PySNV for complex intra-host variation detection.

MOTIVATION: Intra-host variants refer to genetic variations or mutations that occur within an individual host organism. These variants are typically studied in the context of viruses, bacteria, or other pathogens to understand the evolution of pathogens. Moreover, intra-host variants are also explored in the field of tumor biology and mitochondrial biology to characterize somatic mutations and inherited heteroplasmic mutations. Intra-host variants can involve long insertions, deletions, and combinations of different mutation types, which poses challenges in their identification. The performance of current methods in detecting of complex intra-host variants is unknown. RESULTS: First, we simulated a dataset comprising 10 samples with 1869 intra-host variants involving various mutation patterns and benchmarked current variant detection software. The results indicated that though current software can detect most variants with F1-scores between 0.76 and 0.97, their performance in detecting long indels and low frequency variants was limited. Thus, we developed a new software, PySNV, for the detection of complex intra-host variations. On the simulated dataset, PySNV successfully detected 1863 variant cases (F1-score: 0.99) and exhibited the highest Pearson correlation coefficient (PCC: 0.99) to the ground truth in predicting variant frequencies. The results demonstrated that PySNV delivered promising performance even for long indels and low frequency variants, while maintaining computational speed comparable to other methods. Finally, we tested its performance on SARS-CoV-2 replicate sequencing data and found that it reported 21% more variants compared to LoFreq, the best-performing benchmarked software, while showing higher consistency (62% over 54%) within replicates. The discrepancies mostly exist in low-depth regions and low frequency variants. AVAILABILITY AND IMPLEMENTATION: https://github.com/bnuLyndon/PySNV/.

Machine learning evaluation of LV outflow obstruction in hypertrophic cardiomyopathy using three-chamber cardiovascular magnetic resonance.

Left ventricular outflow tract obstruction (LVOTO) is common in hypertrophic cardiomyopathy (HCM), but relationships between anatomical metrics and obstruction are poorly understood. We aimed to develop machine learning methods to evaluate LVOTO in HCM patients and quantify relationships between anatomical metrics and obstruction. This retrospective analysis of 1905 participants of the HCM Registry quantified 11 anatomical metrics derived from 14 landmarks automatically detected on the three-chamber long axis cine CMR images. Linear and logistic regression was used to quantify strengths of relationships with the presence of LVOTO (defined by resting Doppler pressure drop of > 30 mmHg), using the area under the receiver operating characteristic (AUC). Intraclass correlation coefficients between the network predictions and three independent observers showed similar agreement to that between observers. The distance from anterior mitral valve leaflet tip to basal septum (AML-BS) was most highly correlated with Doppler pressure drop (R2 = 0.19, p < 10-5). Multivariate stepwise regression found the best predictive model included AML-BS, AML length to aortic valve diameter ratio, AML length to LV width ratio, and midventricular septal thickness metrics (AUC 0.84). Excluding AML-BS, metrics grouped according to septal hypertrophy, LV geometry, and AML anatomy each had similar associations with LVOTO (AUC 0.71, 0.71, 0.68 respectively, p = ns), significantly less than their combination (AUC 0.77, p < 0.05 for each). Anatomical metrics derived from a standard three-chamber CMR cine acquisition can be used to highlight risk of LVOTO, and suggest further investigation if necessary. A combination of geometric factors is required to provide the best risk prediction.

[Treatment of sciatica by lumbar nerve root canal injection under X-ray angiography].

OBJECTIVE: To investigate the short-term clinical effect of lumbar nerve root canal injection under X-ray angiography in the treatment of sciatica. METHODS: The clincal data of 78 patients with sciatica underwent lumbar nerve root canal injection under X-ray angiography from December 2017 to February 2020 was retrospectively analyzed. Including 31 males and 47 females, aged from 22 to 88 years old with a median of 65 years. There were 55 cases of lumbar disc herniation and 23 cases of lumbar spinal stenosis, the course of disease ranged from 1 to 8 weeks with a median of 3 weeks. There were 71 cases of single segment disc herniation or stenosis, including L3,4 of 5 cases, L4,5 of 61 cases, L5S1 of 5 cases, and 7 cases of multisegment herniation or stenosis. The pain visual analogue scale (VAS) was recorded and Macnab was used to evaluate the clinical effect. RESULTS: All patients completed standardized treatment without serious adverse reactions. VAS were (3.21±0.76) scores immediately after treatment, (2.89±0.33) scores 1 hour after treatment, (1.80±0.27) scores 6 hours after treatment, (1.10±0.20) scores 24 hours after treatment, (2.53±0.35) scores 1 week after treatment and (4.27±0.36) scores 1 month after treatment. There were significant differences in VAS between before treatment(7.83±0.56) and each time period after treatment(P<0.05). According to Macnab low back pain evaluation standard, 42 cases were effective, 34 cases were markedly effective and 2 cases were ineffective within 24 hours after treatment, with an effective rate of 97.4%;38 cases were effective, 25 cases were markedly effective, 15 cases were ineffective within one week after treatment, the effective rate was 80.0%;32 cases were effective, 22 cases were markedly effective, 24 cases were ineffective within one month after treatment, the effective rate was 69.2%. CONCLUSION: The short-term clinical effect of nerve root canal injection under X-ray radiography in the treatment of sciatica is good and it is an effective method to relieve sciatica.

Preoperative Modic changes are related to axial symptoms after anterior cervical discectomy and fusion.

BACKGROUND: The objective of this study was to compare the clinical and radiological outcomes between patients with or without axial symptoms (AS) and investigate the risk factors associated with AS by multivariate regression analysis in anterior cervical discectomy and fusion (ACDF). MATERIALS AND METHODS: The records of 117 patients who underwent ACDF were reviewed for clinical and radiological outcomes. These outcomes were evaluated before and after surgery and at the last follow-up. Preoperative Modic changes (MCs) adjacent to the treated disc were identified. Risk factors for AS were detected through logistic regression analysis. RESULTS: The patients were divided into two groups: one with AS (AS group, n=35) and the other without (NAS group, n=82). Visual Analog Scale values after the operation (P=0.013) and at final follow-up (P<0.001) and preoperative segmental angle (P=0.031) were significantly different between the two groups. There were no significant differences with respect to other clinical and radiographic outcomes between the two groups (P>0.05). Logistic regression analysis revealed that preoperative segmental kyphosis (OR =2.912, P=0.035) and MCs (odds ratio =3.268, P=0.015) were the risk factors for the occurrence of AS. CONCLUSION: AS do not correlate with recovery of neural function in patients treated by ACDF. In addition, preoperative segmental kyphosis and MCs at the fusion segment were found to affect the incidence of AS after ACDF.

miR-342-3p promotes osteogenic differentiation via targeting ATF3.

Through their multiple targets, microRNAs (miRNAs) are involved in numerous physiological and pathological processes. In this study, miR-342-3p was found to be deregulated with ossification of ligament or osteoporosis. We demonstrate that silencing miR-342-3p impairs osteoblast activity and matrix mineralization, while over expression of miR-342-3p promotes osteoblast differentiation significantly. Moreover, miR-342-3p directly targets activating transcription factor 3 (ATF3), which inhibits transcription of pro-osteogenic differentiation-associated genes. In addition, there exists a higher frequency of methylation at the CpG island of the Enah/Vasp-Like (EVL) locus in undifferentiated pre-osteoblasts; however, demethylation of the EVL CpG island induces over expression of miR-342-3p during osteogenic differentiation. This study suggests that miR-342-3p may serves as a potential marker for diagnosis and treatment of ossification of ligament and osteoporosis.

A Transcriptome-Level Study Identifies Changing Expression Profiles for Ossification of the Ligamentum Flavum of the Spine.

Ossification of the ligamentum flavum (OLF) is a common spinal disorder that causes myelopathy and radiculopathy. Non-coding RNAs (ncRNAs) are involved in numerous pathological processes; however, very few ncRNAs have been identified to be correlated with OLF. Here we compared the expression of lncRNA, mRNA, circRNA, and microRNA in OLF tissues from OLF patients and healthy volunteers through mRNA, lncRNA, and circRNA microarrays and microRNA sequencing. A total of 2,054 mRNAs, 2,567 lncRNAs, 627 circRNAs, and 28 microRNAs (miRNAs) were altered during the process of OLF. qPCR confirmed the differential expression of selected mRNAs and ncRNAs. An lncRNA-mRNA co-expression network, miRNA-mRNA target prediction network, and competing endogenous RNA (ceRNA) network of circRNA-miRNA-mRNA were constructed based on a correlation analysis of the differentially expressed RNA transcripts. Subsequently, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for the differentially expressed mRNAs and the predicted miRNAs target genes were performed. In addition, a deregulated miRNA-19b-3p-based miRNA-circRNA-lncRNA-mRNA network was confirmed, by gain-of-function and loss-of-function experiments, to function in the process of ossification. Taken together, this study provides a systematic perspective on the potential function of ncRNAs in the pathogenesis of OLF.

The analgesic effect of intravenous methylprednisolone on acute neuropathic pain with allodynia due to central cord syndrome: a retrospective study.

BACKGROUND: Central cord syndrome (CCS) may be associated with severe neuropathic pain that often resists to conventional pain therapy regimens and affects the patients' quality of life (QoL) seriously. Current treatments for CCS-associated neuropathic pain have limited evidence of efficacy. This retrospective study was performed to present the effects of early treatment with methylprednisolone (MP) on acute neuropathic pain relief and the QoL in CCS patients. PATIENTS AND METHODS: Data were collected from the medical records of CCS patients who suffered from acute neuropathic pain with allodynia. All the patients received intravenous MP treatment for up to 1 week. Patients were evaluated with standard measures of efficacy: neuropathic pain intensity, the area of allodynia, and the QoL at baseline, daily treatment, and at 1 and 3 months after the end of MP treatment. RESULTS: Thirty-four eligible patients were enrolled in our study. By the end of MP treatment, the proportion of patients who gained total or major (visual analog scale [VAS] score decreased by 50% or more) allodynia relief from the treatment was 91.18%, and a decrease in spontaneous pain was also observed. Moreover, this study showed MP could significantly improve the QoL of patients based on McGill Pain Questionnaire Short Form and EuroQol Five Dimensions Questionnaire. Four patients (11.76%) during MP treatment experienced mild or moderate side effects. None of the patients manifested CCS-associated neuropathic pain recurrence and MP-associated side effects at follow-up. CONCLUSION: The current results suggested that MP offered an effective therapeutic alternative for relieving CCS-associated acute neuropathic pain with allodynia. Given the encouraging results of this study, it would be worthwhile to confirm these results in randomized placebo-controlled clinical trials.

Clinical efficacy of calcitonin compared to diclofenac sodium in chronic nonspecific low back pain with type I Modic changes: a retrospective study.

BACKGROUND: The objective of this study was to compare the efficacy of calcitonin with diclofenac sodium in the treatment of patients with nonspecific low back pain (LBP) and type I Modic changes (MC1). PATIENTS AND METHODS: The study was a retrospective observational study with 109 patients who had nonspecific LBP and MC1 that appeared as bone marrow lesions on magnetic resonance imaging (MRI). Between October 2013 and March 2016, 62 patients were injected intramuscularly with calcitonin 50 IU once daily and 47 patients were treated with diclofenac 75 mg once per day for 4 weeks for the treatment of LBP associated with MC1 on MRI. Visual analog scale (VAS) (0-10) and Oswestry Disability Index (ODI) (0-100) questionnaires were acquired from clinical records to evaluate LBP perception and degree of disability. Imaging data were also collected before and after treatment. RESULTS: Significant improvements were found in VAS and ODI at posttreatment compared with baseline in both groups (P < 0.05). Meanwhile, there was a significant difference between calcitonin group and diclofenac group at both 4 weeks and 3 months of follow-up (4 weeks: VAS 4.46 ± 1.58 vs 5.08 ± 1.50, ODI 20.32 ± 9.64 vs 24.35 ± 7.95; 3 months: VAS 3.70 ± 1.74 vs 4.51 ± 1.67, ODI 16.67 ± 9.04 vs 21.18 ± 9.56; P < 0.05 for all). Moreover, the proportion of patients with a significant change in LBP scales was higher in the calcitonin group (4 weeks: VAS 50.00% vs 23.40%, ODI 54.83% vs 25.53%; 3 months: VAS 58.06% vs 38.29%, ODI 59.67% vs 38.29%; P < 0.05 for all). According to MRI, 43.54% patients in the calcitonin group showed improvement compared with 21.27% patients in the diclofenac group (P < 0.05). CONCLUSION: There was greater short-term efficacy of calcitonin compared with diclofenac in patients with LBP and MC1 on MRI.

Association between PPAP2B gene polymorphisms and coronary heart disease susceptibility in Chinese Han males and females.

Little is known about gender-related differences in the association between PPAP2B single nucleotide polymorphisms (SNPs) and coronary heart disease (CHD) in Chinese Han males and females. We therefore conducted a case-control study with 456 cases and 685 healthy controls divided into male and female subgroups. Five PPAP2B polymorphisms (SNPs) were selected and genotyped using Sequenom Mass-ARRAY technology. Odds ratios (OR) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression adjusting for age and gender. Allelic model analysis revealed that for PPAP2B rs1759752, allele frequency distributions differed between cases and controls in the male subgroup (p = 0.015, OR: 1.401, 95%CI: 1.066-1.481). Genetic model analysis revealed that in the male subgroup, rs1759752 was associated with increased CHD risk in the dominant model (p = 0.035) and overdominant model (p = 0.045). In the female subgroup, rs12566304 was associated with a decreased CHD risk in the codominant model (p = 0.038) and overdominant model (p = 0.031). Additionally, the "GC" haplotypes of rs1759752 and rs1930760 were protective against CHD in males. These observations shed new light on gender-related differences in the association between PPAP2B gene polymorphisms and CHD susceptibility in the Chinese Han population.

Increasing gap junction coupling suppresses ibutilide-induced torsades de pointes.

Drug-induced torsades de pointes (TdP) is common with class III antiarrhythmic drugs. Increased transmural dispersion of repolarization (TDR) contributes significantly to the development of TdP. Gap junctions play an important role in maintaining TDR in long QT syndrome. The present study examined the effect of a gap junction enhancer, antiarrhythmic peptide 10 (AAP10), on ibutilide-induced TdP. Coronary-perfused rabbit ventricular wedge preparations were used to evaluate the effect of AAP10 on ibutilide-induced arrhythmia. Transmural electrocardiograms and action potentials were recorded simultaneously. Early afterdepolarizations (EADs), R-on-T extrasystole, TdP and changes in Tpeak-end (Tp-e) and the Tp-e/QT ratio were observed. Changes in the levels of non-phosphorylated connexin 43 (Cx43) were measured by immunoblotting. Compared with those in the control group, the QT interval, Tp-e/QT and incidence rates of EAD and TdP increased with augmented dephosphorylation in the ventricular wedge preparations perfused with ibutilide under conditions of hypokalemia and hypomagnesemia. In the presence of AAP10, the incidence rates of EAD and TdP were reduced and the Tp-e/QT ratio decreased, with a parallel reduction in the level of non-phosphorylated Cx43. The results indicate that AAP10 suppressed ibutilide-induced TdP under conditions of hypokalemia and hypomagnesemia by decreasing TDR. AAP10 reduced TDR, possibly by preventing the dephosphorylation of Cx43 and thereby increasing myocardial cell gap junction coupling.

[Effect of antiarrhythmic peptide on ventricular arrhythmia induced by lysophosphatidic acid].

OBJECTIVE: To investigate the effect and potential mechanism of lysophosphatidic acid (LPA) and antiarrhythmic peptide (AAP10) on rabbit ventricular arrhythmia. METHODS: Twenty-four rabbits were randomly divided into three groups (n = 8 each): control group, LPA group and AAP10 + LPA group. Using arterially perfused rabbit ventricular wedge preparations, transmural ECG and action potentials from both endocardium and epicardium were simultaneously recorded in the whole process of all experiments with two separate floating microeletrodes. The incidence of ventricular arrhythmia post S1S2 stimulation was recorded. Protein levels of nonphosphorylated Cx43 and total Cx43 were evaluated by Western blot. The distribution of nonphosphorylated Cx43 was observed by confocal immunofluorescence microscopy. RESULTS: Compared with the control group, the QT interval, endocardial action potential duration, transmural repolarization dispersion (TDR) and incidence of ventricular arrhythmia were significantly increased and nonphosphorylated Cx43 expression was significantly upregulated in the LPA group. Compared with the LPA group, cotreatment with AAP10 can reduce the QT interval, endocardial action potential duration, TDR and incidence of ventricular arrhythmia (25.0% vs 62.5%, P < 0.01) and downregulate nonphosphorylated Cx43. CONCLUSIONS: LPA could promote the arrhythmia possibly by upregulating nonphosphorylated Cx43 and subsequent gap junction transmission inhibition. Gap junction enhancer AAP10 could attenuate the pro-arrhythmic effect of LPA probably by downregulating myocardial nonphosphorylated Cx43 expression.

Gap junctions enhancer combined with Vaughan Williams class III antiarrhythmic drugs, a promising antiarrhythmic method?

Arrhythmias is one of the leading causes of death in the world. Current antiarrhythmic drugs are limited by unsatisfactory efficacy and adverse effects such as proarrhythmias. Reentry mechanism plays an important role in persistence of arrhythmias. Reentry can only continue when reentry path-length is longer than cardiac wavelength which is equal to the product of conduction velocity (CV) and effective refractory period (ERP). Gap junctions uncoupling is associated with proarrhythmic CV slowing and transmural dispersion of repolarization (TDR) increasing in many cardiac diseases. Vaughan Williams class III antiarrhythmic drugs prolong ERP with an augmented TDR which is the main mechanism of the proarrhythmic effects. Gap junctions enhancer can augment CV and diminish TDR. As a result, gap junctions enhancer combined with class III drugs may be a promising antiarrhythmic method.

[Effects of combined amiodarone and antiarrhythmic peptide use on the cardiac gap junctions and incidence of induced ventricular arrhythmias in healed myocardial infarction rabbit models].

OBJECTIVE: The aim of this study is to observe the effect of combined amiodarone and antiarrhythmic peptide (AAP10) use on the incidence of induced ventricular arrhythmias in healed myocardial infarction (MI) rabbits. METHODS: Twenty Japanese rabbits underwent thoracotomy without coronary artery ligation (Sham, group A), the middle left circumflex branch were ligated to induce MI in 180 Japanese rabbits. Eight weeks after operation, 124 rabbits survived MI operation and were divided into four groups: control group (group B, n = 31), amiodarone group (group C, n = 31), AAP10 group (group D, n = 31) and amiodarone plus AAP10 group (group E, n = 31). The A and B and D groups were treated with saline 2 ml/d, the C and E groups were treated with 2 ml saline containing amiodarone 100 mg×kg(-1)×d(-1). All rabbits were examined by echocardiogram at 12 weeks after operation, then anesthetized by sodium barbital, the left wedge ventricular preparations were cannulated and artery perfused by Tyrode's solution in vitro in the absence (Group A, B and C) and presence of AAP10 (500 nmol/L, Group D and E). The volume electrocardiogram, QT Interval, QRS interval, effective refractory period (ERP), the T-peak to T-end interval (T(p-e)), and ventricular tachycardia episodes induced by programmed stimulation were recorded. The T(p-e)/QT ratio was calculated. After perfusion, gap junctions protein connexin 43 (Cx43) expression was detected by Western blot and immunofluorescence. RESULTS: The incidence of induced ventricular tachycardia episodes of group A, B, C, D, E was 0, 62.5%, 26.9%, 40.0%, 22.2% respectively. The incidence of induced ventricular tachycardia episodes of group E was less than group B. The T(p-e)/QT ratio in group B, C, D were greater than in group A. The T(p-e)/QT ratio of group E was less than group B. The myocardial Cx43 in the group B was down-regulated and disorganized compared to group A, up-regulated in group C and E compared to group B, up-regulated in group E compared to group D. The Cx43 in the heart of group D and E were well organized than in group B and C. CONCLUSIONS: The artery perfused rabbits wedge preparations with healed myocardial infarction with high incidence of induced ventricular tachycardia episodes are good platform for ventricular arrhythmias research. Combined amiodarone and AAP10 use could decrease the T(p-e)/QT ratio and the incidence of induced ventricular tachycardia episodes. Amiodarone and AAP10 have synergistic effects on upregulating Cx43 and preventing ventricular arrhythmias in this rabbit model of healed myocardial infarction.