Identification and characterization of long non-coding RNAs as competing endogenous RNAs in the cold stress response of Triticum aestivum

Long non-coding RNAs (lncRNAs) play important roles in plant development and stress responses. MicroRNAs (miRNAs) are involved in transcriptional and post-transcriptional gene regulation. It is not clear how lncRNA-mediated plant responses to cold stress and how lncRNAs, miRNAs and target mRNAs cooperate subject to the competing endogenous RNA (ceRNA). We interpreted the function of lncRNAs in the winter wheat cultivar Dongnongdongmai 1 (Dn1). A total of 9970 putative lncRNAs were initially identified from three Dn1 lncRNA libraries (5 °C, -10 °C and -25 °C) using high-throughput sequencing. Among the 14,626 genes detected via weighted gene co-expression network analysis, 7435 lncRNAs were co-expressed with 7191 mRNAs. We found six modules related to cold resistance in the lncRNA-mRNA weighted co-expression network, and the functions of mRNAs were similar in each module. Antioxidant systems and hormones played important roles in low-temperature responses. RNA sequencing analysis revealed that interactions between the 384 lncRNAs and 70 miRNAs were required for ceRNA activity. According to ceRNA activity, 225 lncRNAs, 60 miRNAs and 621 target mRNAs were involved in the regulatory networks of the cold stress response. Notably, a conserved region was found in the complementary regions of lncRNAs and miR164/408 but had reverse expression trends in the ceRNA network. Our results reveal possible roles of lncRNAs-mRNAs in the regulatory networks associated with tolerance to low temperature and provide useful information for more strategic use of genomic resources in wheat breeding.

Reduced scaling extended multi-state CASPT2 (XMS-CASPT2) using supporting subspaces and tensor hyper-contraction

We present a reduced scaling formulation of the extended multi-state CASPT2 (XMS-CASPT2) method, which is based on our recently developed state-specific CASPT2 (SS-CASPT2) formulation using supporting subspaces and tensor hyper-contraction. By using these two techniques, the off-diagonal elements of the effective Hamiltonian can be computed with only O(N³) operations and O(N²) memory, where N is the number of basis functions. This limits the overall computational scaling to O(N⁴) operations and O(N²) memory. Thus, excited states can now be obtained at the same reduced (relative to previous algorithms) scaling we achieved for SS-CASPT2. In addition, we also investigate how the energy denominators can be factorized with the Laplace quadrature when some of the denominators are negative, which is critical for excited state calculations. An efficient implementation of the method has been developed using graphical processing units while also exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method by comparison to non-THC formulated XMS-CASPT2 for the excited states of various molecules. In our tests, the THC approximation introduces negligible errors (≈0.01 eV) compared to the non-THC reference method. Scaling behavior and computational timings are presented to demonstrate performance. The new method is also interfaced with quantum mechanics/molecular mechanics (QM/MM). In an example study of green fluorescent protein, we show how the XMS-CASPT2 potential energy surfaces and excitation energies are affected by increasing the size of the QM region up to 278 QM atoms with more than 2300 basis functions.

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

Distribution, combined pollution and risk assessment of antibiotics in typical marine aquaculture farms surrounding the Yellow Sea, North China

This study focused on the distribution, combined pollution, potential source and risk assessment of 17 antibiotics in an aquaculture ecosystem surrounding the Yellow sea, North China. Antibiotics were detected in various matrices (seawater, sediment/biofilm, organism and feed) in different aquaculture modes (greenhouse and outdoor aquaculture) during the wet and dry seasons in coastal areas of Shandong province. The innovation points of the study were as follows: (1) To the best of our knowledge, this study was one of the few to investigate the occurrence and distribution of antibiotics in mariculture environments along the Yellow Sea coast; (2) Biofilms, a focus of the study, might act as a sink for antibiotics in the aquaculture ecosystem; and (3) The correlation of heavy metals and antibiotic concentrations was proved, which could correspondingly be used as an indicator for antibiotic concentrations in the studied area. The levels of antibiotics in water were observed to be relatively low, at the ng/L level. Trimethoprim was the most prevalent antibiotic, and was detected in all water samples. Oxytetracycline was detected at high concentrations in biofilms (up to 1478.29 ng/g). Moreover, biofilms exhibited a higher antibiotic accumulation capacity compared to sediments. Concentrations of oxytetracycline and doxycycline were high in feed, while other antibiotics were almost undetected. Tetracycline was widely detected and the concentration of enrofloxacin was highest in organisms. Correlation analysis demonstrated that environmental parameters and other coexisting contaminants (e.g. heavy metals) significantly affected antibiotic concentrations. In addition, the concentration of Zn was significantly correlated with the total antibiotic concentration and was proportional to several antibiotics in water and sediment (biofilm) samples (p < 0.01). High Mn concentrations were closely related to total and individual (e.g. sulfadiazine, sulfamethazine and enrofloxacin) antibiotic levels, which may result in the combined contamination of the environment. Antibiotics in estuaries and groundwater generally originated from aquaculture wastewater and untreated/treated domestic sewage. Most of the detected antibiotics posed no risk to the environment. Ciprofloxacin and enrofloxacin found in water may present high ecological and resistance risks, while the two antibiotics observed to accumulate in fish may pose a considerable risk to human health through diet consumption. All antibiotics detected in seafood were lower than the respective maximum residue limits. This study can act as a reference for the government for the determination of antibiotic discharge standards in aquaculture wastewater and the establishment of a standardized antibiotic monitoring and management system.

Estimating the burden of lung cancer in Canada attributed to occupational radon exposure using a novel exposure assessment method

Objective

Exposure to radon causes lung cancer. The scope and impact of exposure among Canadian workers have not been assessed. Our study estimated occupational radon exposure in Canada and its associated lung cancer burden.

Methods

Exposed workers were identified among the working population during the risk exposure period (1961–2001) using data from the Canadian Census and Labour Force Survey. Exposure levels were assigned based on 12,865 workplace radon measurements for indoor workers and assumed to be 1800 mg/m³ for underground workers. Lung cancer risks were calculated using the Biological Effects of Ionizing Radiation (BEIR) VI exposure-age-concentration model. Population attributable fractions were calculated with Levin’s equation and applied to 2011 Canadian lung cancer statistics.

Results

Approximately 15.5 million Canadian workers were exposed to radon during the risk exposure period. 79% of exposed workers were exposed to radon levels < 50 Bq/m³ and 4.8% were exposed to levels > 150 Bq/m³. We estimated that 0.8% of lung cancers in Canada were attributable to occupational radon exposure, corresponding to approximately 188 incident lung cancers in 2011.

Conclusions

The lung cancer burden associated with occupational radon exposure in Canada is small, with the greatest burden occurring among those exposed to low levels of radon.

Development and validation of a nomogram to predict the risk of occult cervical lymph node metastases in cN0 squamous cell carcinoma of the tongue

We have explored the relations between clinicopathological features and cervical lymph node metastases (LNM) in patients with cN0 squamous cell carcinoma (SCC) of the tongue, and developed and validated a nomogram for predicting the risk of their development. Clinical data on 230 patients with cN0 SCC of the tongue who had had primary extended excision and lymph node dissection of the neck were collected retrospectively. They were divided into a development cohort and a validation cohort in a 4:1 ratio. Logistic regression analysis was used to assess the risk factors of cervical LNM in patients in the development cohort, and a nomogram was established to predict the risk of such nodes. In the validation cohort, the predictive performance and compliance of the model were evaluated using the consistency index (C-index) and calibration curve, and the clinical value was evaluated by decision curve analysis. Of the 230 patients, 60 had cervical LNM, of which 60 were invaded (26%). Analysis of the development cohort showed that the site of the primary lesion, depth of invasion, size of the tumour, and histopathological grade were included in the prediction model, which was validated in the validation cohort. Consistency was high (C-index=0.846), calibration good, and it was clinically valuable. The nomogram could be used to predict the probability of occult cervical LNM before operation in patients with stage cN0 SCC of the tongue. It could also be used as a reference tool for dissection of cervical nodes and a communication tool between the doctor and the patient.

[Downregulation of Herg1 suppresses osteosarcoma proliferation and invasion by targeting Hippo signaling pathway]

Objective: To detect the effect and regulatory mechanism of human ether à go-go related gene 1 (Herg 1) knockdown on the proliferation and invasion of osteosarcoma (OS). Methods: We constructed a recombinant adenovirus vector (Ad5-Herg1-shRNA) expressing short hair RNA (shRNA) against Herg1 and tested the knockdown efficiency. Then, the effects of Herg 1 knockdown on the proliferation, growth and invasion of osteosarcoma were measured by using cell counting kit-8 (CCK-8), wound healing assay, Transwell assay and xenograft model of nude mice, respectively. Tandem affinity purification, mass spectrometry and dual luciferase reporter assay were used to find out the molecules interacted with Herg1. Western blot was used to detect the expressions of large tumor suppressor gene (LATS1), p-LATS1, Yes-associated protein (YAP) and p-YAP in cells after infection of Ad5-Herg1-shRNA. Results: Compared to Ad5-control-shRNA, Ad5-Herg1-shRNA dramatically inhibited the expression of Herg1 in OS cells. The result of CCK8 array demonstrated that 143B cell vitalities of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were (65.47±3.90)% and (79.90±1.52)%, significantly lower than (100.00±6.14)% of Ad5-control-shRNA group. Meanwhile, U2OS cell vitality of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were (69.69±1.36)% and (76.72±2.75)%, significantly lower than (100.00±3.01)% of Ad5-control-shRNA group (all P<0.001). The results of wound healing array showed that 143B cell migration rates of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were (33.03±2.88)% and (36.47±4.16)%, significantly lower than (97.78±2.28)% of Ad5-control-shRNA group. Meanwhile, U2OS cell migration rates of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were (68.07±0.90)% and (73.97±1.25)%, significantly lower than (96.50±1.12)% of Ad5-control-shRNA group (all P<0.001). The results of Transwell showed that 143B cell invasion numbers of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were 36.50±12.15 and 44.83±7.62, significantly lower than 195.33±19.68 of Ad5-control-shRNA group. Meanwhile, U2OS cell migration rates of Ad5-Herg1-shRNA1 and Ad5-Herg1-shRNA2 group were 21.83±7.99 and 22.85±7.08, significantly lower than 83.33±12.36 of Ad5-control-shRNA group (all P<0.001). The results of xenograft model of OS showed that the tumor volume and weight of Ad5-Herg1-shRNA group were significantly smaller than of Ad5-control-shRNA group after 14 days and 5 weeks of inoculation, respectively (P<0.001). Moreover, knockdown of Herg1 inhibited the metastasis of OS cells. In mechanism, Herg1 protein interacted with NF2 protein. Knockdown of Herg1 significantly suppressed the expression levels of LATS1 and YAP protein, and promoted the phosphorylation of LATS1 and YAP in OS cells (all P<0.001). Conclusion: Our findings suggest that Herg1 participates in the proliferation and motility of OS cells and may serve as a potential therapeutic target for osteosarcoma patients.

Emergent dynamics of extremes in a population driven by common information sources and new social media algorithms

We quantify how and when extreme subpopulations emerge in a model society despite everyone having the same information and available resources – and show that counterintuitively these extremes will likely be enhanced over time by new social media algorithms designed to reduce division. We verify our analysis mathematically, and show it reproduces (a) the time-dependent behavior observed in controlled experiments on humans, (b) the findings of a recent study of online behavior by Facebook concerning the impact of ‘soft’ and ‘hard’ news, (c) the observed temporal emergence of extremes in U.S. House of Representatives voting, and (d) the real-time emergence of a division in national opinion during the ongoing peace process in Colombia. We uncover a novel societal tipping point which is a ‘ghost’ of a nearby saddle-node bifurcation from dynamical systems theory, and which provides a novel policy opportunity for preventing extremes from emerging.

Car-Parrinello Monitor for More Robust Born-Oppenheimer Molecular Dynamics

Born-Oppenheimer molecular dynamics (BOMD) is a promising simulation method for exploring the possible reaction pathways of a chemical system, but one significant challenge is the increased difficulty of converging the self-consistent field (SCF) calculation that often accompanies the breaking and forming of chemical bonds. To address this challenge, we developed an enhancement to the BOMD simulation method called the Car-Parrinello monitor (CPMonitor) that uses Car-Parrinello molecular dynamics (CPMD) to recover from SCF convergence failures. CPMonitor works by detecting SCF convergence failures in BOMD and switching to a CPMD Hamiltonian to propagate through the region of configuration space where the SCF calculation is unable to converge, then switching back to BOMD when good convergence behavior is re-established. We present a series of simulation studies that use CPMonitor, including detailed studies of the thermodynamic and dynamical properties of simple systems, as well as ab initio nanoreactor simulations containing transition metal atoms that were previously not possible to simulate using standard BOMD methods. Our studies show that CPMonitor can make BOMD simulations robust to SCF convergence difficulties and improve simulation performance and stability in reaction discovery applications.

ZB transposon and chicken vasa homologue (Cvh) promoter interact to increase transfection efficiency of primordial germ cells in vivo

1. In order to increase the efficiency of generating transgenic chicken, this trial focused on two points: primordial germ cells (PGCs）transfection in vivo and a germline-specific promoter.2. In order to transfect PGCs in vivo, two plasmids (pZB-CAG-GFP, pCMV-ZB）were co-injected into chicken embryos via the subgerminal cavity at Hamburger and Hamilton (HH) stage 2-3 or via blood vessel at HH stage 13-14. Results showed that the percentage of GFP+ embryos, viability and hatching rate of embryos injected at HH stage 13-14 were significantly higher than that at HH stage 2-3.3. Two plasmid transposon systems were used for chicken embryo micro-injections. The donor plasmid, with a green fluorescent protein (GFP) reporter gene, was mediated by the ZB transposon. The helper plasmid was a transposase expression vector driven by the promoter of the chicken vasa homologue (Cvh) gene or Human cytomegalovirus (CMV) promoter. Results showed that 60.98% of gonads in Cvh group expressed GFP, which was 52.50% higher than seen in the CMV group. Only gonad tissue from the Cvh group showed any GFP signal, whereas both gonads and other tissues in the CMV group showed green fluorescence.4. The data suggested that ZB transposon-mediated gene transfer was efficient for transfecting PGCs in vivo; the Cvh promoter drove the transposase gene specifically in the germline and increased the efficiency of germline transmission. Blood vessels injection at HH stage 13-14 may be a more efficient route for PGCs transfection in vivo.

The efficacy and safety of menatetrenone in the management of osteoporosis: a systematic review and meta-analysis of randomized controlled trials

In our systematic review and meta-analysis, we comprehensively evaluated menatetrenone in the management of osteoporosis. We found that menatetrenone decreased the ratio of undercarboxylated osteocalcin to osteocalcin (ucOC/OC) and improved lumbar BMD compared with placebo based on the 18 studies assessed. However, its benefit in fracture risk control was uncertain.

INTRODUCTION

We performed a systematic review and meta-analysis of the efficacy and safety of menatetrenone in managing osteoporosis.

METHODS

PubMed, Cochrane Library, Embase, ClinicalTrials.gov , and three Chinese literature databases (CNKI, CBM, Wanfang) were searched for relevant randomized controlled trials (RCTs) published before October 5, 2017, comparing menatetrenone with other anti-osteoporotic drugs or placebo in treating osteoporosis. The pooled risk ratio (RR) or mean difference (MD) and 95% confidence interval (CI) were calculated using fixed-effects or random-effects meta-analysis.

RESULTS

Eighteen RCTs (8882 patients) were included. Pooled analyses showed that menatetrenone was more effective than placebo in improving lumbar bone mineral density (BMD) (five studies, N = 658, MD = 0.05 g/cm², 95% CI 0.01 to 0.09 g/cm²) and decreasing ucOC/OC (two studies, N = 75, MD = - 21.78%, 95% CI - 33.68 to - 9.87%). Compared with placebo, menatetrenone was associated with a nonsignificantly decreased risk of vertebral fracture (five studies, N = 5508, RR = 0.87, 95% CI 0.64 to 1.20). Evidence on other anti-osteoporotic drugs as comparators was limited and revealed no significantly different effects of menatetrenone on BMD or fracture risks. Furthermore, compared with placebo, menatetrenone significantly increased the incidence of adverse events (AEs) (two studies, N = 1949, RR = 1.47, 95% CI 1.07 to 2.02) and adverse drug reactions (four studies, N = 6102, RR = 1.29, 95% CI 1.07 to 1.56). However, no significant difference in the incidence of serious AEs was found between menatetrenone and placebo.

CONCLUSIONS

Menatetrenone significantly decreases ucOC and might improve lumbar BMD in osteoporotic patients. However, its benefit in fracture risk control is uncertain.

Single-Neuron Level One-Photon Voltage Imaging With Sparsely Targeted Genetically Encoded Voltage Indicators

Voltage imaging of many neurons simultaneously at single-cell resolution is hampered by the difficulty of detecting small voltage signals from overlapping neuronal processes in neural tissue. Recent advances in genetically encoded voltage indicator (GEVI) imaging have shown single-cell resolution optical voltage recordings in intact tissue through imaging naturally sparse cell classes, sparse viral expression, soma restricted expression, advanced optical systems, or a combination of these. Widespread sparse and strong transgenic GEVI expression would enable straightforward optical access to a densely occurring cell type, such as cortical pyramidal cells. Here we demonstrate that a recently described sparse transgenic expression strategy can enable single-cell resolution voltage imaging of cortical pyramidal cells in intact brain tissue without restricting expression to the soma. We also quantify the functional crosstalk in brain tissue and discuss optimal imaging rates to inform future GEVI experimental design.