A compression method for DNA

The development of high-throughput sequencing technology has generated huge amounts DNA data. Many general compression algorithms are not ideal for compressing DNA data, such as the LZ77 algorithm. On the basis of Nour and Sharawi's method,we propose a new, lossless and reference-free method to increase the compression performance. The original sequences are converted into eight intermediate files and six final files. Then, the LZ77 algorithm is used to compress the six final files. The results show that the compression time is decreased by 83% and the decompression time is decreased by 54% on average.The compression rate is almost the same as Nour and Sharawi's method which is the fastest method so far. What's more, our method has a wider range of application than Nour and Sharawi's method. Compared to some very advanced compression tools at present, such as XM and FCM-Mx, the time for compression in our method is much smaller, on average decreasing the time by more than 90%.

[The role of CT coronary angiography in improving the positive rate of coronary angiography in patients with low-or moderate-risk non-ST segment elevation myocardial infarction]

Objective: To investigate whether CT coronary angiography (CTA) can safely and effectively reduce the number of invasive coronary angiography (ICA) in patients with non-ST-segment elevation myocardial infarction (NSTEMI) whose Grace score is low-or moderate-risk, and increase ICA positive rate. Methods: One hundred and two NSTEMI patients, including 61 males and 41 females, aged 38-80 (58±12) years, were prospectively included and treated in Henan Provincial People's Hospital from February 2017 to February 2018. By using random number method, the patients were divided into control group (51 cases) and experimental group (51 cases). Patients in the control group were arranged for elective ICA examination according to the risk stratification. If further intervention or surgical treatment was required, the ICA examination was positive; in the experimental group, the CTA examination was completed through the green channel first. If the CTA showed that the main coronary artery and its main branches were severe or extreme stenosis, further ICA examination was arranged; otherwise, a secondary prophylactic drug treatment was developed and the patients were then discharged and followed up for 1 year. ICA number, ICA positive rate, length of hospital stay, hospital cost, hospital anxiety and depression score (HADS), major cardiovascular events (MACE) within 1 year, and other serious adverse events related to examination or surgery were compared between the two groups. Results: A total of 37 patients in the experimental group underwent ICA, and the positive rate of ICA was 94.59% (35/37), which was significantly higher than that of the control group [62.75% (32/51)] (P<0.05). The average length of hospital stay and the HADS score before ICA in the experimental group were significantly lower than those in the control group [(3.8±2.2) d vs (4.8±2.4) d; 8.8±4.5 vs 11.4±6.8] (all P<0.05). There was no significant difference in the cumulative incidence of MACE (3 cases vs 5 cases, P=0.423) and other serious adverse events (8 cases vs 10 cases, P=0.548) within 1 year between the two groups. Conclusion: CTA significantly reduces the number of ICA and the average length of hospital stay, and increases the positive rate of ICA in NSTEMI patients whose Grace score is low-or moderate-risk. There is no increase in cardiovascular risks within 1 year.

Einstein-Podolsky-Rosen Energy-Time Entanglement of Narrow-Band Biphotons

We report the direct characterization of energy-time entanglement of narrow-band biphotons produced from spontaneous four-wave mixing in cold atoms. The Stokes and anti-Stokes two-photon temporal correlation is measured by single-photon counters with nanosecond temporal resolution, and their joint spectrum is determined by using a narrow linewidth optical cavity. The energy-time entanglement is verified by the joint frequency-time uncertainty product of 0.063±0.0044, which does not only violate the separability criterion but also satisfies the continuous variable Einstein-Podolsky-Rosen steering inequality.

miR-126 suppresses neuronal apoptosis in rats after cardiopulmonary resuscitation via regulating p38MAPK

In this study, we aimed to evaluate the effect of microRNA-126 (miR-126) on neuronal apoptosis in cardiopulmonary resuscitation rats and to explore the related molecular mechanism. The expression of miR-126 in brain tissues of rats after cardiopulmonary resuscitation was measured by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR). The basic parameters of cardiopulmonary resuscitation were recorded by miR-126 mimic injection in rats after cardiopulmonary resuscitation. Hematoxylin-eosin staining was used to observe the pathological changes of hippocampus. Immunohistochemistry was used to observe the expression of p38 and caspase-3 protein. Furthermore, the expression of p38 mitogen-activated protein kinase (p38MAPK), Jun N-terminal kinase (JNK), and extracellular signal-regulated kinase 1/2 (ERK1/2) in rat hippocampus was detected by RT-qPCR and Western blot. In order to confirm whether miR-126 takes part in the p38MAPK pathway in the hippocampus of rats after cardiopulmonary resuscitation, the p38MAPK pathway inhibitor (SB203580) and activator (anisomycin) were added. The results showed overexpression of miR-126 could significantly increase the neurological function score and improve the pathological morphology of hippocampus in rats after cardiopulmonary resuscitation. miR-126 overexpression also could reduce the neuronal apoptosis, p38, and caspase-3 expression in the hippocampus. Moreover, the p38MAPK and JNK expression was downregulated and ERK1/2 expression was upregulated after miR-126 mimic injection (p < 0.05). The results of inhibition of p38MAPK pathway were consistent with those of overexpression of miR-126 (p > 0.05). This study indicated miR-126 could significantly reduce neuronal apoptosis of hippocampus in rats after cardiopulmonary resuscitation, which might be involved in the regulation of p38MAPK pathway.

Identification of E2F8 as a Transcriptional Regulator of Gluconeogenesis in Primary Mouse Hepatocytes

The dysregulation of hepatic gluconeogenesis is a major factor in the pathogenesis of type 2 diabetes mellitus (T2DM). Hepatic gluconeogenesis is known to be tightly regulated at the transcription/expression level. The aim of this study was to evaluate the role of the E2F8 transcription factor in glucose metabolism. Here, we found that hepatic expression levels of E2F8 were increased in db/db and high-fat-diet-induced obese mice. Adenovirus-mediated overexpression of E2F8 in primary mouse hepatocytes upregulated expression of gluconeogenic genes, including those for PGC-1α, PEPCK, and G6Pase, subsequently increasing cellular glucose output. We demonstrated that E2F8 overexpression impairs insulin sensitivity in vitro. Furthermore, knockdown of E2F8 expression increased insulin sensitivity in primary hepatocytes. In summary, these findings indicated that E2F8 is involved in gluconeogenesis and insulin resistance and may represent a new therapeutic target in T2DM prevention.

Final results for the neutron -asymmetry parameter A0 from the UCNA experiment

The UCNA experiment was designed to measure the neutron β-asymmetry parameter A0 using polarized ultracold neutrons (UCN). UCN produced via downscattering in solid deuterium were polarized via transport through a 7 T magnetic field, and then directed to a 1 T solenoidal electron spectrometer, where the decay electrons were detected in electron detector packages located on the two ends of the spectrometer. A value for A0 was then extracted from the asymmetry in the numbers of counts in the two detector packages. We summarize all of the results from the UCNA experiment, obtained during run periods in 2007, 2008–2009, 2010, and 2011–2013, which ultimately culminated in a 0.67% precision result for A0.

δ-Quench Measurement of a Pure Quantum-State Wave Function

The measurement of a quantum state wave function not only acts as a fundamental part in quantum physics but also plays an important role in developing practical quantum technologies. Conventional quantum state tomography has been widely used to estimate quantum wave functions, which usually requires complicated measurement techniques. The recent weak-value-based quantum measurement circumvents this resource issue but relies on an extra pointer space. Here, we theoretically propose and then experimentally demonstrate a direct and efficient measurement strategy based on a δ-quench probe: by quenching its complex probability amplitude one by one (δ quench) in the given basis, we can directly obtain the quantum wave function of a pure ensemble by projecting the quenched state onto a postselection state. We confirm its power by experimentally measuring photonic complex temporal wave functions. This new method is versatile and can find applications in quantum information science and engineering.

Anti-Parity-Time Symmetric Optical Four-Wave Mixing in Cold Atoms

Non-Hermitian optical systems with parity-time (PT) symmetry have recently revealed many intriguing prospects that outperform conservative structures. The previous works are mostly rooted in complex arrangements with controlled gain-loss interplay. Here, we demonstrate anti-PT symmetry inherent in the nonlinear optical interaction based upon forward optical four-wave mixing in a laser-cooled atomic ensemble with negligible linear gain and loss. We observe that the pair of frequency modes undergo a nontrivial anti-PT phase transition between coherent power oscillation and optical parametric amplification in presence of a large phase mismatch.

Ti n+1C n MXenes with fully saturated and thermally stable Cl terminations

MXenes are a rapidly growing family of 2D materials that exhibit a highly versatile structure and composition, allowing for significant tuning of the materials properties. These properties are, however, ultimately limited by the surface terminations, which are typically a mixture of species, including F and O that are inherent to the MXene processing. Other and robust terminations are lacking. Here, we apply high-resolution scanning transmission electron microscopy (STEM), corresponding image simulations and first-principles calculations to investigate the surface terminations on MXenes synthesized from MAX phases through Lewis acidic melts. The results show that atomic Cl terminates the synthesized MXenes, with mere residual presence of other termination species. Furthermore, in situ STEM-electron energy loss spectroscopy (EELS) heating experiments show that the Cl terminations are stable up to 750 °C. Thus, we present an attractive new termination that widely expands the MXenes' functionalization space and enables new applications.

Visualization of Protein Sorting at the Trans-Golgi Network and Endosomes Through Super-Resolution Imaging

The trans-Golgi network (TGN) and endosomes are essential protein sorting stations in the secretory transport pathway. Protein sorting is fundamentally a process of spatial segregation, but the spatial relationships among the proteins that constitute the sorting machinery have not been systematically analyzed at high resolution in mammalian cells. Here, using two-color STORM imaging, we show that the TGN/endosome-localized cargo adaptors, AP-1, GGA2 and epsinR, form elongated structures of over 250 nm in length at the juxta-nuclear Golgi area. Many of these structures are associated with clathrin. We found that AP-1 is spatially segregated from AP-3 and GGA2, whereas a fraction of AP-1 and GGA2 punctae are associated with epsinR. Moreover, we observed that the planar cell polarity cargo proteins, Vangl2 and Frizzled6 associate with different cargo adaptors—AP-1 and GGA2 or epsinR, respectively—when exiting the TGN. Knockdown analysis confirms the functional significance of this segregation. Our data indicates that TGN/endosome-localized cargo adaptors have distinct spatial relationships. The spatially segregated cargo adaptors GGA2 and AP-1 regulate sorting of Frizzled6 and Vangl2, respectively and spatially associated cargo adaptors can cooperatively regulate a specific sorting process.

Genetic polymorphisms in IL1B predict susceptibility to steroid-induced osteonecrosis of the femoral head in Chinese Han population

The purpose of this research was to examine if the IL1B gene polymorphism has impact on the risk of steroid-induced ONFH in Chinese population. We found that IL1B rs1143630 decreased the SANFH's risk and IL1B rs2853550 increased the risk of steroid-induced ONFH. So, we guess that IL1B gene influences the genetic susceptibility of steroid-induced ONFH.

INTRODUCTION

Genetic polymorphisms in IL1B gene could be related in the pathogenesis of osteonecrosis. Discusses on the relationship between the IL1B gene and steroid-induced osteonecrosis of the femoral head (steroid-induced ONFH) is still less in Chinese Han population. So, in this research, we want to examine whether the IL1B gene polymorphism has impact on the risk of steroid-induced ONFH in Chinese population.

METHODS

A total of 286 steroid-induced ONFH patients and 441 controls were recruited, and seven SNPs (rs2853550, rs1143643, rs3136558, rs1143630, rs1143627, rs16944, and rs1143623) in IL1B gene were selected; unconditional logistic regression analysis was used to research the influence on the risk of steroid-induced ONFH. Functional annotations of IL1B variants were performed by RegulomeDB and HaploReg.

RESULTS

rs1143630 (A>C) in the IL1B gene decreased the risk of steroid-induced ONFH in the allele model (OR = 0.69, 95%CI 0.51-0.93, p = 0.014). Further genetic model analyses found that IL1B rs2853550 AG genotype increased the risk of steroid-induced ONFH compared with the people who are carriers of the IL1B rs2853550 GG genotype (OR = 1.69, 95%CI 1.16-2.46, p = 0.012). In the dominant model, IL1B rs1143630 GG-GT genotype decreased the risk of steroid-induced ONFH (OR = 0.62, 95%CI 0.44-0.87, p = 0.0051). And further haplotype analysis was performed, while the result was not significant. Using RegulomeDB and HaploReg, rs2853550 is likely to affect TF binding, any motif and DNase peak.

CONCLUSIONS

We guess that IL1B gene influences the genetic susceptibility of steroid-induced ONFH.

[Biomarkers screening for viral myocarditis through proteomics analysis of plasma exosomes]

Objective: To compare and analyze the differentially expressed plasma exosomic proteome between healthy control group (Control group) and viral myocarditis group (VMC group) to search for biomarkers that maybe used for early diagnosis of VMC. Methods: Fifty plasma samples of Control group and VMC group were collected respectively from Henan Provincial People's Hospital (from January 2016 to December 2017), and then 5 samples (1 ml) of each group were selected randomly, after exosomes extraction with ultra-centrifugation, difference gel electrophoresis (DIGE) was used to isolate the total proteins, and then the protein spots with more than 2-fold changes between VMC and Control group were picked up after the software analysis, afterward, the varied proteins were identified by MALDI-TOF/TOF mass spectrometry. Finally, the specifically related protein was selected to be verified by ELISA with the plasma exosomic samples of Control (n=40) and VMC (n=40). Results: A total of 10 varied protein spots were found including 8 up-regulated proteins and 2 down-regulated proteins between VMC and Control group. After MS analysis, the up-regulated proteins in VMC group contained KRT2, KRT5, KRT9, KRT77, KRT78, AZGP1, HP and RBP4, whereas the down-regulated ones were CD5L and C1QB. RBP4 was selected to validate by ELISA analysis, and the corresponding results showed that RBP4 was increased specifically in plasma exosomes of VMC group (P<0.05) after comparing with Control group, which was consistent with DIGE. Conclusion: Ten proteins related to VMC are detected in total, and RBP4 might serve as a potential specific biomarker for early screening and diagnosis of VMC.

Intracavity cold atomic ensemble with high optical depth

We describe the apparatus of an optical cavity loaded with cold ⁸⁵Rb atoms of high optical depth (OD) in the weak coupling regime. The relevant cavity-atom parameters are the single-photon Rabi frequency g₀ = 2π × 0.25 MHz, the cavity power decay rate κ = 2π × 9.0 MHz, and the atomic excited state decay rate Γ = 2π × 5.75 MHz. In this bad-cavity configuration where the atomic natural linewidth (Γ/2π) is less than the cavity linewidth (κ/2π), the cavity enhancement factor for the longitudinal OD is about 188. We obtain a cavity enhanced OD up to 7600, corresponding to an atomic ensemble with a bare single-pass OD of 40, coupled to the cavity mode. Our intracavity cold atomic ensemble with high OD may have many applications in studying collective atom-light interaction inside an optical cavity.

TEFM Enhances Transcription Elongation by Modifying mtRNAP Pausing Dynamics

Regulation of transcription elongation is one of the key mechanisms employed to control gene expression. The single-subunit mitochondrial RNA polymerase (mtRNAP) transcribes mitochondrial genes, such as those related to ATP synthesis. We investigated how mitochondrial transcription elongation factor (TEFM) enhances mtRNAP transcription elongation using a single-molecule optical-tweezers transcription assay, which follows transcription dynamics in real time and allows the separation of pause-free elongation from transcriptional pauses. We found that TEFM enhances the stall force of mtRNAP. Although TEFM does not change the pause-free elongation rate, it enhances mtRNAP transcription elongation by reducing the frequency of long-lived pauses and shortening their durations. Furthermore, we demonstrate how mtRNAP passes through the conserved sequence block II, which is the key sequence for the switch between DNA replication and transcription in mitochondria. Our findings elucidate how both TEFM and mitochondrial genomic DNA sequences directly control the transcription elongation dynamics of mtRNAP.