB immune response level. Results: There were 104 children in the case group and 159 in the control group. The median (Q₁, Q₃) level of anti-HBs in two groups were 62.34 (30.06, 98.88) mIU/ml and 1 089.10 (710.35, 1 233.45) mIU/ml. The methylation levels of IFNG_1 gene 44 and 93 locus in the case group were higher than those in the control group (P<0.05). The unconditional logistic regression model showed that the DNA methylation level of IFNG_1 gene at 44 (OR=1.18, 95%CI: 1.03-1.35) and 93 (OR=1.21, 95%CI: 1.07-1.38) locus was associated with the HepB response level. Conclusion: The changes of DNA methylation at locus 44 and 93 of IFNG_1 gene may be relevant factors affecting the response level of HepB in Han nationality children from Guangxi province.

[Clinical features of epilepsy in 5 children with Mowat-Wilson syndrome]

Objective: To summarize and investigate the clinical characters of epilepsy in children with Mowat-Wilson syndrome (MWS), thus to improve the understanding of this disease. Methods: Clinical characters of epilepsy episodes in 5 children with MWS admitted to Department of Pediatrics, Peking University First Hospital from June to December 2020 were retrospectively reviewed. Clinical data including onset age of seizures, clinical features, characters of electroencephalogram (EEG), magnetic resonance imaging (MRI) findings, results of ZEB2 gene testing and responses to the anti-seizure medications (ASM) were summarized. Results: The onset age of seizures in the 5 patients (3 males and 2 females) ranged from 6 months to 4 years. Four patients showed focal motor seizures with diverse expressions, while the other 1 patient had epileptic spasms. All the 5 patients showed distinctive face, different degrees of intellectual disability, development delay and other congenital malformations. EEG of 4 patients presented the slowing of background rhythm and epileptiform discharges mainly occurred in the posterior region of the brain. The other 1 patient showed hypsarrhythmia at the beginning of the disease, changing into multifocal discharges mainly occurred in posterior region later. Corpus callosum abnormality and white matter disability were found from investigations of MRI in 2 patients, respectively. All the 5 patients carried a de novo heterozygous variation in the ZEB2 gene, 4 were nonsense variants and 1 was frame-shift variant. Within the follow-up of 14 months to 20 months, 3 patients achieved seizure-free more than 1 year, 2 patients achieved seizure-free more than 6 months. Two patients used valproate only and 2 patients received valproate combined with other ASM. Conclusions: Epileptic seizures are common clinical phenotype of MWS. Focal motor seizure may be the most common seizure type and epileptic spasms exist. The manifestations of EEG can be age-related. The most common type of variation of the ZEB2 gene is de novo nonsense variation. Valproate might be the first-line ASM for patients with MWS.

Paternal Radiofrequency Electromagnetic Radiation Exposure Causes Sex-Specific Differences in Body Weight Trajectory and Glucose Metabolism in Offspring Mice

Nowadays, concerns about the harmful effects of radiofrequency electromagnetic radiation (RF-EMR) on male fertility and offspring health are growing. In the present study, we investigated the effects of long-term exposure (at least 10 weeks) to the RF-EMR [2.0 GHz; power density, 2.5 W/m2; whole-body specific absorption rate (SAR), 0.125-0.5 W/kg] on male mice fertility and F1 growth and glucose metabolism. No significant injuries were observed in testis organization, sperm quality, and pregnancy rate. However, mice exposed to RF-EMR exhibited a significantly elevated apoptosis rate in testis germ cells. Interestingly, paternal RF-EMR exposure resulted in sex-specific weight trajectory differences and glucose metabolism changes in male F1 mice but not in female F1 mice. The changed glucose metabolism in F1 male may result from the altered gene expression of liver Gck. These data collectively suggested that 2.0 GHz RF-EMR whole-body exposure of male mice does not cause obvious impairment in testis, sperm quality, and pregnancy rate. Paternal RF-EMR exposure causes male-specific alterations in body weight trajectories and glucose metabolism of F1.

[METTL27 is a prognostic biomarker of colon cancer and associated with immune invasion]

OBJECTIVE

To investigate the expression and gene function of methyltransferase-like protein 27 (METTL27) in colon cancer, its association with immune infiltration and its prognostic significance.

METHODS

We analyzed the expression levels of METTL27 in 33 cancers using R language and identified METTL27 as a differential gene in colon cancer. The related signaling pathways of METTL27 were analyzed by gene functional annotation and enrichment. SsGSEA algorithm was used to analyze immune infiltration, and logistic analysis was used to evaluate the correlation between METTL27 expression and clinicopathological features of the patients. Kaplan-meier analysis, univariate and multivariate Cox regression analysis were performed to construct a nomogram for evaluating the correlation between METTL27 expression and clinical prognosis. The expression level of METTL27 was further verified in colorectal cancer cell lines and 16 clinical specimens of colorectal cancer tissues using qPCR and Western blotting.

RESULTS

METTL27 was highly expressed in 21 cancers, and its expression was significantly higher in colon cancer than in adjacent tissues (P < 0.001). METTL27-related genes were identified by differential analysis, and functional annotation revealed that METTL27 was significantly enriched in transmembrane transport and lipid metabolism, and 5 related signaling pathways were identified by GSEA. METTL27 expression was negatively correlated with different T helper cells and central memory T cells (P < 0.001). The patients with a high METTL27 mRNA expression had a poor survival outcome. Cox regression analysis showed that METTL27 expression was an independent prognostic factor of the overall survival. The expression level of METTL27 was significantly higher in the colorectal cancer cell line than in normal cells (P < 0.05).

CONCLUSION

METTL27 is overexpressed in colon cancer and is associated with a poor prognosis of the patients. A high expression of METTL27 showed is associated less T cell immune infiltration, suggesting the potential of METTL27 as a prognostic marker of colon cancer.

Distance-based support vector machine to predict DNA N6-methyladenine modification

Background:

DNA N6-methyladenine plays an important role in the restriction-modification system to isolate invasion from adventive DNA. The shortcomings of the high time-consumption and high costs of experimental methods have been exposed, and some computational methods have emerged. The support vector machine theory has received extensive attention in the bioinformatics field due to its solid theoretical foundation and many good characteristics.

Objective:

General machine learning methods include an important step of extracting features. The research has omitted this step and replaced with easy-to-obtain sequence distances matrix to obtain better results

Method:

First sequence alignment technology was used to achieve the similarity matrix. Then a novel transformation turned the similarity matrix into a distance matrix. Next, the similarity-distance matrix is made positive semi-definite so that it can be used in the kernel matrix. Finally, the LIBSVM software was applied to solve the support vector machine.

Results:

The five-fold cross-validation of this model on rice and mouse data has achieved excellent accuracy rates of 92.04% and 96.51%, respectively. This shows that the DB-SVM method has obvious advantages compared with traditional machine learning methods. Meanwhile this model achieved 0.943,0.982 and 0.818 accuracy,0.944, 0.982, and 0.838 Matthews correlation coefficient and 0.942, 0.982 and 0.840 F1 scores for the rice, M. musculus and cross-species genome datasets, respectively.

Conclusion:

These outcomes show that this model outperforms the iIM-CNN and csDMA in the prediction of DNA 6mA modification, which are the lastest research on DNA 6mA.

TMPpred: A support vector machine-based thermophilic protein identifier

MOTIVATION

The thermostability of proteins will cause them to break the temperature binding and play more functions. Using machine learning, we explored the mechanism of and reasons for protein thermostability characteristics.

RESULTS

Different from other methods that only pursue the performance of models, we aim to find important features so as to provide a powerful reference for in vitro experiments. We transformed this problem into a binary classification problem, that is, the distinction between thermophilic proteins and nonthermophilic proteins. Using support vector machine-based model construction and analysis, we inferred that Gly, Ala, Ser and Thr may be the most important components at the residue level that determine the thermal stability of proteins. It is also noteworthy that our proposed model obtains an Sn of 0.892, an Sp of 0.857, an ACC of 0.87566 and an AUC of 0.874. To facilitate other researchers, we wrapped our model and deployed it as a web server, which is accessible at http://112.124.26.17:7000/TMPpred/index.html.

Butyl-fructooligosaccharides modulate gut microbiota in healthy mice and ameliorate ulcerative colitis in a DSS-induced model

Butyl-fructooligosaccharides (B-FOSs) are newly synthesized prebiotics composed of short-chain FOS (GF2, 1-kestose; GF3, nystose; GF4, fructofuranosyl-nystose; GF5, 1-F-(1-b-D-fructofuranosyl)-2-nystose) bound with one or two butyric groups by ester bonds. Previous in...

Association of Serum Uric Acid With Retinal Capillary Plexus

BACKGROUND

To determine the association between serum uric acid (SUA) and the retinal capillary plexus (RCP) using optical coherence tomography angiography (OCTA).

METHODS

This cross-sectional study evaluated data from August 2019 to January 2020 from participants recruited from the Jidong community (Tangshan, Hebei, China). All participants completed detailed anthropometrical measurements, laboratory tests and comprehensive ophthalmic examinations. We assessed the vessel density in RCP using OCTA. We used multivariable analysis to evaluate the sex-specific association between SUA and RCP after adjusting for confounders.

RESULTS

A total of 2730 participants were included in this study. The mean age of the participants was 44.0 ± 11.6 years, and 1463 (53.6%) were women. The multivariable βs and 95% confidence intervals (CIs) of superficial RCP vessel density in the second through fourth SUA quartiles compared with the lowest SUA quartiles were -0.27 (-0.56 - 0.03), -0.30 (-0.60 - 0.01), and -0.46 (-0.78 - -0.14) (P for trend = 0.007) in men.

CONCLUSIONS

Higher SUA levels were significantly associated with lower RCP vessel density in men. Our findings provide evidence for the detrimental effect of high SUA levels on the retinal microvasculature and imply the importance of modulating SUA to prevent the microvascular alternation especially for men.

Research on the Computational Prediction of Essential Genes

Genes, the nucleotide sequences that encode a polypeptide chain or functional RNA, are the basic genetic unit controlling biological traits. They are the guarantee of the basic structures and functions in organisms, and they store information related to biological factors and processes such as blood type, gestation, growth, and apoptosis. The environment and genetics jointly affect important physiological processes such as reproduction, cell division, and protein synthesis. Genes are related to a wide range of phenomena including growth, decline, illness, aging, and death. During the evolution of organisms, there is a class of genes that exist in a conserved form in multiple species. These genes are often located on the dominant strand of DNA and tend to have higher expression levels. The protein encoded by it usually either performs very important functions or is responsible for maintaining and repairing these essential functions. Such genes are called persistent genes. Among them, the irreplaceable part of the body’s life activities is the essential gene. For example, when starch is the only source of energy, the genes related to starch digestion are essential genes. Without them, the organism will die because it cannot obtain enough energy to maintain basic functions. The function of the proteins encoded by these genes is thought to be fundamental to life. Nowadays, DNA can be extracted from blood, saliva, or tissue cells for genetic testing, and detailed genetic information can be obtained using the most advanced scientific instruments and technologies. The information gained from genetic testing is useful to assess the potential risks of disease, and to help determine the prognosis and development of diseases. Such information is also useful for developing personalized medication and providing targeted health guidance to improve the quality of life. Therefore, it is of great theoretical and practical significance to identify important and essential genes. In this paper, the research status of essential genes and the essential genome database of bacteria are reviewed, the computational prediction method of essential genes based on communication coding theory is expounded, and the significance and practical application value of essential genes are discussed.

DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA

MOTIVATION

N4-acetylcytidine (ac4C) is the only acetylation modification that has been characterized in eukaryotic RNA, and is correlated with various human diseases. Laboratory identification of ac4C is complicated by factors, such as sample hydrolysis and high cost. Unfortunately, existing computational methods to identify ac4C do not achieve satisfactory performance.

RESULTS

We developed a novel tool, DeepAc4C, which identifies ac4C using convolutional neural networks (CNNs) using hybrid features composed of physicochemical patterns and a distributed representation of nucleic acids. Our results show that the proposed model achieved better and more balanced performance than existing predictors. Furthermore, we evaluated the effect that specific features had on the model predictions and their interaction effects. Several interesting sequence motifs specific to ac4C were identified.

AVAILABILITY AND IMPLEMENTATION

The webserver is freely accessible at https://ac4c.webmalab.cn/, the source code and datasets are accessible at Zenodo with URL https://doi.org/10.5281/zenodo.5138047 and Github with URL https://github.com/wangchao-malab/DeepAc4C.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Application of Sparse Representation in Bioinformatics

Inspired by L1-norm minimization methods, such as basis pursuit, compressed sensing, and Lasso feature selection, in recent years, sparse representation shows up as a novel and potent data processing method and displays powerful superiority. Researchers have not only extended the sparse representation of a signal to image presentation, but also applied the sparsity of vectors to that of matrices. Moreover, sparse representation has been applied to pattern recognition with good results. Because of its multiple advantages, such as insensitivity to noise, strong robustness, less sensitivity to selected features, and no “overfitting” phenomenon, the application of sparse representation in bioinformatics should be studied further. This article reviews the development of sparse representation, and explains its applications in bioinformatics, namely the use of low-rank representation matrices to identify and study cancer molecules, low-rank sparse representations to analyze and process gene expression profiles, and an introduction to related cancers and gene expression profile database.

[N-glycosylation modification of heat shock protein gp96 affects its immunological function]

N-glycosylation modification, one of the most common protein post-translational modifications, occurs in heat shock protein gp96. The purpose of this study is to investigate the effect of N-glycosylation modification on immunologic function of the recombinant gp96 using the mutant gp96 in N-glycosylation sites. Firstly, wild-type and mutant gp96 proteins were expressed by insect expression system and their glycosylation levels were detected. To determine the effect of N-glycosylation on gp96 antigen presentation function, the IFN-γ+ CD8+ T cells in gp96-immunized mice and secretion level of IFN-γ were examined by flow cytometry and ELISA. The ATPase activity of gp96 was further detected by the ATPase kit. Finally, the effect of N-glycosylation on adjuvant function of gp96 for influenza vaccine was investigated in immunized mice. It was found that total sugar content of mutant recombinant gp96 was reduced by 27.8%. Compared to the wild type recombinant gp96, mutations in N-glycosylation sites resulted in decreased antigen presentation ability and ATPase activity of gp96. Furthermore, influenza vaccine-specific T cell levels induced by mutant gp96 as adjuvant were dramatically reduced compared to those by wild type recombinant gp96. These results demonstrate that N-glycosylation modification is involved in regulation of ATPase activity and antigen presentation function of gp96, thereby affecting its adjuvant function. The results provide the technical bases for development of gp96- adjuvanted vaccines.

Characterizing viral circRNAs and their application in identifying circRNAs in viruses

Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism, which play an important role in a variety of biological activities. Viruses can encode circRNA, and viral circRNAs have been found in multiple single-stranded and double-stranded viruses. However, the characteristics and functions of viral circRNAs remain unknown. Sequence alignment showed that viral circRNAs are less conserved than circRNAs in animal, indicating that the viral circRNAs may evolve rapidly. Through the analysis of the sequence characteristics of viral circRNAs and circRNAs in animal, it was found that viral circRNAs and animals circRNAs are similar in nucleic acid composition, but have obvious differences in secondary structure and autocorrelation characteristics. Based on these characteristics of viral circRNAs, machine learning algorithms were employed to construct a prediction model to identify viral circRNA. Additionally, analysis of the interaction between viral circRNA and miRNAs showed that viral circRNA is expected to interact with 518 human miRNAs, and preliminary analysis of the role of viral circRNA. And it has been also found that viral circRNAs may be involved in many KEGG pathways related to nervous system and cancer. We curated an online server, and the data and code are available: http://server.malab.cn/viral-CircRNA/.

The Next Generation of Machine Learning in DDIs Prediction

Drug-drug interactions may occur when combining two or more drugs may cause some adverse events such as cardiotoxicity, central neurotoxicity, hepatotoxicity, etc. However, a large number of researchers who are proficient in pharmacokinetics and pharmacodynamics have been engaged in drug assays and trying to find out the side effects of all kinds of drug combinations. However, at the same time, the number of new drugs is increasing dramatically, and the drug assay is an expensive and time-consuming process. It is impossible to find all the adverse reactions through drug experiments. Therefore, new attempts have been made in using computational techniques to deal with this problem. In this review, we conduct a review of the literature on applying the computational method for predicting drug-drug interactions. We first briefly introduce the widely used data sets. After that, we elaborate on the existing state-of-art deep learning models for drug-drug interactions prediction. We also discussed the challenges and opportunities of applying the computational method in drug-drug interactions prediction.