Development of an online calculator for the prediction of seizure freedom following pediatric hemispherectomy using the Hemispherectomy Outcome Prediction Scale (HOPS)

OBJECTIVES

Although hemispheric surgeries are among the most effective procedures for drug-resistant epilepsy (DRE) in the pediatric population, there is a large variability in seizure outcomes at the group level. A recently developed HOPS score provides individualized estimation of likelihood of seizure freedom to complement clinical judgement. The objective of this study was to develop a freely accessible online calculator that accurately predicts the probability of seizure freedom for any patient at 1-, 2-, and 5-years post-hemispherectomy.

METHODS

Retrospective data of all pediatric patients with DRE and seizure outcome data from the original Hemispherectomy Outcome Prediction Scale (HOPS) study were included. The primary outcome of interest was time-to-seizure recurrence. A multivariate Cox proportional-hazards regression model was developed to predict the likelihood of post-hemispheric surgery seizure freedom at three time points (1-, 2- and 5- years) based on a combination of variables identified by clinical judgment and inferential statistics predictive of the primary outcome. The final model from this study was encoded in a publicly accessible online calculator on the International Network for Epilepsy Surgery and Treatment (iNEST) website (https://hops-calculator.com/).

RESULTS

The selected variables for inclusion in the final model included the five original HOPS variables (age at seizure onset, etiologic substrate, seizure semiology, prior non-hemispheric resective surgery, and contralateral fluorodeoxyglucose-positron emission tomography [FDG-PET] hypometabolism) and three additional variables (age at surgery, history of infantile spasms, and magnetic resonance imaging [MRI] lesion). Predictors of shorter time-to-seizure recurrence included younger age at seizure onset, prior resective surgery, generalized seizure semiology, FDG-PET hypometabolism contralateral to the side of surgery, contralateral MRI lesion, non-lesional MRI, non-stroke etiologies, and a history of infantile spasms. The area under the curve (AUC) of the final model was 73.0%.

SIGNIFICANCE

Online calculators are useful, cost-free tools that can assist physicians in risk estimation and inform joint decision-making processes with patients and families, potentially leading to greater satisfaction. Although the HOPS data was validated in the original analysis, the authors encourage external validation of this new calculator.

Corrigendum: Hydroxychloroquine attenuates autoimmune hepatitis by suppressing the interaction of GRK2 with PI3K in T lymphocytes

[This corrects the article DOI: 10.3389/fphar.2022.972397.].

[Protective effect of Liujing Toutong Tablets on rats with permanent cerebral ischemia via NF-κB signaling pathway]

This study investigated the neuroprotective effects and underlying mechanism of Liujing Toutong Tablets(LJTT) on a rat model of permanent middle cerebral artery occlusion(pMCAO). The pMCAO model was established using the suture method. Eighty-four male SPF-grade SD rats were randomly divided into a sham operation group, a model group, a nimodipine group(0.020 g·kg~(-1)), and high-, medium-, and low-dose LJTT groups(2.8, 1.4, and 0.7 g·kg~(-1)). The Longa score, adhesive removal test and laser speckle contrast imaging technique were used to evaluate the degree of neurological functional impairment and changes in local cerebral blood flow. The survival and mortality of rats in each group were recorded daily. After seven days of continuous administration following the model induction, the rats in each group were euthanized, and brain tissue and blood samples were collected for corresponding parameter measurements. Nissl staining was used to examine pathological changes in brain tissue neurons. The levels of tumor necrosis factor-alpha(TNF-α), interleukin-6(IL-6), IL-1β, vascular endothelial growth factor(VEGF), calcitonin gene-related peptide(CGRP), beta-endorphin(β-EP), and endogenous nitric oxide(NO) in rat serum were measured using specific assay kits. The entropy weight method was used to analyze the weights of various indicators. The protein expression levels of nuclear factor kappa-B(NF-κB), inhibitor kappaB alpha(IκBα), phosphorylated IκBα(p-IκBα), and phosphorylated inhibitor of NF-κB kinase alpha(p-IKKα) in brain tissue were determined using Western blot. Immunohistochemistry was used to detect the protein expression of chemokine-like factor 1(CKLF1) and C-C chemokine receptor 5(CCR5) in rat brain tissue. Compared with the sham operation group, the model group showed significantly higher neurological functional impairment scores, prolonged adhesive removal time, decreased cerebral blood flow, increased neuronal damage, reduced survival rate, significantly increased levels of TNF-α, IL-1β, IL-6, CGRP, and NO in serum, significantly decreased levels of VEGF and β-EP, significantly increased expression levels of NF-κB p65, p-IκBα/IκBα, and p-IKKα in rat brain tissue, and significantly upregulated protein expression of CKLF1 and CCR5. Compared with the model group, the high-dose LJTT group significantly improved the neurological functional score of pMCAO rats after oral administration for 7 days. LJTT at all doses significantly reduced adhesive removal time and restored cerebral blood flow. The high-and medium-dose LJTT groups significantly improved neuronal damage. The LJTT groups at all doses showed reduced levels of TNF-α, IL-1β, IL-6, CGRP, and NO in rat serum, increased VEGF and β-EP levels, and significantly decreased expression levels of NF-κB p65, p-IκBα/IκBα, p-IKKα, and CCR5 protein in rat brain tissue. The entropy weight analysis revealed that CGRP and β-EP were significantly affected during the model induction, and LJTT exhibited a strong effect in reducing the release of inflammatory factors such as TNF-α and IL-1β. LJTT may exert a neuroprotective effect on rats with permanent cerebral ischemia by reducing neuroinflammatory damage, and its mechanism may be related to the inhibition of the NF-κB signaling pathway and the regulation of the CKLF1/CCR5 axis. Additionally, LJTT may exert certain analgesic effects by reducing CGRP and NO levels and increasing β-EP levels.

Corrigendum: Diazoxide post-conditioning activates the HIF-1/HRE pathway to induce myocardial protection in hypoxic/reoxygenated cardiomyocytes

[This corrects the article DOI: 10.3389/fcvm.2021.711465.].

The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D

Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850 K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1 A, 2 A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., glial scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 mapped explicitly to biological pathways related to neurodegeneration, biogenesis of the extracellular matrix (ECM) components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.

Effects of the termination of LC30 imidacloprid stress on the multigeneration adaptive strategies of Aphis glycines population

Aphis glycines Matsumura (Hemiptera: Aphididae) is a major soybean pest that often poses a serious threat to soybean production. Imidacloprid is one of the commonly used insecticides to control the soybean aphid. To investigate the effect of termination of imidacloprid stress on the adaptive strategies of soybean aphid populations, we studied the growth, development, and related metabolism changes when the stress was terminated after 24 generations of imidacloprid stress on A. glycines. The results show that the A. glycines population accelerated its recovery and expanded its population size across generations. The longevity of the adults of the recovering population in the F12, F18, and F24 generations, respectively, was 1.11, 1.15, and 1.11 times longer than the control, while the fecundity was 10.38%, 11.74%, and 11.61% higher than that of the control. The net reproductive rate (R 0) of the recovering population was always significantly higher than that of the control in the F1 to F24 generations. In addition, metabolisms related to the regulation of cell proliferation and oocyte meiosis were significantly upregulated in the recovering population. Even when the imidacloprid pressure disappeared, intergenerational stimuli still affected the adaptive strategies of soybean aphid populations. This effect was manifested as inhibiting the growth and development of the soybean aphid in the early generations and improving the fecundity of the soybean aphid in the later generations. Adaptive soybean aphid populations would surge in the absence of imidacloprid pressure. This study provides an important reference for exploring the adaptability of the A. glycines population under termination of stress from low lethal concentrations of imidacloprid across generations. It also provides important data for monitoring the population dynamics of A. glycines in the field and analyzing the degree of pharmacodynamic stress.

Single-atom-anchored microsweepers for H. pylori inhibition through dynamically navigated reciprocating locomotion

Catalytic microsweepers with a single-iron-atom center were designed to search for and inhibit Helicobacter pylori. Under dynamic navigation, the microsweepers displayed a large-range wall-adhering reciprocating motion, which increased the opportunity for interaction between microsweepers and H. pylori and further inhibited H. pylori through acid-responsive reactive oxygen species generation.

[Effects of Combined Application of Fungal Residue and Chemical Fertilizer on Soil Microbial Community Composition and Diversity in Paddy Soil]

Fungal residue is a unique abundant organic material undervalued in agricultural production. The application of chemical fertilizer combined with fungal residue can not only improve soil quality but also regulate the microbial community. However, it is unclear whether the response of soil bacteria and fungi to the combined application of fungal residue and chemical fertilizer is consistent. Therefore, a long-term positioning experiment in a rice field was conducted with a total of nine treatments. Chemical fertilizer (C) and fungal residue (F) were applied at 0, 50%, and 100% to evaluate 1 the change in soil fertility properties and microbial community structure and 2 the main driving factors of soil microbial diversity and species composition. The results showed that soil total nitrogen (TN) was highest after treatment C₀F₁₀₀ (55.56% higher than in the control), and the carbon to nitrogen ratio (C/N), total phosphorus (TP), dissolved organic carbon (DOC), and available phosphorus (AP) contents were highest after treatment with C₁₀₀F₁₀₀(26.18%, 26.46%, 17.13%, and 279.54% higher than in the control, respectively). The amounts of soil organic carbon (SOC), available nitrogen (AN), available potassium (AK), and pH were highest after treatment with C₅₀F₁₀₀ (85.57%, 41.61%, 29.33%, and 4.62% higher than in the control, respectively). Following the application of fungal residue with chemical fertilizer, there were significant changes in the α-diversity of bacteria and fungi in each treatment. Compared with that of the control (C₀F₀), different long-term applications of fungal residue with chemical fertilizer did not significantly change soil bacterial β-diversity but resulted in significant differences in fungal β-diversity, and the relative abundance of soil fungal Ascomycota and Sordariomycetes significantly decreased after the application of C₅₀F₁₀₀. The random forest prediction model indicated that AP and C/N were the main driving factors of bacterial and fungal α-diversity, respectively, and AN, pH, SOC, and DOC were the main driving factors of bacterial β-diversity, whereas AP and DOC were the main driving factors of fungal β-diversity. Correlation analysis suggested that the relative abundance of soil fungal Ascomycota and Sordariomycetes had a significantly negative correlation with SOC, TN, TP, AN, AP, AK, and C/N. PERMANOVA showed that variation in soil fertility properties, dominant species of soil bacteria at the phylum and class level, and dominant species of soil fungi at the phylum and class level were all best explained by fungal residue (46.35%, 18.47%, and 41.57%, respectively), and variation in bacterial diversity was best explained by fungal residue (23.84%) and to a lesser extent by the interaction between fungal residue and chemical fertilizer (9.90%). In contrast, the variation in fungal diversity was best explained by the interaction between fungal residue and chemical fertilizer (35.00%) and to a lesser extent by fungal residue (10.42%). In conclusion, the application of fungal residue has more advantages than chemical fertilizer in influencing soil fertility properties and microbial community structure changes.

[Sinusitis, otitis media and diffuse bronchiectasis in both lungs]

Primary ciliary dyskinesia (PCD) is a rare autosomal recessive or X-linked biallelic mutations inherited disease, characterized by motile cilia dysfunction. Typical manifestations include bronchiectasis, secretory otitis media, sinusitis, situs inversus, and infertility. PCD often needs to be differentiated from cystic fibrosis (CF) because of similar clinical manifestations. In this paper, a juvenile female who presented with recurrent cough and expectoration with fever since early childhood, had a history of secretory otitis media and sinusitis, and had been considered for the diagnosis of CF. After the discovery of compound heterozygous mutations in PCD related pathogenic genes by gene sequencing, combined with the clinical manifestations and imaging characteristics, PCD was finally diagnosed.

Gender-related differences in the effects of Inonotus obliquus polysaccharide on intestinal microorganisms in SD rats model

Natural edible fungal polysaccharides are of research and application value for the prevention of diseases by improving the microenvironment within the intestine. Inonotus obliquus polysaccharide (IOP) extracts have strong antioxidant, anti-inflammatory, and other biological activities, and as such, it could be used as prebiotics to improve the viability of intestinal microbes, maintain intestinal homeostasis and improve intestinal immunity. The effects of sex on intestinal microbiota after IOP absorption was determined. In this study, IOP had different effects on the intestinal flora of male and female rats, with the diversity and richness showing opposite changes. At the same time, after IOP intervention, changes in the dominant intestinal flora of female rats was less compared with that of males. In addition, while Clostridia, Lactobacillus and Roseburia were the dominant intestinal microbes in female rats, males had mainly Bacteroidota from different families and genera, along with an increasing proportion of Muribaculaceae from different families and genera. IOP could further regulate the intestinal microenvironment of male and female SD rats by enhancing the vitality of their dominant microorganisms, and for both sexes, this enabled the screening of dominant microflora that were conducive to the balance of the intestinal flora. These results help to understand the effects of sex-related differences on the composition of the intestinal microbiota as well as on diseases.

Hydroxychloroquine attenuates autoimmune hepatitis by suppressing the interaction of GRK2 with PI3K in T lymphocytes

Hydroxychloroquine (HCQ) is derivative of the heterocyclic aromatic compound quinoline, which has been used for the treatment of autoimmune diseases. The central purpose of this study was to investigate therapeutic effects and inflammatory immunological molecular mechanism of HCQ in experimental autoimmune hepatitis (AIH). Treatment with HCQ ameliorated hepatic pathologic damage, inflammatory infiltration, while promoted regulatory T cell (Treg) and down-regulated CD8+T cell differentiation in AIH mice induced by S-100 antigen. In vitro, HCQ also suppressed pro-inflammatory cytokine (IFN-γ, TNF-α, and IL-12) secretion, promoted anti-inflammatory cytokine (TGF-β1) secretion. HCQ mainly impaired T cell lipid metabolism but not glycolysis to promote Treg differentiation and function. Mechanistically, HCQ down-regulated GRK2 membrane translocation in T cells, inhibited GRK2-PI3K interaction to reduce the PI3K recruiting to the membrane, followed by suppressing the phosphorylation of PI3K-AKT-mTOR signal. Pretreating T cells with paroxetine, a GRK2 inhibitor, disturbed HCQ effect to T cells. HCQ also reversed the activation of the PI3K-AKT axis by 740 Y-P (PI3K agonist). Meanwhile, HCQ inhibited the PI3K-AKT-mTOR, JAK2-STAT3-SOCS3 and increased the AMPK signals in the liver and T cells of AIH mice. In conclusion, HCQ exhibited specific and potent therapeutic effects on AIH and attendant liver injury, which was attributed to HCQ acted on GRK2 translocation, inhibited metabolism-related PI3K-AKT and inflammation-related JAK2-STAT3 signal in T lymphocytes, thereby modulating lipid metabolism of T cell function to regulate Treg differentiation and function.

[Prevalence and trend analysis of severe multiple disabling birth defects in Chongqing City from 2007 to 2020]

Objective: To explore the prevalence and change trend of severe multiple disabling birth defects in Chongqing City from 2007 to 2020, and to provide a basis for comprehensive prevention and control measures of severe multiple disabling birth defects. Methods: Based on hospital monitoring data, 1 103 children with severe multiple disabling birth defects monitored by all birth defects monitoring institutions in Chongqing City from January 2007 to December 2020 were included in the study. They were grouped by year, perinatal gender, maternal permanent residence (urban/rural), maternal age, different regions and other categories. Chi-square test was used to analyze the differences in the incidence of severe multiple disabling birth defects in different categories, and linear trend test was used to analyze the change trend. Results: From 2007 to 2020, a total of 1 022 314 perinatal births and 1 103 severe multiple disabling birth defects were monitored in Chongqing City, with an incidence of 10.79/10 000, including 11.47/10 000 in urban areas and 9.48/10 000 in rural areas, with an incidence higher in urban areas than in rural areas(χ²=8.424,P=0.004). Male was 10.47/10 000, female was 10.97/10 000, there was no significant difference between male and female(χ²=0.606,P=0.436). The incidence of maternal in different age groups was u-shaped, and there was statistical difference in incidence among different age groups (χ²=59.465, P<0.001). The incidence of maternal in<20 years old and ≥35 years old was higher, and in 25-29 years old was lower. The incidence rate was 17.96/10 000 in 2007 and 7.18/10 000 in 2020, which decreased by 60.02% in 2007-2020. The incidence of neural tube defect, chromosome syndrome, limb shortening and abdominal wall defect decreased by 78.12%, 77.38%, 80.55% and 91.30%, respectively. Severe Congenital heart disease rose by 456.16%. From 2007 to 2020, the overall incidence of the disease showed a decreasing trend (χ²_trend =117.046, P<0.001), except for the rise of severe congenital heart disease, (χ²_trend=8.744, P=0.003), the other four types of diseases were on the decline (neural tube defects χ²_trend =48.618, P<0.001; chromosome syndrome χ²_trend=50.999, P<0.001; limb shortening χ²_trend=73.464, P<0.001; abdominal wall defect χ²_trend=79.863, P<0.001). Conclusion: From 2007 to 2020, the incidence of severe disabling birth defects in Chongqing City showed a downward trend, and there were regional and age differences. The incidence of severe congenital heart disease is on the rise.

Postnatal Cytomegalovirus Infection May Increase the Susceptibility of Tuberous Sclerosis Complex to Autism Spectrum Disorders

Autism spectrum disorder (ASD), a highly hereditary and heterogeneous neurodevelopmental disorder, is influenced by genetic and environmental factors. Tuberous sclerosis complex (TSC) is a common syndrome associated with ASD. Cytomegalovirus (CMV) infection is an environmental risk factor for ASD. The similarities in pathological and mechanistic pathways of TSC and CMV intrigued us to investigate whether CMV and TSC interacted in ASD's occurrence. We detected CMV IgG seroprevalence of 308 TSC patients from our prospective cohort (September 2011 to March 2021) and 93 healthy children by magnetic particle indirect chemiluminescence immunoassay. A total of 206 TSC patients enrolled were divided into ASD and non-ASD groups, and the relationship between ASD and CMV seroprevalence was analyzed. Nested PCR and Western blot were used to detect CMV DNAs and proteins in cortical malformations of seven TSC patients with and without ASD. No difference was found in CMV seroprevalence between TSC patients and healthy children (74.0% versus 72.0%, P = 0.704). Univariate analysis showed the seroprevalence in TSC patients with ASD was higher than that in TSC patients without ASD (89.2% versus 75.1%, P = 0.063), and multifactorial analysis showed that CMV seroprevalence was a risk factor for ASD in TSC patients (OR = 3.976, 95% CI = 1.093 to 14.454). Moreover, CMV was more likely to be detected in the cortical malformations in TSC patients with ASD but not in those without ASD. The findings demonstrated that CMV may increase the susceptibility of TSC to ASD. IMPORTANCE CMV is an environmental risk factor for ASD, but its role in syndromic autism with known genetic etiology has been rarely studied. The pathogenesis of ASD is related to the interaction between environmental and genetic factors. This study demonstrated that CMV can contribute to the occurrence of ASD related to TSC, a common genetic syndrome associated with ASD. Our findings provided support for the theory of gene-environment interaction (G × E) in pathogenesis of ASD and a new perspective for the prevention and therapy for TSC related ASD.

[Analysis of A Pedigree with Hereditary Coagulation Factor Ⅻ Deficiency Caused by Compound Heterozygous Mutations]

OBJECTIVE

To analysis clinical phenotype and potential genetic cause of a family affected with hereditary coagulation factor Ⅻ deficiency.

METHODS

The prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen (FIB), D-Dimer (D-D), coagulation factor Ⅻ activity (FⅫ:C) and coagulation factor Ⅻ antigen (FⅫ:Ag) were determined for phenotype diagnosis of the proband and his family members(3 generations and 5 people). Targeted capture and whole exome sequencing were performed in peripheral blood sample of the proband. Possible disease-causing mutations of F12 gene were obtained and further confirmed by Sanger sequencing. The corresponding mutation sites of the family members were analyzed afterwards. The online bioinformatics software AutoPVS1 and Mutation Taster was used to predict the effects of mutation sites on protein function.

RESULTS

The APTT of the proband was significantly prolonged, reaching 180.9s. FⅫ:C and FⅫ:Ag of the proband was significantly reduced to 0.8% and 4.17%, respectively. The results of whole exome sequencing displayed that there were compound heterozygous mutations in F12 gene of the proband, including the c.1261G＞T heterozygous nonsense mutation in exon 11 (causing p.Glu421*) and the c.251dupG heterozygous frameshift mutation in exon 4 (causing p.Trp85Metfs*53). Both mutations are loss of function mutations with very strong pathogenicity, leading to premature termination of the protein. AutoPVS1 and Mutation Taster software predicted both mutations as pathogenic mutations. The results of Sanger sequencing revealed that c.1261G＞T heterozygous mutation of the proband was inherited from his mother, for which his brother and his daughter were c.1261G＞T heterozygous carriers. Genotype-phenotype cosegregation was observed in this family.

CONCLUSION

The c.1261G＞T heterozygous nonsense mutation in exon 11 and the c.251dupG heterozygous frameshift mutation in exon 4 of the F12 gene probably account for coagulation factor Ⅻ deficiency in this family. This study reports two novel pathogenic F12 mutations for the first time worldwide.

[Effects of postoperative urine protein levels on predicting acute kidney injury in critically ill patients undergoing non-cardiac surgery]

Objective: To investigate the predictive value of postoperative urine protein level in critically ill patients undergoing non-cardiac surgery with acute kidney injury (AKI). Methods: A total of 661 critically ill patients undergoing non-cardiac surgery, who visited the Department of Critical Care Medicine of Peking University First Hospital from May 20, 2019 to November 24, 2020, were enrolled in this prospective study. The clinical data of the patient's age, gender, body mass index, laboratory examination, surgical status, etc. were collected. AKI diagnostic criteria of the 2012 KDIGO guidelines were used to diagnose the occurrence of AKI after surgery. The independent predictors of AKI were determined by multivariate logistic regression. Results: The age of this patient cohort was (69±15) years. The prevalence of AKI was 45.4% (300/661). Multivariate logistic regression showed that urine protein semi-quantitative ≥2+(OR=2.62, 95%CI: 1.05-6.56, P=0.039) was independent factor for postoperative AKI in critically ill patients undergoing non-cardiac surgery, other independent factors include higher age (OR=1.04, 95%CI: 1.02-1.06, P=0.001), higher body mass index (BMI) (OR=1.12, 95%CI: 1.04-1.21, P=0.004), lower plasma hemoglobin level (OR=0.98, 95%CI: 0.97-1.00, P=0.019), lower central venous pressure (OR=0.89, 95%CI: 0.83-0.97, P=0.005) and lower total hypotension time (OR=1.01, 95%CI: 1.00-1.01, P=0.041). Conclusions: Urine protein semi-quantitative ≥2+after surgery is an independent predictive factor for the occurrence of postoperative AKI in critically ill patients undergoing non-cardiac surgery. It is important to check urine routine immediately after surgery to detect and deal with high-risk patients.

pValid 2: A deep learning based validation method for peptide identification in shotgun proteomics with increased discriminating power

Tandem mass spectrometry has been the principal method in shotgun proteomics for peptide and protein identification. However, incorrect identifications reported by proteome search engines are still unknown, and further validation methods are needed. We have proposed a validation method pValid before, but its scope of application is limited because two features used in pValid are related to open database search and sub-optimal peptide candidates for tandem mass spectra, and the performance on complex datasets still has room for improvement. In this study, we developed a more comprehensive validation method, pValid 2, to break these limitations by removing the two features and bringing in a new feature related to the retention time predicted by a deep learning-based method pPredRT. pValid 2 yielded an average false positive rate of 0.03% and an average false negative rate of 1.37% on three testing datasets, better than those of pValid, and flagged 8.47% to 11.31% more incorrect identifications than pValid on two complex datasets. Moreover, pValid 2 flagged almost all decoy identifications in validating the open-search datasets. In addition, the function of validating identifications given by MaxQuant and MS-GF+ was implemented in pValid 2, and the validation results showed that pValid 2 performed dramatically better than three metabolic labeling validation methods. Further considering its cost-effectiveness as a pure computational approach, pValid 2 has the potential to be a widely used validation tool for peptide identifications of any proteome search engines in shotgun proteomics. SIGNIFICANCE: Identification results given by shotgun proteomics are vital to life science research. The correctness of identifications deeply affects the precision of the subsequent studies about protein structures and functions, protein-protein interactions, pathogenic mechanism, and targeted drugs. Thus, validating the correctness of identifications is crucial and urgent. In 2019, we developed an identification credibility validation method named pValid, whose false positive rate (FPR) is 0.03% and false negative rate (FNR) is 1.79%, comparable to those of the gold standard, i.e., the Synthetic-peptide validation method. However, pValid can only be used for validating the results from pFind, and its validation performance on a few complex datasets still has room for improvement. So, in this submission, we proposed pValid 2, a more comprehensive computational validation method that can validate identifications from any proteome search engines with increased discriminating power.

Diazoxide Post-conditioning Activates the HIF-1/HRE Pathway to Induce Myocardial Protection in Hypoxic/Reoxygenated Cardiomyocytes

Background: Previous studies have shown that diazoxide can protect against myocardial ischemia-reperfusion injury (MIRI). The intranuclear hypoxia-inducible factor-1 (HIF-1)/hypoxia-response element (HRE) pathway has been shown to withstand cellular damage caused by MIRI. It remains unclear whether diazoxide post-conditioning is correlated with the HIF-1/HRE pathway in protective effect on cardiomyocytes. Methods: An isolated cardiomyocyte model of hypoxia-reoxygenation injury was established. Prior to reoxygenation, cardiomyocytes underwent post-conditioning treatment by diazoxide, and 5-hydroxydecanoate (5-HD), N-(2-mercaptopropionyl)-glycine (MPG), or dimethyloxallyl glycine (DMOG) followed by diazoxide. At the end of reoxygenation, ultrastructural morphology; mitochondrial membrane potential; interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), reactive oxygen species (ROS), and HIF-1α levels; and downstream gene mRNA and protein levels were analyzed to elucidate the protective mechanism of diazoxide post-conditioning. Results: Diazoxide post-conditioning enabled activation of the HIF-1/HRE pathway to induce myocardial protection. When the mitoKATP channel was inhibited and ROS cleared, the diazoxide effect was eliminated. DMOG was able to reverse the effect of ROS absence to restore the diazoxide effect. MitoKATP and ROS in the early reoxygenation phase were key to activation of the HIF-1/HRE pathway. Conclusion: Diazoxide post-conditioning promotes opening of the mitoKATP channel to generate a moderate ROS level that activates the HIF-1/HRE pathway and subsequently induces myocardial protection.

Comparison of the real-world effectiveness of vertical versus lateral functional hemispherotomy techniques for pediatric drug-resistant epilepsy: A post hoc analysis of the HOPS study

Objective

This study was undertaken to determine whether the vertical parasagittal approach or the lateral peri‐insular/peri‐Sylvian approach to hemispheric surgery is the superior technique in achieving long‐term seizure freedom.

Methods

We conducted a post hoc subgroup analysis of the HOPS (Hemispheric Surgery Outcome Prediction Scale) study, an international, multicenter, retrospective cohort study that identified predictors of seizure freedom through logistic regression modeling. Only patients undergoing vertical parasagittal, lateral peri‐insular/peri‐Sylvian, or lateral trans‐Sylvian hemispherotomy were included in this post hoc analysis. Differences in seizure freedom rates were assessed using a time‐to‐event method and calculated using the Kaplan–Meier survival method.

Results

Data for 672 participants across 23 centers were collected on the specific hemispherotomy approach. Of these, 72 (10.7%) underwent vertical parasagittal hemispherotomy and 600 (89.3%) underwent lateral peri‐insular/peri‐Sylvian or trans‐Sylvian hemispherotomy. Seizure freedom was obtained in 62.4% (95% confidence interval [CI] = 53.5%–70.2%) of the entire cohort at 10‐year follow‐up. Seizure freedom was 88.8% (95% CI = 78.9%–94.3%) at 1‐year follow‐up and persisted at 85.5% (95% CI = 74.7%–92.0%) across 5‐ and 10‐year follow‐up in the vertical subgroup. In contrast, seizure freedom decreased from 89.2% (95% CI = 86.3%–91.5%) at 1‐year to 72.1% (95% CI = 66.9%–76.7%) at 5‐year to 57.2% (95% CI = 46.6%–66.4%) at 10‐year follow‐up for the lateral subgroup. Log‐rank test found that vertical hemispherotomy was associated with durable seizure‐free progression compared to the lateral approach (p = .01). Patients undergoing the lateral hemispherotomy technique had a shorter time‐to‐seizure recurrence (hazard ratio = 2.56, 95% CI = 1.08–6.04, p = .03) and increased seizure recurrence odds (odds ratio = 3.67, 95% CI = 1.05–12.86, p = .04) compared to those undergoing the vertical hemispherotomy technique.

Significance

This pilot study demonstrated more durable seizure freedom of the vertical technique compared to lateral hemispherotomy techniques. Further studies, such as prospective expertise‐based observational studies or a randomized clinical trial, are required to determine whether a vertical approach to hemispheric surgery provides superior long‐term seizure outcomes.

Genetically Encoded Sensor Enables Endogenous RNA Imaging with Conformation-Switching Induced Fluorogenic Proteins

Genetically encoded molecular tools are crucial for live cell RNA imaging, and few are available for endogenous RNA imaging. We develop a new genetically encoded sensor using conformation switching RNA induced fluorogenic proteins that enable multicolor and signal-amplified imaging of endogenous RNAs. The sensor system is designed with an RNA sensing module and a degron-fused fluorescent protein reporter. Target RNA induces conformation switching of the RNA sensing module to form RNA aptamers that stabilize the degron-fused protein for fluorogenic imaging. This sensor is demonstrated for high-contrast imaging of survivin mRNA abundance and dynamics in live cells. Moreover, the sensor system is extended to a multicolor palette by screening fluorogenic proteins of distinct colors, and engineered into a signal amplifier using the split fluorescent protein design. The sensor is further exploited for imaging lncRNA MALAT-1 and its translocation dynamics during mitosis. Our sensor system can afford a valuable platform for RNA imaging in biomedical research and clinical theranostics.

[Effect of gMDSCs on natural killer cell functionality in chronic hepatitis C patients treated with direct-acting antiviral agents]

Objective: To investigate the changes of natural killer(NK) cell function, and clarify the effect of granulocytic myeloid derived suppressor cells (G-MDSCs) on NK cell functionality in patients with treatment-naive chronic hepatitis C (CHC) who were cured by direct-acting antiviral agents (DAAs). Methods: Thirteen treatment-naive CHC patients and 13 healthy controls were prospectively included in this study from March 2016 to January 2017. They were divided into case group and control group, respectively. The patients of case group,6 males and 7 females aged 21-65 years old with an average of (37±14),were treated with daclatasvir and asunaprevir combination (DCV/ASV) at the Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital. While 13 healthy individuals, 6 males and 7 females aged 21-57 (36±11) years old, were enrolled as healthy controls(control group). Flow cytometry was used to determine the immunological characteristics of peripheral blood NK cells subset, and detect the frequencies of gMDSCs in peripheral blood of people in two groups. It was specifically notes that CHC patients of case group would be detected before, during and after treatment. The correlations between gMDSCs and each NK cell subset function were also examined. The impact of gMDSCs on NK cell functionalities and the relevant regulatory mechanisms were explored using co-culture experiments of sorted NK cells and gMDSCs in vitro. Results: Compared with healthy controls, the decreased IFN-γ production[M(Q1,Q3)] [3.182 (2.757, 4.237) vs 6.675 (4.476, 8.280),1.434 (1.127, 2.434) vs 3.045 (1.680, 4.856), 2.611 (1.749, 3.498) vs 5.160 (4.232, 7.683)] and increased CD107a degranulation [9.314 (7.838, 13.543) vs 3.480 (2.938, 6.824), 2.544 (1.366, 4.768) vs 0.552 (0.408, 1.560), 10.339 (9.145, 12.534) vs 3.488 (3.117, 5.651)] (all P<0.05) were found on NK cell and its subsets. The frequencies of gMDSCs and plasma concentration of arginase-1 in CHC patients was significantly higher than that in healthy controls [7.050 (4.180, 12.538) vs 1.440 (0.444, 2.261), 114.278 (68.492, 163.724) vs 64.753 (50.809, 93.278)](all P<0.05). The production of IFN-γ was increased and the secretion of CD107a was decreased in NK cell and its subsets after DAAs treatment (P<0.05). The frequencies of gMDSCs and plasma arignase I levels were also decreased in CHC patients treated with DAAs (P<0.05).The results of the study indicated that the frequencies of G-MDSCs were inversely associated with the levels of IFN-γproduction of NK cells and CD56^dim NK cells in CHC patients (r=0.668, -0.750, respectively, both P<0.05). In addition, the frequencies of gMDSCs were positively associated with the expression of CD107a in the CD56^bright NK cell subset (r=0.711, P=0.021). In vitro, the inhibition of gMDSCs on the IFN-γ production of NK cells was demonstrated in the co-culture experiments of sorted NK cells and gMDSCs, and blocking arginase I can significantly increase the ability of NK cells to produce IFN-γ, restore NK cell IFN-γ production. Conclusions: gMDSCs in peripheral blood of CHC patients has been shown to suppress NK cell IFN-γ production in an arginase I-dependent manner. Direct-acting antiviral-mediated clearance of HCV is associated with the normalization of NK cell function and gMDSCs frequency.

Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure

Inadequate endometrial receptivity may be responsible for the low implantation rate of transferred embryos in in vitro fertilization (IVF) treatments. Patients with repeated implantation failure (RIF) impact the clinical pregnancy rate for IVF. We collected endometrial tissue during the implantation window of hysteroscopy biopsies from September 2016 to December 2019 and clinical data were collected simultaneously. Patients were divided into RIF and pregnant controls group according to pregnancy outcomes. A total of 82 differentially expressed endometrial proteins were identified, including 55 up-regulated proteins (>1.50-fold, P < 0.05) and 27 down-regulated proteins (<0.67-fold, P < 0.05) by iTRAQ labeling coupled with the 2D LC MS/MS technique in the RIF group. String analysis found interactions between these proteins which assembled in two bunches: ribosomal proteins and blood homeostasis proteins. The most significant enriched Gene Ontology terms were negative regulation of hydrolase activity, blood microparticle, and enzyme inhibitor activity. Our results emphasized the corticosteroid-binding globulin and fetuin-A as the specific proteins of endometrial receptivity by Western-blot. Our study provided experimental data to establish the objective indicator of endometrial receptivity, and also provided new insight into the pathogenesis of RIF.

Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes

Autophagy and endocytosis are essential in regulating cellular homeostasis and cancer immunotherapeutic responses. Existing methods for autophagy and endocytosis imaging are susceptible to cellular micro-environmental changes, and direct fluorogenic visualization of their fluxes remains challenging. We develop a novel strategy via clicking of organelle-enriched probes (COP), which comprises a pair of trans-cyclooctenol (TCO) and tetrazine probes separately enriched in lysosomes and mitochondria (in autophagy) or plasma membrane (in endocytosis). These paired probes are merged and boost a fluorogenic click reaction in response to autophagic or endocytic flux that ultimately fuses mitochondria or plasma membrane into lysosomes. We demonstrate that this strategy enables direct visualization of autophagic and endocytic fluxes, and confer insight into correlation of autophagic or endocytic flux to cell surface expression of immunotherapeutic targets such as MHC-I and PD-L1. The COP strategy provides a new paradigm for imaging autophagic and endocytic fluxes, and affords potential for improved cancer immunotherapy using autophagy or endocytosis inhibitors.

NAMPT promotes hepatitis B virus replication and liver cancer cell proliferation through the regulation of aerobic glycolysis

Nicotinamide phosphoribosyltransferase (NAMPT) is a critical rate-limiting enzyme involved in NAD synthesis that has been shown to contribute to the progression of liver cancer. However, the potential role and mechanism of NAMPT in hepatitis B virus (HBV)-associated liver cancer remain unclear. The present study assessed the expression of NAMPT in HBV-positive and -negative liver cancer cells, and investigated whether HBV-induced NAMPT expression is dependent on HBV X protein (HBx). In addition, the role of NAMPT in HBV replication and transcription, and in HBV-mediated liver cancer cell growth was explored. The effects of NAMPT on the glycolytic pathway were also evaluated. Reverse transcription-quantitative PCR and western blotting results revealed that NAMPT expression levels were significantly higher in HBV-positive liver cancer cells than in HBV-negative liver cancer cells, and this effect was HBx-dependent. Moreover, the activation of NAMPT was demonstrated to be required for HBV replication and transcription. The NAMPT inhibitor FK866 repressed cell survival and promoted cell death in HBV-expressing liver cancer cells, and these effects were attenuated by nicotinamide mononucleotide. Furthermore, the inhibition of NAMPT was associated with decreased glucose uptake, decreased lactate production and decreased ATP levels in HBV-expressing liver cancer cells, indicating that NAMPT may promote the aerobic glycolysis. Collectively, these findings reveal a positive feedback loop in which HBV enhances NAMPT expression and the activation of NAMPT promotes HBV replication and HBV-mediated malignant cell growth in liver cancer. The present study highlights the important role of NAMPT in the regulation of aerobic glycolysis in HBV-mediated liver cancer, and suggests that NAMPT may be a promising treatment target for patients with HBV-associated liver cancer.

Hemispherectomy Outcome Prediction Scale: Development and validation of a seizure freedom prediction tool

OBJECTIVE

To develop and validate a model to predict seizure freedom in children undergoing cerebral hemispheric surgery for the treatment of drug-resistant epilepsy.

METHODS

We analyzed 1267 hemispheric surgeries performed in pediatric participants across 32 centers and 12 countries to identify predictors of seizure freedom at 3 months after surgery. A multivariate logistic regression model was developed based on 70% of the dataset (training set) and validated on 30% of the dataset (validation set). Missing data were handled using multiple imputation techniques.

RESULTS

Overall, 817 of 1237 (66%) hemispheric surgeries led to seizure freedom (median follow-up = 24 months), and 1050 of 1237 (85%) were seizure-free at 12 months after surgery. A simple regression model containing age at seizure onset, presence of generalized seizure semiology, presence of contralateral 18-fluoro-2-deoxyglucose-positron emission tomography hypometabolism, etiologic substrate, and previous nonhemispheric resective surgery is predictive of seizure freedom (area under the curve = .72). A Hemispheric Surgery Outcome Prediction Scale (HOPS) score was devised that can be used to predict seizure freedom.

SIGNIFICANCE

Children most likely to benefit from hemispheric surgery can be selected and counseled through the implementation of a scale derived from a multiple regression model. Importantly, children who are unlikely to experience seizure control can be spared from the complications and deficits associated with this surgery. The HOPS score is likely to help physicians in clinical decision-making.

In vivo mRNA imaging based on tripartite DNA probe mediated catalyzed hairpin assembly

Herein, we develop a novel tripartite DNA probe to transport phosphorothioated substrate hairpins and an aptamer for the intramolecular CHA circuit, which achieves detection of a low amount of specific mRNA in living cells and mice. Our study provides an improved strategy to promote in vivo fluorescence imaging applications in early-stage clinical diagnosis.

Sarcopenia is associated with the presence of nonalcoholic fatty liver disease in Zhejiang Province, China: a cross-sectional observational study

Background

Currently, both non-alcoholic fatty liver disease (NAFLD) and sarcopenia have attracted extensive attention in public health. However, the relationship between NAFLD and sarcopenia remains unclear. This study aimed to clarify the sex-specific association between sarcopenia and NAFLD according to the Asian Working Group for Sarcopenia (AWGS).

Methods

Dual-energy X-ray absorptiometry (DXA) and hepatic ultrasonography were measured in 578 participants (92 men and 486 women) during their annual health examinations. Multivariate logistic regression models were used to explore the association between NAFLD and sarcopenia with its two components.

Results

A total of 154 participants (30 men and 124 women) had NAFLD. The prevalence of sarcopenia was higher among the participants with NAFLD than among those without NAFLD (men: 20.0% vs. 9.7%, P = 0.295, women: 15.3% vs. 8.0%, P = 0.019). Low muscle mass (LMM) was independently associated with NAFLD in both men and women (men: odds ratio [OR], 2.88; 95% confidence interval [CI] 1.52–5.46; women: OR, 2.08; 95% CI 1.63–2.67). However, low muscle strength (LMS) was independently associated with NAFLD only in male participants, with an OR of 1.15 (95% CI 1.02–1.28).

Conclusion

The occurrence of sarcopenia was associated with a higher risk of NAFLD, especially in men, as demonstrated by lower muscle mass and lower muscle strength.

[Long-term clinical effect of full-mouth implant fixation in middle-aged and elderly patients with static computer-assisted implant surgery]

Objective: To evaluate long-term clinical outcome of implant-supported fixed prosthesis with the guidance of computer-aided design/computer-aided manufacturing (CAD/CAM) surgical template in old patients. Methods: Fifteen 50-67(58.6±5.3) year-old patients (11 males and 4 females) who received the digital implant surgery with the guidance of CAD/CAM surgical template and implant-supported fixed prosthesis in Department of Oral Implantology, Yantai Stomatological Hospital Affiliated to Binzhou Medical College from August, 2013 to Janurary, 2016 were included. There are 15 edentulous maxillas, 8 edentulous mandibles on which 145 implants were placed in total. After the placement of implant, the accuracy of CAD/CAM surgical template was assessed by comparing the post-operative 3-dimensional location of implant with the pre-operative design. The 5-year survival rate of implant and prosthesis was recorded, and marginal bone loss around implants and the development of complication were evaluated by radiological and clinical examination respectively. Results: The result on accuracy of CAD/CAM surgical template showed that deviations in neck and apex of implants were (0.78±0.59) and (1.38±0.63) mm respectively, depth deviation was (0.65±0.35) mm and angle deviation was 4.12°±2.77°. The 5-year cumulative survival rate of implants was 98.6%(143/145). In all 145 implants, the prevalence of implant-related biological complication was 4.1%(6/145). The prosthesis-related mechanical complication rate was 57%(13/23). After 5-year function, mean peri-implant bone loss was (0.69±0.35) mm. Conclusions: This 5-year follow-up retrospective study showed that implant-supported fixed prosthesis with the guidance of CAD/CAM surgical template in middle aged and elderly patients could achieve good long-term clinical outcome and patient satisfaction.

[Nutritional recovery after discharge in hospitalized children with malnutrition]

OBJECTIVE

To investigate the nutritional recovery status of children with moderate or severe malnutrition during hospitalization after discharge.

METHODS

The children with moderate or severe malnutrition were given nutrition support during hospitalization. They received a regular follow-up and nutrition guidance after discharge. The weight-for-age and height-for-age Z-scores reaching above -2 SD were considered the nutrition criterion for ending follow-up.

RESULTS

Among the 298 children with moderate or severe malnutrition, 174 (58.4%) reached the criterion for ending follow-up, 100 (33.6%) were lost to follow-up, 18 (6.0%) died, and 6 (2.0%) did not reach the criterion for ending follow-up after 18 months of follow-up. The children with malnutrition in the department of surgery had a significantly higher proportion of children reaching the criterion for ending follow-up than those in the department of internal medicine (P<0.05). The children with severe malnutrition had a significantly higher loss to follow-up rate than those with moderate nutrition (P<0.05). The majority of children with emaciation reached the criterion for ending follow-up at month 3 after discharge, while those with growth retardation reached such the criterion at months 3-6 after discharge. Up to 1 year after discharge, more than 80% of the children with different types of malnutrition reached the nutrition criterion for ending follow-up.

CONCLUSIONS

Most of the children with malnutrition who adhere to follow-up can reach the expected nutrition criterion within 1 year after discharge. The children with growth retardation have slower nutritional recovery than those with emaciation.

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

MOTIVATION

De novo peptide sequencing based on tandem mass spectrometry data is the key technology of shotgun proteomics for identifying peptides without any database and assembling unknown proteins. However, owing to the low ion coverage in tandem mass spectra, the order of certain consecutive amino acids cannot be determined if all of their supporting fragment ions are missing, which results in the low precision of de novo sequencing.

RESULTS

In order to solve this problem, we developed pNovo 3, which used a learning-to-rank framework to distinguish similar peptide candidates for each spectrum. Three metrics for measuring the similarity between each experimental spectrum and its corresponding theoretical spectrum were used as important features, in which the theoretical spectra can be precisely predicted by the pDeep algorithm using deep learning. On seven benchmark datasets from six diverse species, pNovo 3 recalled 29-102% more correct spectra, and the precision was 11-89% higher than three other state-of-the-art de novo sequencing algorithms. Furthermore, compared with the newly developed DeepNovo, which also used the deep learning approach, pNovo 3 still identified 21-50% more spectra on the nine datasets used in the study of DeepNovo. In summary, the deep learning and learning-to-rank techniques implemented in pNovo 3 significantly improve the precision of de novo sequencing, and such machine learning framework is worth extending to other related research fields to distinguish the similar sequences.

AVAILABILITY AND IMPLEMENTATION

pNovo 3 can be freely downloaded from http://pfind.ict.ac.cn/software/pNovo/index.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Seroprevalence of Toxoplasma gondii infection in people in southeast Hubei province, China

Toxoplasma gondii is a world-widely spread zoonotic parasite. However, scarce knowledge is known about the prevalence of T. gondii infection in people in Hubei province, China. This study herein was to perform epidemiological investigation of T. gondii infection in people in this region. A total 12527 blood samples were obtained during 2015-2018, and were assayed for T. gondii antibodies of IgG and IgM, respectively by employing an indirect hemagglutination test (IHA). The results discovered that the prevalence of T. gondii in people was 2.44% and 6.1%, respectively based on antibodies of IgG and IgM, respectively. The prevalence was ranged from 0.3% to 5.4% during 2015-2018 based on IgM antibodies. For genders, the prevalence was 0.7% and 2.6% in males and females, respectively based on IgM antibodies. In different years, the prevalence was ranged from 4.9% to 14.0% based on IgG antibodies. The prevalence of T. gondii was 4.9% and 6.6% in males and femalesy based on IgG antibodies. The current results may be helpful for the implementation of preventive measures against Toxoplasma infection among people living in this region.

[Prognostic value of myocardial injury in patients with COVID-19]

Objective: To analyze the prognostic value of myocardial injury in patients with COVID-19. Method: Confirmed cases of COVID-19 patients admitted from January 31st to February 5th at isolation ward of Renmin Hospital of Wuhan University were divided into non-survival group and survival group according to the clinical outcomes 5 weeks after admission. Data including demographics, comorbidities, vital signs, laboratory results were obtained. Cardiac injury was defined as serum concentration of high sensitivity cardiac troponin I (hs-cTnI) above 0.04 μg/L. Univariate and multivariate Cox regression were used to analyze the prognostic value of myocardial injury in patients with COVID-19. Kaplan-Meier analysis was used to plotted survival curve and analyze the impact of myocardial injury on the survival outcome of COVID-19 patients. Results: A total of 202 patients were included, the age was 63 (51, 70) years old, 88 (43.6%) of them were male, 85 (42.1%) of them had comorbidities, 125 (61.9%) of them were severely to critically ill. Till March 11, 33 patients died, all of them were critically ill patients. The age, proportion of males, comorbidities, respire rate, serum levels of hs-cTnI and incidence of heart failure in the non-survival group were significantly higher than those in the survival group (all P<0.05). The hospitalization time of non-survival group was significantly shorter than that of survival group (6(4, 9) vs. 32(23, 36), P<0.001). Myocardial injury was an important prognostic factor of COVID-19 (HR=5.382, 95%CI 2.404-12.05, P<0.001). Kaplan-Meier survival analysis showed that the presence of myocardial injury was significantly associated with the reduced survival rate among COVID-19 patients (P<0.001). Conclusion: Myocardial injury is an important prognostic factor of COVID-19, COVID-19 patients with myocardial injury face a significantly higher risk of death.

[Analysis of genotypes, EEG and phenotypes of tuberous sclerosis complex patients]

Objective: Tuberous sclerosis complex (TSC) is a multi-system disease with TSC1 and TSC2 genes as the pathogenic genes. The purpose of our study was to analyze the gene mutation in patients with TSC with epilepsy as the main clinical manifestation. The relationship between genotype and phenotype, scalp EEG in patients was analyzed. Methods: The peripheral blood was extracted from 43 patients and their families. TSC gene was detected by second-generation sequencing. Long-term video EEG monitoring and MRI examination were performed to determine the onset area, seizure type and location of nodules. Results: 39 patients had TSC gene mutation, 4 patients did not detect the gene mutation.11 had TSC1 mutations and 28 had TSC2 mutations. 22 mutations were de novo. Patients with TSC2 mutations had earlier seizure and more nodules than patients with TSC1 mutations, but no significant difference in intelligence and spasm were observed. 28 patients had focal origin of scalp EEG, of which 85.7% of TSC2 mutations patients had focal origin. Conclusions: Patients of TSC2 mutations always has an early onset age. Although MRI shows multiple nodules, the onset of EEG is mainly focal origin.

[Identification of a Novel Mutation of EPB41 Gene in a Family Affected with Hereditary Elliptocytosis]

OBJECTIVE

To analyse potential genetic cause of a family affected with hereditary elliptocytosis （HE）.

METHODS

Peripheral blood samples from this HE family were collected. Targeted capture and high-throughput sequencing of 4 813 genetic disease-associated genes was performed in four members of the family. Possible causative genetic variation was obtained and further confirmed by Sanger sequencing. Fifty healthy control subjects were recruited for detection of the candidate variation.

RESULTS

High-throughput sequencing detected a nonsense mutation c.1215G>A（p.Trp405Ter）in exon 13 of the EPB41 gene in the proband and his mother presenting with moderate anemia. The pathogenicity of this loss-of-function mutation is very strong, because the G→A transition leads to introduce the premature stop codon instead of tryptophan codon at position 405, which producing a truncating protein with loss of important functional domains. This causative mutation is extremely rare in the population, and it has not yet been reported. The grandmother of the proband was heterozygous for the same mutation. Genotype-phenotype cosegregation was observed in this family. This mutation was not found in the 50 unrelated healthy controls.

CONCLUSION

The c.1215G>A mutation of the EPB41 gene probably accounts for the disease in this HE family. This study reports a pathogenic EPB41 mutation in a Chinese HE family for the first time.

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, ¹⁵N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.

The identification of cross-linked peptides at a proteome scale for interactome analyses represents a complex challenge. Here the authors report an efficient and reliable search engine pLink 2 for proteome-scale cross-linking mass spectrometry analyses, and demonstrate how to systematically evaluate the credibility of search engines.

Surgical outcomes in patients with epilepsy after viral encephalitis: contribution of SEEG study

Background

Nowadays, few surgery analysis has been reported in cases of epilepsy after viral encephalitis(VE). Herein, this study was to evaluate the efficacy of surgery and capability of stereoelectroencephalography (SEEG) in the definition of the epileptogenic zone (EZ) after VE, and also to explore the relationship between the SEEG features and the surgical outcomes.

Methods

We retrospectively analyzed 10 surgically treated patients that identified to suffer from epilepsy secondary to VE using SEEG, and investigated the SEEG features associated with surgical outcomes in these patients. Besides visual analysis, we used the epileptogenicity index (EI), a semi-quantitative and supplementary tool to evaluate the validity of SEEG in the context of VE.

Results

Among the 10 operated patients, 3 of them became completely seizure-free. The patients who got totally seizure free or significant improvement, the seizure onset was located either in the antero-mesial temporal structures or focal gyrus; patients who got worthwhile improvement or no improvement, the seizure started from multiple brain lobes. The number of electrodes classified as epileptogenic visually involved were closely correlated with EI positive onses.Anatomic areas defined and shown as EZ on MRI by visual assessment were also defined as epileptogenic by the EI in these cases.

Conclusion

Apart from exploring the surgical outcome related to epilepsy after VE, we also bring insight into the relationship between the SEEG features and surgical outcome with the application of the supplementary methods.

[Application value of shear wave elastography technique in qualitative and quantitative diagnosis of breast masses]

Objective: To explore the value of shear wave elastography(SWE)stiff rim sign and SWE stiff rim sign combined with BI-RADS classification in qualitative diagnosis and multiple SWE parameters in quantitative diagnosis of benign and malignant breast masses. Methods: One hundred and eighty-eight patients, 18-83 (44±14) years old, with 199 breast masses (maximum diameter, 0.4-5.0 (2.1±1.0) cm) by ultrasound were selected.Qualitative diagnosis was made by SWE stiff rim sign, and SWEmax, SWEmean, SWEmin, SWE1max, SWE2max, SWE3max, SWE1mean, SWE2mean, SWE3mean were obtained. The ROC of each quantitative parameter was drawn, then the AUC was calculated. Results: There were 75 malignant masses and 124 benign masses in 199 breast masses confirmed by pathology. Qualitative diagnosis of BI-RADS classification (χ(2)=155.181) and of SWE stiff rim sign (χ(2)=117.304)and quantitative diagnosis of SWEmax, SWEmean (t=6.869,6.305), SWE1max, SWE2max, SWE3max (t=8.768,9.059,9.180), SWE1mean, SWE2mean, SWE3mean (t=10.041,10.312,10.576) were all statistically significant (all P<0.01). But there was no statistically significance in quantitative diagnosis of SWEmin (P>0.05). The AUC value of qualitative diagnosis of SWE stiff rim sign combined with BI-RADS classification was 0.967, and the sensitivity was 92.0%.For BI-RADS 4a masses,the positive rate of puncture could be increased from 15.3% to 77.8% by combination of SWE hard ring sign. Conclusions: Qualitative diagnosis of SWE stiff rim sign and quantitative diagnosis of multiple SWE parameters are of high accuracy in differentiating benign or malignant breast masses. The combination of SWE stiff rim sign and BI-RADS classification could further improve the sensitivity of qualitative diagnosis, and increase the positive rate of puncture for 4a masses.

pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

As the de facto validation method in mass spectrometry-based proteomics, the target-decoy approach determines a threshold to estimate the false discovery rate and then filters those identifications beyond the threshold. However, the incorrect identifications within the threshold are still unknown and further validation methods are needed. In this study, we characterized a framework of validation and investigated a number of common and novel validation methods. We first defined the accuracy of a validation method by its false-positive rate (FPR) and false-negative rate (FNR) and, further, proved that a validation method with lower FPR and FNR led to identifications with higher sensitivity and precision. Then we proposed a validation method named pValid that incorporated an open database search and a theoretical spectrum prediction strategy via a machine-learning technology. pValid was compared with four common validation methods as well as a synthetic peptide validation method. Tests on three benchmark data sets indicated that pValid had an FPR of 0.03% and an FNR of 1.79% on average, both superior to the other four common validation methods. Tests on a synthetic peptide data set also indicated that the FPR and FNR of pValid were better than those of the synthetic peptide validation method. Tests on a large-scale human proteome data set indicated that pValid successfully flagged the highest number of incorrect identifications among all five methods. Further considering its cost-effectiveness, pValid has the potential to be a feasible validation tool for peptide identification.

[Correlation between single nucleotide polymorphisms of rs4778137 located in OCA2 gene and clinical response of breast cancer patients receiving neoadjuvant chemotherapy]

Objective: To evaluate the correlation between single nucleotide polymorphisms (SNPs) of rs4778137 located in OCA2 gene and clinical response of breast cancer patients receiving neoadjuvant chemotherapy. Methods: A total of 140 breast cancer patients receiving neoadjuvant chemotherapy were enrolled to detect DNA in blood sample by DNA extraction kit and the rs4778137 polymorphism by sequenom. The relationship between SNPs of rs4778137 and pathologic complete response (pCR) were analyzed. Results: The frequency of CC, GC and GG genetype of rs4778137 was 48.6%, 31.4% and 20.0%,respectively. Thirty cases (21.4%) achieved pCR with CC allele in 9 cases(13.2%),GC allele in 10 cases (22.7%) and GG allele in 11 cases (39.3%),respectively,with a statistically significant difference(P<0.05). When conducting stratified analysis in accordance with the estrogen receptor (ER) status,only in ER negative group pCR was significantly associated with SNPs of rs4778137 (P<0.05). SNPs of Rs4778137, targeted therapy,subtypes,tumor stage were independent predictors of pCR in multivariate logistic regression analysis (P<0.05),and SNPs of rs4778137 was an independent predictors of pCR in ER negative group (P<0.05), but not in ER positive group group (P>0.05). Conclusion: SNPs of rs4778137 was associated with pCR only in ER negative patients receiving neoadjuvant therapy, and breast cancer patients with the GG allele were more likely to achieve pCR.

Plasma levels of IL-1Ra are associated with schizophrenia

AIM

Although peripheral low-grade inflammation and brain-derived neurotrophic factor (BDNF) levels have been implicated in schizophrenia (SCZ), the interactions between them remain to be fully revealed. We aimed to compare BDNF and cytokines in patients with SCZ and healthy controls (HC). Additionally, we aimed to investigate the association between peripheral levels of cytokines and BDNF in patients with SCZ.

METHODS

Plasma levels of BDNF, interferon gamma, interleukin (IL)-10, IL-12, IL-1, IL-6, IL-8, tumor necrosis factor alpha, macrophage migration inhibitory factor, IL-1 receptor antagonist (IL-1Ra), and CD40 Ligand were compared in 45 SCZ patients and 38 HC using Luminex technology.

RESULTS

Compared to HC, patients had significantly higher IL-1Ra levels (P = 0.031). We found a strong positive association between BDNF and CD40 Ligand in the patient group (rho = 0.858, P < 0.001) as well as in the HC group (rho = 0.822, P < 0.001), respectively. Furthermore, there was a negative association between BDNF and tumor necrosis factor alpha in patients (rho = -0.429, P = 0.030) as well as in HC (rho = -0.649, P < 0.001).

CONCLUSION

These results suggest that the cytokine IL-1Ra may play a role in SCZ pathophysiology. Additionally, the interaction between cytokines and BDNF levels further indicated the diverse actions of these cytokines.

[Retraction Note: Association of Gene Polymorphisms in Wnt Signal Pathway with Tuberculosis in Chinese Tibetan Population.2016,47(6):920-925.]

This corrects the article DOI: 10.13464/j.scuxbyxb.2016.06.021.

[Methylation Chip Screening and Verification of Differential Genes Related to Tuberculosis Infection]

OBJECTIVE

To screen the genes with significant changes in DNA methylation level in active tuberculosis patients, we used the methylation chips and expanded the sample size to verify candidate genes.

METHODS

① This study enrolled 9 cases of active tuberculosis patients, 3 cases of latent tuberculosis patients and 3 cases of healthy controls whose age and gender were all matched. Genome DNA was extracted from peripheral blood mononuclear cell in blood samples collected from these candidates, and bisulfite conversion treatment was then conducted. After hybridization with the Illumina HD 450K Infinium Mehtylation BeadChip, the results were compared between patients group and control group, and GO and KEGG pathway analyses were performed to evaluate the function of differentially expressed genes. ② We further enrolled 60 cases of active tuberculosis patients and 60 cases of health controls (age-and gender-matched), DNA was extracted from their peripheral blood and also followed bisulfite conversion treatment. Pyrosequencing method was used to detect the methylation levels of candidate genes (IFNGR2, PTPN6, CRK1, ATP6V0B, WIF1, DKK1 and SFRP1) screened by gene chip.

RESULTS

Compared with healthy controls, the fragments in the patients that showed low methylation change accounted for the vast majority. Most of the methylation differential fragments (DMRs) were located in the main body region, followed by the upstream region of transcription initiation site, and the lowest DMRs distribution area was 3´UTR area. GO and Pathway analysis showed that the functions of the differentially methylated regions related genes are mainly enriched in the biological processes of the regulation of leukocyte differentiation, apoptosis, cytokine regulation and inflammatory response which are closely related to tuberculosis. There were 32 CpG sites involved in the verified 7 tuberculosis related genes, and 16 CpG locus showed significant difference (P<0.05), they were distributed in 6 genes: PTPN6, WIF1, CRK1, SFRP1, DKK1 and IFNGR2.Of these genes with significant difference, PTPN6 genes showed hypermethylation status and WIF1, CRK1, SFRP1, DKK1 and IFNGR2 genes exhibited demethylation status in the patients group compared to the health controls. SFRP1 and CRK-1 mRNA up-regulated in the patients group compared with health controls.

CONCLUSION

In the course of MTB infection, the methylation status of genomic DNA is altered, and most of the differentially methylated regions (DMRs) are showed status of demethylation. The expressions ofSFRP1and CRK-1gene up-regulate in tuberculosis infection.

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an ultra-large search space that includes coeluting peptides, unexpected modifications and digestions. Our method detects peptides with higher precision and speed than seven other search engines. Open-pFind identified 70-85% of the tandem mass spectra in four large-scale datasets and 14,064 proteins, each supported by at least two protein-unique peptides, in a human proteome dataset.

[The transformation of microcystin-LR during tap water treatment process and analysis of its degradation products]

Objective: To establish a liquid chromatography-tandem mass spectrometry (LC/MS/MS) method for the determination of microcystin-LR (MC-LR) in drinking water, investigate its removal efficiency during tap water advanced treatment process and analyze its degradation products in the tap water. Methods: Two parallel water samples were collected from each point of tap water advanced treatment process in September 2015, November 2015 and January 2016, respectively, and treated by mixing, filtration, concentration, elution, nitrogen blow and re-dissolvement. The samples were analyzed by LC/MS/MS to determine the MC-LR concentration and its removal efficiency during treatment process. The combination of actual water enrichment (including source water enrichment of 50 times and 1 500 times concentrated, finished water enrichment of 50 times and 2 500 times concentrated) and laboratory simulated water (including the mixture of MC-LR and liquid chlorine in the mass ratio of 1∶10, 1∶20, 1∶100 and 1∶1 000, respectively) were used to qualitative analyze the MC-LR degradation products by Orbitrap mass spectrometry. Results: The linearity of MC-LR ranged from 2 to 200 μg/L with the detection limit of 0.007 9 μg/L and the limit of quantification of 0.026 3 μg/L. The recovery rate of MC-LR from different contration in drinking water were from 94.88%-101.47%. The intra-day precision was 2.51%-7.93% and the intra-day precision was 3.24%-8.41%. The average concentration of MC-LR in source water was (0.631±0.262) μg/L, 94.0% of which can be removed by ozone exposure while the concentrate was (0.038±0.016) μg/L, biological pre-treatment and chlorination. The remaining can hardly be removed by sand filtration, ozone exposure, activated carbon, ultrafiltration and other processes. The MC-LR average concentration in the finished water maintained at about (0.036±0.016) μg/L. Degradation products including hydroxy-microcystin, methyl-hydroxy-microcystin, methyl-microcystin were identified in the laboratory simulated water of the mixture of MC-LR and liquid chlorine in the mass ratio of 1∶10. Conclusion: The established MC-LR detection method can be well applied to the monitoring of MC-LR in drinking water due to its simple pre-treatment process and good methodological validation parameters. The degradation products of treatment processes was different.