Sequence variation and selection of small RNAs in domesticated rice

<p>Abstract</p> <p>Background</p> <p>Endogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined.</p> <p>Results</p> <p>A polymorphism survey of 94 small RNA loci (88 <it>MIRNAs</it>, four <it>TAS3 </it>loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 <it>MIRNAs </it>(12.5% of the investigated <it>MIRNAs</it>). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection.</p> <p>Conclusions</p> <p>Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.</p

Auto-correlative weak-value amplification under strong noise background

In the general optical metro-logical protocols based on the weak-value amplification(WVA) approach, it is beneficial to choose the pre-selected state and the post-selected one to be nearly orthogonal for improving the sensitivity. However, the orthogonality of the post-selection decreases the probability of detecting photons and makes the weak measurement difficult, especially when there is strong noise background and the pointer is drowned in noise. In this article, we investigate a modified weak measurement protocol with a temporal pointer, namely, the auto-correlative weak-value amplification (AWVA) approach. We find it can significantly improve the precision of optical metrology under Gaussian white noise, especially with a negative signal-to-noise ratio. With the AWVA approach, a small longitudinal time delay (tiny phase shift) $\tau$ of a Gaussian pulse is measured by implementing two auto-correlative weak measurements. The small quantities are obtained by measuring the auto-correlation coefficient of the pulses instead of fitting the shift of the mean value of the probe. Simulation results show that the AWVA approach outperforms the standard WVA technique in the time domain, remarkably increasing the precision of weak measurement under strong noise background.Comment: 15 pages, 10 figure

Survival after alcohol septal ablation versus conservative therapy in obstructive hypertrophic cardiomyopathy

Background: The impact of alcohol septal ablation (ASA) on the survival of patients with drug-refractory obstructive hypertrophic cardiomyopathy (HCM) remains unresolved. The aim of this study was to compare survival after ASA vs. conservative therapy. Methods: We studied a consecutive cohort of 274 patients with severe drug-refractory obstructive HCM, 229 in ASA group and 45 in conservative group. The primary endpoint was a composite of all-cause mortality and aborted cardiac arrest. Results: With a median follow-up of 4.3 years, primary endpoint occurred in 13 (5.7%) patients in the ASA group, and 8 (17.8%) patients in the conservative group. The 5- and 10-year survival free from primary endpoint of the ASA group (94.5% and 93.0%, respectively) was significantly better than that of the conservative group (78.3% and 72.2%, respectively, log-rank p = 0.009). Independent determinants of primary endpoint were ASA therapy (hazard ratio [HR] 0.22; 95% confidence interval [CI] 0.08–0.60; p = 0.003) and maximal septal thickness (HR 1.14; 95% CI 1.03–1.27; p = 0.011). Conclusions: In patients with severe drug-refractory obstructive HCM, survival after ASA is favorable and better than that of conservative therapy. ASA seems to improve survival

Analysis of the influencing factors of interface operation in femtosecond laser assisted cataract surgery

AIM: To discuss the influencing factors of interface operation in femtosecond laser assisted cataract surgery(FLACS). METHODS: From March 2016 to October 2017, 44 patients(44 eyes)were enrolled in this study who had adverse cases occurred in interface operation in femtosecond laser assisted cataract surgery. A questionnaire survey was conducted to find out the relevant factors. RESULTS: The patient's emotion, comfort and external environment can influence the process and safety of interface operation in femtosecond laser assisted cataract surgery. The positive detection rate of patients with state anxiety was 73%, with mild and moderate status anxiety, among which there was no statistical difference between male and female state(P>0.05). The patient's comfort level was 89% and the satisfaction rate was 96%. CONCLUSION: The emotional, comfort, and environmental factors of patients in femtosecond laser assisted cataract surgery may affect the process and safety of interface operations, effective nursing and management measures can be implemented to improve patient surgical coordination and comfort, and reduce intraoperative complications

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

BACKGROUND: Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of S. flexneri genomes further, we have sequenced the complete genome of S. flexneri 5b strain 8401 (abbreviated Sf8401) and compared it with S. flexneri 2a (Sf301). RESULTS: The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI). Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS). There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the pheV locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of iut/iuc genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known Shigella genomes. CONCLUSION: Our data show that the two S. flexneri genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the S. flexneri 5b genome by recombination, but stabilized in the S. flexneri 2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of S. flexneri

Genetic Variations in Plasma Circulating DNA of HBV-Related Hepatocellular Carcinoma Patients Predict Recurrence after Liver Transplantation

BACKGROUND: Recurrence prediction of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients undergoing liver transplantation (LT) present a great challenge because of a lack of biomarkers. Genetic variations play an important role in tumor development and metastasis. METHODS: Oligonucleotide microarrays were used to evaluate the genetic characteristics of tumor DNA in 30 HBV-related HCC patients who were underwent LT. Recurrence-related single-nucleotide polymorphism were selected, and their prognostic value was assessed and validated in two independent cohorts of HCC patients (N = 102 and N = 77), using pretransplant plasma circulating DNA. Prognostic significance was assessed by Kaplan-Meier survival estimates and log-rank tests. Multivariate analyses were performed to evaluate prognosis-related factors. RESULTS: rs894151 and rs12438080 were significantly associated with recurrence (P = .003 and P = .004, respectively). Multivariate analyses demonstrated that the co-index of the 2 SNPs was an independent prognostic factor for recurrence (P = .040). Similar results were obtained in the third cohort (N = 77). Furthermore, for HCC patients (all the 3 cohorts) exceeding Milan criteria, the co-index was a prognostic factor for recurrence and survival (P<.001 and P = .002, respectively). CONCLUSIONS: Our study demonstrated first that genetic variations of rs894151 and rs12438080 in pretransplant plasma circulating DNA are promising prognostic markers for tumor recurrence in HCC patients undergoing LT and identify a subgroup of patients who, despite having HCC exceeding Milan criteria, have a low risk of post-transplant recurrence