Systematic identification and characterization of exon-intron circRNAs.

Exon-intron circRNAs (EIciRNAs) are a circRNA subclass with retained introns. Global features of EIciRNAs remain largely unexplored, mainly owing to the lack of bioinformatic tools. The regulation of intron retention (IR) in EIciRNAs and the associated functionality also require further investigation. We developed a framework, FEICP, which efficiently detected EIciRNAs from high-throughput sequencing (HTS) data. EIciRNAs are distinct from exonic circRNAs (EcircRNAs) in aspects such as with larger length, localization in the nucleus, high tissue specificity, and enrichment mostly in the brain. Deep learning analyses revealed that compared with regular introns, the retained introns of circRNAs (CIRs) are shorter in length, have weaker splice site strength, and have higher GC content. Compared with retained introns in linear RNAs (LIRs), CIRs are more likely to form secondary structures and show greater sequence conservation. CIRs are closer to the 5'-end, whereas LIRs are closer to the 3'-end of transcripts. EIciRNA-generating genes are more actively transcribed and associated with epigenetic marks of gene activation. Computational analyses and genome-wide CRISPR screening revealed that SRSF1 binds to CIRs and inhibits the biogenesis of most EIciRNAs. SRSF1 regulates the biogenesis of EIciLIMK1, which enhances the expression of LIMK1 in cis to boost neuronal differentiation, exemplifying EIciRNA physiological function. Overall, our study has developed the FEICP pipeline to identify EIciRNAs from HTS data, and reveals multiple features of CIRs and EIciRNAs. SRSF1 has been identified to regulate EIciRNA biogenesis. EIciRNAs and the regulation of EIciRNA biogenesis play critical roles in neuronal differentiation.

Friend or foe: role of pathological tau in neuronal death.

Neuronal death is one of the most common pathological hallmarks of diverse neurological diseases, which manifest varying degrees of cognitive or motor dysfunction. Neuronal death can be classified into multiple forms with complicated and unique regulatory signaling pathways. Tau is a key microtubule-associated protein that is predominantly expressed in neurons to stabilize microtubules under physiological conditions. In contrast, pathological tau always detaches from microtubules and is implicated in a series of neurological disorders that are characterized by irreversible neuronal death, such as necrosis, apoptosis, necroptosis, pyroptosis, ferroptosis, autophagy-dependent neuronal death and phagocytosis by microglia. However, recent studies have also revealed that pathological tau can facilitate neuron escape from acute apoptosis, delay necroptosis through its action on granulovacuolar degeneration bodies (GVBs), and facilitate iron export from neurons to block ferroptosis. In this review, we briefly describe the current understanding of how pathological tau exerts dual effects on neuronal death by acting as a double-edged sword in different neurological diseases. We propose that elucidating the mechanism by which pathological tau affects neuronal death is critical for exploring novel and precise therapeutic strategies for neurological disorders.

The P38MAPK/ATF2 signaling pathway is involved in PND in mice.

Accumulating evidence indicates that microglia-mediated neuroinflammation in the hippocampus contributes to the development of perioperative neurocognitive disorder (PND). P38MAPK, a point of convergence for different signaling processes involved in inflammation, can be activated by various stresses. This study aims to investigate the role of the P38MAPK/ATF2 signaling pathway in the development of PND in mice. Aged C57BL/6 mice were subjected to tibial fracture surgery under isoflurane anesthesia to establish a PND animal model. The open field test was used to evaluate the locomotor activity of the mice. Neurocognitive function was assessed with the Morris water maze (MWM) and fear conditioning test (FCT) on postoperative days 1, 3 and 7. The mice exhibited cognitive impairment accompanied by increased expression of proinflammatory factors (IL-1ß, TNF-α), proapoptotic molecules (caspase-3, bax) and microglial activation in the hippocampus 1, 3 and 7 days after surgery. Treatment with SB239063 (a P38MAPK inhibitor) decreased the expression of proinflammatory factors, proapoptotic molecules and Iba-1 in the CA1 region of the hippocampus. The number of surviving neurons was significantly increased. Inhibition of the P38MAPK/ATF2 signaling pathway attenuates hippocampal neuroinflammation and neuronal apoptosis in aged mice with PND, thus improving the perioperative cognitive function of the mice.

HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes.

Exonic circular RNAs (ecircRNAs) in animal cells are generated by backsplicing, and the biogenesis of ecircRNAs is regulated by an array of RNA binding proteins (RBPs). HNRNPD is a heterogeneous nuclear ribonucleoprotein family member with both cytoplasmic and nuclear roles, and whether HNRNPD regulates the biogenesis of circRNAs remains unknown. In this study, we examine the role of HNRNPD in the biogenesis of ecircRNAs. The levels of ecircRNAs are primarily increased upon depletion of HNRNPD. HNRNPD preferentially binds to motifs enriched with A and U nucleotides, and the flanking introns of ecircRNAs tend to have more numbers and higher intensity of HNRNPD binding sites. The levels of mRNAs are generally not significantly altered in HNRNPD knockout cells. For a small set of genes, the circRNA:mRNA ratio is substantially affected, and the mRNA levels of some of these genes demonstrate a significant decrease in HNRNPD knockout cells. CDK1 is identified as a key gene modulated by HNRNPD in the context of circRNA biogenesis. HNRNPD suppresses the biogenesis of circCDK1 and favours the generation of CDK1 mRNA, and the CDK1 protein is a critical regulator of the cell cycle and apoptosis. HNRNPD can participate in cellular physiology, including the cell cycle and apoptosis, and plays roles in clear cell renal cell carcinoma (ccRCC) by modulating circRNA biogenesis and the mRNA levels of key genes, such as CDK1.

Tunable underwater sound absorption characteristics of 0-3 piezoelectric anechoic coating.

Piezoelectric composite materials (PCMs) with shunt damping circuits are used widely in hydroacoustics because of the flexible adjustability of their parameters. PCMs offer good underwater sound absorption, but shortcomings remain, such as poor low-frequency sound absorption, narrow bandwidth, and a single dissipation mechanism. In this paper, the tunable underwater sound absorption of a 0-3 PCM combined with a cavity structure and shunt circuit (PCMC) is studied systematically. First, the equivalent material parameters of 0-3 PCM are derived based on the Yamada model, and then a theoretical electroacoustic model is established for solving the absorption coefficient and is mutually verified with the numerical simulation method. On this basis, the tunable absorption characteristics of the structure are analyzed. The results show that coupling the energy dissipation mechanism of 0-3 PCM with the acoustic mechanism of the cavity structure not only achieves strong absorption at lower frequencies but also enriches the absorption mode in the mid-high frequencies by connecting the shunt circuits. Moreover, the influence of piezoelectric control variables and acoustic cavity morphology characteristics on structural sound absorption performance is further explored. Finally, the acoustic performance of PCMC is improved further via shape optimization and parameter optimization.

Continuous Analysis of Critical Incidents for 92,136 Postanesthesia Care Unit Patients of a Chinese University Hospital.

PURPOSE: To determine the spectrum of critical incidents in postanesthesia care unit (PACU) and the possible prediction and prevention of the worse scenario-associated critical incidents. DESIGN: A retrospective observational study. METHODS: The critical incidents in PACU comprising 92,136 patients were recorded. The incidents included the following disorders: delayed recovery, pain, bleeding, hypothermia, unplanned transfer to intensive care unit, shivering, agitation, nausea and vomiting, and respiratory or cardiovascular-related critical incidents. We then performed descriptive analyses and t test or χ2 test on the collected data. FINDINGS: A total of 1,760 critical incidents were recorded in 1,417 patients among 92,136 patients. Most critical incidents were associated with the patients after general anesthesia and general or gynecologic surgery. The most common critical incidents noted in the present study were pain, followed by cardiovascular-related and respiratory-related incidents. The average length of stay in PACU was 61.50 ± 44.40 minutes for the patients with critical incidents and 28.50 ± 19.40 minutes for the patients without critical incidents. CONCLUSIONS: Critical incidents lead to longer length of stay in the PACU. Regular inspection and immediate response for critical incidents in the PACU is essential for the maintenance of the quality of the immediate postoperative care.

Neuroprotective effect of the traditional decoction Tian-Si-Yin against Alzheimer's disease via suppression of neuroinflammation.

ETHNOPHARMACOLOGICAL RELEVANCE: Alzheimer's disease (AD) is the most prevalent neurodegenerative disease among old adults. As a traditional Chinese medicine, the herbal decoction Tian-Si-Yin consists of Morinda officinalis How. and Cuscuta chinensis Lam., which has been widely used to nourish kidney. Interestingly, Tian-Si-Yin has also been used to treat dementia, depression and other neurological conditions. However, its therapeutic potential for neurodegenerative diseases such as AD and the underlying mechanisms remain unclear. AIM OF THE STUDY: To evaluate the therapeutic effect of the herbal formula Tian-Si-Yin against AD and to explore the underlying mechanisms. MATERIALS AND METHODS: The N2a cells treated with amyloid ß (Aß) peptide or overexpressing amyloid precursor protein (APP) were used to establish cellular models of AD. The in vivo anti-AD effects were evaluated by using Caenorhabditis elegans and 3 × Tg-AD mouse models. Tian-Si-Yin was orally administered to the mice for 8 weeks at a dose of 10, 15 or 20 mg/kg/day, respectively. Its protective role on memory deficits of mice was examined using the Morris water maze and fear conditioning tests. Network pharmacology, proteomic analysis and ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry (UHPLC-MS/MS) were used to explore the underlying molecular mechanisms, which were further investigated by Western blotting and immunohistochemistry. RESULTS: Tian-Si-Yin was shown to improve cell viability of Aß-treated N2a cells and APP-expressing N2a-APP cells. Tian-Si-Yin was also found to reduce ROS level and extend lifespan of transgenic AD-like C. elegans model. Oral administration of Tian-Si-Yin at medium dose was able to effectively rescue memory impairment in 3 × Tg mice. Tian-Si-Yin was further shown to suppress neuroinflammation by inhibition of glia cell activation and downregulation of inflammatory cytokines, diminishing tau phosphoralytion and Aß deposition in the mice. Using UHPLC-MS/MS and network pharmacology technologies, 17 phytochemicals from 68 components of Tian-Si-Yin were identified as potential anti-AD components. MAPK1, BRAF, TTR and Fyn were identified as anti-AD targets of Tian-Si-Yin from network pharmacology and mass spectrum. CONCLUSIONS: This study has established the protective effect of Tian-Si-Yin against AD and demonstrates that Tian-Si-Yin is capable of improving Aß level, tau pathology and synaptic disorder by regulating inflammatory response.

Local influence measure of zero-inflated generalized Poisson mixture regression models.

In many practical applications, count data often exhibit greater or less variability than allowed by the equality of mean and variance, referred to as overdispersion/underdispersion, and there are several reasons that may lead to the overdispersion/underdispersion such as zero inflation and mixture. Moreover, if the count data are distributed as a generalized Poisson or a negative binomial distribution that accommodates extra variation not explained by a simple Poisson or a binomial model, then the dispersion occurs too. In this paper, we deal with a class of two-component zero-inflated generalized Poisson mixture regression models to fit such data and propose a local influence measure procedure for model comparison and statistical diagnostics. At first, we formally develop a general model framework that unifies zero inflation, mixture as well as overdispersion/underdispersion simultaneously, and then we mainly investigate two types of perturbation schemes, the global and individual perturbation schemes, for perturbing various model assumptions and detecting influential observations. Also, we obtain the corresponding local influence measures. Our method is novel for count data analysis and can be used to explore these essential issues such as zero inflation, mixture, and dispersion related to zero-inflated generalized Poisson mixture models. On the basis of the results of model comparison, we could further conduct the sensitivity analysis of perturbation as well as hypothesis test with more accuracy. Finally, we employ here a simulation study and a real example to illustrate the proposed local influence measures.

A Simple Method for the Synthesis of a Coral-like Boron Nitride Micro-/Nanostructure Catalyzed by Fe.

Catalyzed by Fe, novel a coral-like boron nitride (BN) micro-/nanostructure was synthesized from B2O3 by a ball milling and annealing process. Observations of the morphology of the product indicated that the coral-like BN micro-/nanostructure consists of a bamboo-shaped nanotube stem and dense h-BN nanoflakes growing outward on the surface of the nanotube. Experimental results showed that the morphology of the BN nanotube was greatly dependent on the anneal process parameters. With the annealing time increasing from 0.5 h to 4 h, the morphology developed from smooth BN nanotubes, with a diameter size of around 100 nm, to rough, coral-like boron nitride with a large diameter of 3.6 µm. The formation mechanism of this coral-like BN micro-/nanostructure is a two-stage growth process: bamboo-shaped BN nanotubes are first generated through a vapor-liquid-solid (VLS) mechanism and then nanoflakes grow surrounding the surface of the nanotube. Acid pickling and a hydrolysis process were carried out to remove Fe, iron nitrogen and unreacted B2O3 impurities.

Biaxial tensile test and meso damage numerical simulation of HTPB propellant.

Aiming at the shortcomings of the current research on the mechanical properties of solid propellants under complex stress conditions, an effective cross-shaped test piece configuration and variable-scale biaxial tensile test method are designed in this paper, and the meso-simulation model of propellant is constructed by Micro-CT test and random filling algorithm. Then, based on the Hook-Jeeves method and the cohesive force model, the mechanical performance parameters of each mesoscopic component were obtained, and finally the damage evolution process of the propellant was numerically simulated. The results show that the stress-strain curve of the propellant under biaxial loading is similar to that of uniaxial stretching, and has obvious rate dependence and stress state dependence. The mechanical properties of the propellant under biaxial tensile loading are significantly lower than those in uniaxial stretching, and the maximum elongation is only 45-85% of that in uniaxial stretching. The fracture process of propellant can be divided into initial linear stage, damage evolution stage and fracture stage. The dewetting phenomenon generally occurs at the interface between the large-sized AP particles and the matrix. With the loading of the load, the pores formed by the dewetting and matrix tearing continue to converge into cracks and expand in the direction perpendicular to the resultant force, and finally fracture. The propellant dehumidifies more easily under high strain rate loading, but the degree of dewetting is lower when the same strain is reached.

[Cloning of y3 gene encoding a tobacco mosaic virus inhibitor from Coprinus comatus and transformation to Nicotiana tabacum].

OBJECTIVE: The protein Y3 was a TMV inhibitor which was encoded by y3 gene. The aim of this work was to clone the full length of y3 gene from Coprinus comatus and to reveal its inhibitory function to TMV in in vivo conditions. METHODS: We amplified the unknown 5'- terminal cDNA sequence of y3 gene with 5'- Full RACE Core Set (TaKaRa), obtained the full length of this gene by RT-PCR, constructed the expression plasmid pCAMBIA1301-y3 via inserting gene y3 sequence, CaMV 35 S promoter, and NOS terminator at MCS and transformed it into Nicotiana tabacum via agrobacterium-mediation. RESULTS: The full length of y3 gene was 534 bps including one ORF encoding 130 amino acid residues (GenBank Accession No. GQ859168; EMBL FN546262). The cDNA sequence and its deduced amino acid sequence showed high similarity (94%) to the published fragment of y3 gene sequence. Northern blot analysis proved the transcription of y3 gene in transgenic tobacco plants. The transgenic plants inoculated with TMV expressed the inhibitory activity to TMV. CONCLUSION: We cloned the full length of y3 gene and obtained transgenic tobacco plants. The expression of y3 gene in transgenic plants improved the inhibitory activity to TMV. The cloning and expression analysis of y3 gene might provide background information for future studying of y3 gene.

Statistical inference of risk difference in K correlated 2 x 2 tables with structural zero.

K correlated 2 x 2 tables with structural zero are commonly encountered in infectious disease studies. A hypothesis test for risk difference is considered in K independent 2 x 2 tables with structural zero in this paper. Score statistic, likelihood ratio statistic and Wald-type statistic are proposed to test the hypothesis on the basis of stratified data and pooled data. Sample size formulae are derived for controlling a pre-specified power or a pre-determined confidence interval width. Our empirical results show that score statistic and likelihood ratio statistic behave better than Wald-type statistic in terms of type I error rate and coverage probability, sample sizes based on stratified test are smaller than those based on the pooled test in the same design. A real example is used to illustrate the proposed methodologies.

Prediction of oxidoreductase subfamily classes based on RFE-SND-CC-PSSM and machine learning methods.

Oxidoreductase is an enzyme that widely exists in organisms. It plays an important role in cellular energy metabolism and biotransformation processes. Oxidoreductases have many subclasses with different functions, creating an important classification task in bioinformatics. In this paper, a dataset of 2640 oxidoreductase sequences was used to perform an analysis and comparison. The idea of dipeptides was introduced to process the Position Specific Score Matrix (PSSM), since each dipeptide consists of two amino acids and each column of PSSM corresponds to the information of one amino acid. Two kinds of dipeptide scores were proposed, the Standardization Normal Distribution PSSM (SND-PSSM) and the Correlation Coefficient PSSM (CC-PSSM). Recursive Feature Elimination (RFE) is used to extract features from the SND-PSSM and CC-PSSM, and the two sets of extracted features are combined to form a new feature matrix, the RFE-SND-CC-PSSM. The results show that, with the proposed method and a kernel-based nonlinear SVM classifier, the accuracy can reach 95.56% by the Jackknife test. Our method greatly improves the accuracy of oxidoreductase subclass prediction. Using this method to predict the categories of the 6 major types of enzymes effectively improves its prediction accuracy to 94.54%, indicating that this method has general applicability to other protein problems. The results show that our method is effective and universally applicable, and might be complementary to the existing methods.

Anesthetic management of radical nephrectomy in patients with renal cell carcinoma involving renal vein or inferior vena cava.

OBJECTIVE: To investigate the perioperative anesthetic management of patients diagnosed with renal cell carcinoma (RCC) metastasized into the renal vein or inferior vena cava (IVC) after undergoing radical nephrectomy to provide clinical evidence for rational anesthetic interventions. METHODS: A total of 81 patients with RCC extending into the renal vein or IVC, aged 17-73 years, undergoing radical nephrectomy were recruited. Preoperative status, intraoperative management, average operation time, average estimated blood loss, postanesthesia outcomes, and postoperative complications were retrospectively analyzed. RESULTS: The mean operation time was 288 minutes (range 146-825 minutes). The mean estimated blood loss was recorded as 1905 mL (range 200-7000 mL). Among 81 cases, 9 patients (11.1%, 1 level II, 3 level III, and 5 level IV) were switched to undergo cardiopulmonary bypass. Significant hemodynamic fluctuations were observed in 39 patients who presented with level II-IV of tumor thrombus. One patient had pulmonary embolism and died of active cardiopulmonary resuscitation. The mean postoperative hospital stay was 12.8 days. Twenty-five cases with level III-IV tumor thrombus were transferred to the intensive care unit with endotracheal intubation due to massive intraoperative blood loss. The remaining 55 cases were transferred to the postanesthesia care unit 2 hours before being transferred to the ward. One patient had postoperative acute coronary syndrome and was discharged after effective interventions. CONCLUSION: Anesthetic management and intensive postoperative care play a pivotal role in the success of complete resection of RCC that metastasize into the IVC.

Risk factors for acute kidney injury after orthotopic liver transplantation: A single-center data analysis.

Acute kidney injury (AKI) is a common complication following orthotopic liver transplantation (OLT) and is associated with increased morbidity and mortality. The aim of the current study was to determine the risk factors for AKI in patients undergoing OLT. A total of 103 patients who received OLT between January 2015 and May 2016 in Tongji Hospital, China, were retrospectively analyzed. Their demographic characteristics and perioperative parameters were collected, and AKI was diagnosed using 2012 Kidney Disease: Improving Global Outcomes (KDIGO) staging criteria. It was found that the incidence of AKI was 40.8% in this cohort and AKI was significantly associated with body mass index, urine volume, operation duration (especially > 480 min), and the postoperative use of vasopressors. It was concluded that relative low urine output, long operation duration, and the postoperative use of vasopressors are risk factors for AKI following OLT.

Elimination of allosteric modulation of myocardial KATP channels by ATP and protons in two Kir6.2 polymorphisms found in sudden cardiac death.

The major cause of sudden cardiac death (SCD) is ventricular arrhythmias due to unstable myocardial electrical activity in which the ATP-sensitive K+ (KATP) channels play a role. Genetic disruption of these channels predisposes the myocardium to arrhythmias. Two point mutations in the Kir6.2 subunit are found in SCD with acute myocardial infarction. Here we show evidence for the functional consequences of the P266T and R371H variants. Baseline single-channel properties, expression density, and channel modulations were studied in patch clamp. We focused on channel modulations by intracellular ATP and protons, as the concentration of these two important KATP channel regulators changes widely with hypoxic ischemia. We found that both variants expressed functional currents even though they occur at two highly conserved regions. The open state probability of P266T was twice as high as the wild-type (WT) channel, whereas its channel density was only approximately 20% of the WT channel. Although the outward current was not affected by these two mutations at neutral pH, it was approximately 20% lower at acidic pH in the P266T than in the WT channel. Both P266T and R371H mutations significantly reduced ATP sensitivity and increased pH sensitivity. More dramatically, allosteric regulation by intracellular ATP and protons was almost completely eliminated in the polymorphic P266T and R371H channels. Such an abnormality was seen in both inward and outward currents. Given the importance and beneficial effects of allosteric regulation in cellular responses to metabolic stress, the loss of such a regulatory mechanism in the P266T and R371H variants appears consistent with the adverse consequences occurring during acute myocardial infarction in patients.

Single nucleotide polymorphisms in K(ATP) channels: muscular impact on type 2 diabetes.

ATP-sensitive K+ channels (K(ATP) channels) play an important role in glucose homeostasis. A single nucleotide polymorphism (SNP) in the Kir6.2 subunit causes a point mutation of Glu23 to lysine and reduces the ATP sensitivity of pancreatic K(ATP) channels. The SNP found in 58% of Caucasians accounts for 15% of type 2 diabetes. Here we show evidence for dysregulations of muscular K(ATP) channels with the E23K variation. We were particularly interested in the channel modulation by intracellular protons, as pH changes widely and frequently in skeletal muscles. Surprisingly, we found that the defect of the E23K variant was more related to pH than ATP. A level of intracellular acidification seen during exercise not only activated the E23K channel more readily than the wild type, but also relieved the channel inhibition by ATP, leading to a vast increase in the channel open-state probability by approximately sevenfold at pH 6.8 over the wild-type channel at pH 7.4. Considering the reduction in sarcolemmal excitability, muscle fatigue, and impairment of muscular glucose uptake found previously by genetically disrupting K(ATP) channels, it is likely that the E23K variant in muscular K(ATP) channels affects systemic glucose homeostasis and poses an important risk factor for type 2 diabetes and obesity.

Hypercapnic acidosis activates KATP channels in vascular smooth muscles.

ATP-sensitive K+ channels (KATP) couple intermediary metabolism to cellular activity, and may play a role in the autoregulation of vascular tones. Such a regulation requires cellular mechanisms for sensing O2, CO2, and pH. Our recent studies have shown that the pancreatic KATP isoform (Kir6.2/SUR1) is regulated by CO2/pH. To identify the vascular KATP isoform(s) and elucidate its response to hypercapnic acidosis, we performed these studies on vascular smooth myocytes (VSMs). Whole-cell and single-channel currents were studied on VSMs acutely dissociated from mesenteric arteries and HEK293 cells expressing Kir6.1/SUR2B. Hypercapnic acidosis activated an inward rectifier current that was K+-selective and sensitive to levcromakalim and glibenclamide with unitary conductance of approximately 35pS. The maximal activation occurred at pH 6.5 to 6.8, and the current was inhibited at pH 6.2 to 5.9. The cloned Kir6.1/SUR2B channel responded to hypercapnia and intracellular acidification in an almost identical pattern to the VSM current. In situ hybridization histochemistry revealed expression of Kir6.1/SUR2B mRNAs in mesenteric arteries. Hypercapnia produced vasodilation of the isolated and perfused mesenteric arteries. Pharmacological interference of the KATP channels greatly eliminated the hypercapnic vasodilation. These results thus indicate that the Kir6.1/SUR2B channel is a critical player in the regulation of vascular tones during hypercapnic acidosis.