Molecular evolution and phylogeographic analysis of wheat dwarf virus.

Wheat dwarf virus (WDV) has caused considerable economic loss in the global production of grain crops. Knowledge of the evolutionary biology and population history of the pathogen remain poorly understood. We performed molecular evolution and worldwide phylodynamic analyses of the virus based on the genes in the protein-coding region of the entire viral genome. Our results showed that host-driven and geography-driven adaptation are major factors that affects the evolution of WDV. Bayesian phylogenetic analysis estimates that the average WDV substitution rate was 4.240 × 10-4 substitutions/site/year (95% credibility interval, 2.828 × 10-4-5.723 × 10-4), and the evolutionary rates of genes encoding proteins with virion-sense transcripts and genes encoding proteins with complementary-sense transcripts were different. The positively selected sites were detected in only two genes encoding proteins with complementary-sense, and WDV-barley are subject to stronger purifying selection than WDV-wheat. The time since the most recent common WDV ancestor was 1746 (95% credibility interval, 1517-1893) CE. Further analyses identified that the WDV-barley population and WDV-wheat population experienced dramatic expansion-decline episodes, and the expansion time of the WDV-barley population was earlier than that of the WDV-wheat population. Our phylogeographic analysis showed that the WDV population originating in Iran was subsequently introduced to Europe, and then spread from Eastern Europe to China.

Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes.

Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10- 4 (4.700 × 10- 4-1.228 × 10- 3) and 8.671 × 10- 4 (6.143 × 10- 4-1.130 × 10- 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040-1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities.

Content-based multiple evidence fusion on EEG and eye movements for mild depression recognition.

BACKGROUND AND OBJECTIVE: Depression is a serious neurological disorder that has become a major health problem worldwide. The detection of mild depression is important for the diagnosis of depression in early stages. This research seeks to find a more accurate fusion model which can be used for mild depression detection using Electroencephalography and eye movement data. METHODS: This study proposes a content-based multiple evidence fusion (CBMEF) method, which fuses EEG and eye movement data at decision level. The method mainly includes two modules, the classification performance matrix module and the dual-weight fusion module. The classification performance matrices of different modalities are estimated by Bayesian rule based on confusion matrix and Mahalanobis distance, and the matrices were used to correct the classification results. Then the relative conflict degree of each modality is calculated, and different weights are assigned to the above modalities at the decision fusion layer according to this conflict degree. RESULTS: The experimental results show that the proposed method outperforms other fusion methods as well as the single modality results. The highest accuracies achieved 91.12%, and sensitivity, specificity and precision were 89.20%, 93.03%, 92.76%. CONCLUSIONS: The promising results showed the potential of the proposed approach for the detection of mild depression. The idea of introducing the classification performance matrix and the dual-weight model to multimodal biosignals fusion casts a new light on the researches of depression recognition.

Air and surface contamination by SARS-CoV-2 virus in a tertiary hospital in Wuhan, China.

BACKGROUND: Few studies have explored air and surface contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare settings. METHODS: Air and surface samples were collected from the isolation wards and intensive care units designated for coronavirus disease 2019 (COVID-19) patients. Clinical data and the results of nasopharyngeal specimen and serum antibody testing were also collected for the patient sample. RESULTS: A total of 367 air and surface swab samples were collected from the patient care areas of 15 patients with mild COVID-19 and nine patients with severe/critical COVID-19. Only one air sample taken during the intubation procedure tested positive. High-touch surfaces were slightly more likely to be contaminated with SARS-CoV-2 RNA than low-touch surfaces. Contamination rates were slightly higher near severe/critical patients than near mild patients, although this difference was not statistically significant (p > 0.05). Surface contamination was still found near the patients with both positive IgG and IgM. CONCLUSIONS: Air and surface contamination with viral RNA was relatively low in these healthcare settings after the enhancement of infection prevention and control. Environmental contamination could still be found near seroconverted patients, suggesting the need to maintain constant vigilance in healthcare settings to reduce healthcare-associated infection during the COVID-19 pandemic.

lncRNA RMRP Prevents Mitochondrial Dysfunction and Cardiomyocyte Apoptosis via the miR-1-5p/hsp70 Axis in LPS-Induced Sepsis Mice.

Both long non-coding RNA (lncRNA) RMRP and heat shock protein (HSP) 70 have been known to play crucial roles in inflammation. The present study investigated the roles of lncRNA RMRP and HSP70 protein 4 (HSPA4) in lipopolysaccharide (LPS)-induced sepsis. The C57BL/6 mice were treated with LPS, following which the cardiomyocytes were isolated for in vitro experiments. Further, a cardiac muscle cell line, HL-1 was transfected with plasmids expressing RMRP and HSPA4, si-NC, si-HSPA4, miR-1-5p mimic, and controls in vitro. Cell apoptosis, mitochondrial membrane potential (MMP), and levels of intracellular reactive oxygen species (ROS), mRNAs, and proteins were detected in the transfected mice tissues and cells. The LPS treatment significantly reduced the expression levels of RMRP, MMP, and mitochondrial cytochrome C. Moreover, it enhanced the cardiomyocyte apoptosis, intracellular ROS levels, cytoplasm cytochrome C levels, and the expression of caspase-3 and caspase-9 and nuclear factor κB (NF-κB) p65 subunit. The predicted RMRP-miR-1-5p-HSPA4 network was validated by co-transfection experiments in vitro in HL-1 cells. The transfection of miR-1-5p-treated cells with pcDNA-RMRP enhanced the levels of the protein HSPA4; however, no change at the mRNA level was observed. Moreover, miR-1-5p mimic attenuated the protective effect of pcDNA-HSPA4 against LPS-induced mitochondrial damage and apoptosis. In addition, we observed that silencing of HSPA4 increased the expression of nuclear p65; however, this effect could be reversed by co-transfection with pcDNA-RMRP. The lncRNA RMRP axis acts as a sponge for miR-1-5p. RMRP inhibits LPS-induced apoptosis of cardiomyocytes and mitochondrial damage by suppressing the post-transcriptional regulatory function of miR-1-5p on HSPA4. We believe that RMRP exhibits therapeutic potential for LPS-induced myocardial dysfunction both in vitro and in vivo.

Genetic structure and variability of tobacco vein banding mosaic virus populations.

Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC). Further analysis indicated that the spatial genetic structure of TVBMV populations is likely to have been caused by natural selection. Phylogeographic analysis provided strong support for spatial diffusion pathways between the Southwest and Northwest tobacco-producing regions. The TVBMV CP gene was found to be under negative selection, and no significant positive selection of amino acids was detected in the SW group; however, the isolates of the MC group experienced significant positive selection pressure at the first and third amino acid sites of CP. This study suggests that natural selection and habitat heterogeneity are important evolutionary mechanisms affecting the genetic structure of the TVBMV population.

Specific Genes Identified in Pathotype 4 of the Clubroot Pathogen Plasmodiophora brassicae.

Clubroot is an important disease of cruciferous crops caused by Plasmodiophora brassicae, and pathotypes are classified based on the response of differential hosts. This study was conducted to identify genetic markers able to differentiate pathotypes. Differential expression of genes between pathotype 4 (P4) and pathotype 7 (P7) was assessed according to transcriptome data of molecular marker screening. Among the pathotypes (P2, P4, P5, P7, P9, P10, and P11) tested, six genes were exclusive to P4, dividing the isolates into three types: PBRA_003263 and PBRA_003268 were present in all P4 isolates, PBRA_000003/Novel512 were found in a type of P4 (P4-1), and Novel137/PBRA_005772 were found in another P4 type, P4-2. Amplicons for all six genes were produced for only one isolate, which we named P4-3. This study is the first to establish a molecular identification system for P4 the, predominant pathotype in China. The genes identified might serve as molecular markers for differentiation of P4 from other pathotypes and may also distinguish different types of P4.

Characterization of Five Molecular Markers for Pathotype Identification of the Clubroot Pathogen Plasmodiophora brassicae.

Clubroot disease is an important disease on cruciferous crops caused by Plasmodiophora brassicae infections. The pathotypes have been classified based on the reactions of differential hosts. However, molecular markers of particular pathotypes for P. brassicae are limited. In this study, we found five genetic markers in association with different pathotypes. Different gene expression patterns among different pathotypes (P4, P7, P9, and P11) were assayed according to the transcriptome data. The assay indicated that molecular markers PBRA_007750 and PBRA_009348 could be used to distinguish P11 from P4, P7, and P9; PBRA_009348 and Novel342 could distinguish P9 from P4, P7, and P11; and PBRA_008439 and Novel342 could represent a kind of P4. Polymerase chain reaction cycles ranging from 25 to 30 were able to identify the predominant pathotype in general. Therefore, these molecular markers would be a valuable tool to identify and discriminate pathotypes in P. brassicae population.

Pregnancy outcomes and superiorities of prophylactic cervical cerclage and therapeutic cervical cerclage in cervical insufficiency pregnant women.

PURPOSE: To compare the clinical effect of prophylactic cervical cerclage and therapeutic cervical cerclage on pregnancy outcome and operative factors in cervical insufficiency pregnant women. METHODS: A retrospective study was conducted between June 2014 and September 2016 in a maternity ward, which included women who have had a single pregnancy and have been carried out a McDonald cerclage. All maternal medical records were reviewed. The efficacy of cerclage for preventing late foetal loss was assessed using multivariable logistic regression analysis. RESULTS: The results showed that there were significant associations between cerclage operations and pregnancy outcomes in the duration of pregnancy prolongation in terms of live births, gestation age, live birth and cesarean section rate. In prophylactic cervical cerclage, compared with therapeutic cervical cerclage, cervical length before surgery was significantly longer (32.7 ± 5.8 vs 19.9 ± 7.3 mm, p < 0.0001). Mean operative duration and postoperative length of hospital stay in prophylactic cervical cerclage were shorter than those in therapeutic cervical cerclage (22.1 ± 10.3 vs 28.9 ± 13.0 min, p = 0.0241 and 5.6 ± 1.8 vs 7.0 ± 2.8 days, p = 0.0354), respectively. Compared with therapeutic cerclage, prophylactic cerclage had more advantages in gestational age at delivery (35.2 ± 5.5 and 31.7 ± 6.5 weeks, p = 0.0061), deliveries < 37 gestational weeks (40 vs 69.2%, p = 0.0159), live births (93.3 vs 69.2%, p = 0.0143) and the duration of pregnancy prolongation in terms of live births (19.5 ± 5.0 vs 12.0 ± 8.2 weeks, p = 0.0002). There was a higher cesarean section rate in prophylactic group than that in therapeutic group (50 vs 25.6%, p = 0.0383). The logistic analysis showed that the cervical length before surgery was the only independent prognostic factor [OR 2.860 (1.425, 5.742) p = 0.0031] for pregnancy outcome, and that is the cervical length before surgery affected late foetal loss. CONCLUSIONS: Our study suggests that, both prophylactic cervical cerclage and therapeutic cervical cerclage reduce the incidence of recurrent abortion or preterm birth and efficiently extend the length of the pregnancy with live births. The prophylactic cervical cerclage has more advantages in operative time, length of hospital stay after surgery, gestational age at delivery, live births and preterm birth. The length of the cervical before surgery is an independent risk factor for pregnancy outcomes when pregnant women appear in the cervical shortening is less than normal. Cervical cerclage is an effective surgical technique to prevent recurrent abortion or late foetal loss.

Comparison of Patterns of Use of Unrecorded and Recorded Spirits: Survey of Adult Drinkers in Rural Central China.

About 70% of the beverage alcohol consumed in China annually is spirits. Recorded spirits make up most spirit consumption, but about 25% of total alcohol consumption (1.7 L pure alcohol per capita annually) is unrecorded spirits (bai jiu), either homemade or made in unregulated distilleries. In some parts of China, the consumption of unrecorded spirits is higher than average. This paper compares the patterns of use of unrecorded distilled spirits and recorded distilled spirits among rural residents in Central China. Interviews were conducted with 3298 individuals in 21 towns/villages in 10 counties in the Hubei, Anhui, and Hebei provinces in the People's Republic of China. Unrecorded bai jiu drinkers chose it because of its taste and its low price. It was consumed mostly by older men, mostly at home with family, more regularly and at higher alcohol by volume (ABV) compared to recorded alcohol. Recorded bai jiu drinkers were more likely to drink away from their homes, consumed more bai jiu at memorable drinking occasions, and reported feeling sick after drinking more often than unrecorded bai jiu drinkers. This comparison of patterns of use of unrecorded bai jiu and recorded bai jiu does not suggest that unrecorded bai jiu is more problematic for drinkers.

Atmospheric mercury deposition and its contribution of the regional atmospheric transport to mercury pollution at a national forest nature reserve, southwest China.

Atmospheric mercury deposition by wet and dry processes contributes to the transformation of mercury from atmosphere to terrestrial and aquatic systems. Factors influencing the amount of mercury deposited to subtropical forests were identified in this study. Throughfall and open field precipitation samples were collected in 2012 and 2013 using precipitation collectors from forest sites located across Mt. Jinyun in southwest China. Samples were collected approximately every 2 weeks and analyzed for total (THg) and methyl mercury (MeHg). Forest canopy was the primary factor on THg and MeHg deposition. Simultaneously, continuous measurements of atmospheric gaseous elemental mercury (GEM) were carried out from March 2012 to February 2013 at the summit of Mt. Jinyun. Atmospheric GEM concentrations averaged 3.8 ± 1.5 ng m(-3), which was elevated compared with global background values. Sources identification indicated that both regional industrial emissions and long-range transport of Hg from central, northeast, and southwest China were corresponded to the elevated GEM levels. Precipitation deposition fluxes of THg and MeHg in Mt. Jinyun were slightly higher than those reported in Europe and North America, whereas total fluxes of MeHg and THg under forest canopy on Mt. Jiuyun were 3 and 2.9 times of the fluxes of THg in wet deposition in the open. Highly elevated litterfall deposition fluxes suggest that even in remote forest areas of China, deposition of atmospheric Hg(0) via uptake by vegetation leaf may be a major pathway for the deposition of atmospheric Hg. The result illustrates that areas with greater atmospheric pollution can be expected to have greater fluxes of Hg to soils via throughfall and litterfall.

Association of red blood cell transfusion and in-hospital mortality in patients admitted to the intensive care unit: a systematic review and meta-analysis.

INTRODUCTION: Previous research has debated whether red blood cell (RBC) transfusion is associated with decreased or increased mortality in patients admitted to the intensive care unit (ICU). We conducted a systematic review and meta-analysis to assess the relationship of RBC transfusion with in-hospital mortality in ICU patients. METHODS: We carried out a literature search on Medline (1950 through May 2013), Web of Science (1986 through May 2013) and Embase (1980 through May 2013). We included all prospective and retrospective studies on the association between RBC transfusion and in-hospital mortality in ICU patients. The relative risk for the overall pooled effects was estimated by random effects model. Sensitivity analyses were conducted to assess potential bias. RESULTS: The meta-analysis included 28,797 participants from 18 studies. The pooled relative risk for transfused versus nontransfused ICU patients was 1.431 (95% CI, 1.105 to 1.854). In sensitivity analyses, the pooled relative risk was 1.211 (95% CI, 0.975 to 1.505) if excluding studies without adjustment for confounders, 1.178 (95% CI, 0.937 to 1.481) if excluding studies with relative high risk of bias, and 0.901 (95% CI, 0.622 to 1.305) if excluding studies without reporting hazard ratio (HR) or relative risk (RR) as an effect size measure. Subgroup analyses revealed increased risks in studies enrolling patients from all ICU admissions (RR 1.513, 95%CI 1.123 to 2.039), studies without reporting information on leukoreduction (RR 1.851, 95%CI 1.229 to 2.786), studies reporting unadjusted effect estimates (RR 3.933, 95%CI 2.107 to 7.343), and studies using odds ratio as an effect measure (RR 1.465, 95%CI 1.049 to 2.045). Meta-regression analyses showed that RBC transfusion could decrease risk of mortality in older patients (slope coefficient -0.0417, 95%CI -0.0680 to -0.0154). CONCLUSIONS: There is lack of strong evidence to support the notion that ICU patients who receive RBC transfusion have an increased risk of in-hospital death. In studies adjusted for confounders, we found that RBC transfusion does not increase the risk of in-hospital mortality in ICU patients. Type of patient, information on leukoreduction, statistical method, mean age of patient enrolled and publication year of the article may account for the disagreement between previous studies.

Association between soy isoflavone intake and breast cancer risk for pre- and post-menopausal women: a meta-analysis of epidemiological studies.

BACKGROUND: Conclusions drawn from meta-analyses on the association between soy isoflavone intake and breast cancer risk for pre- and post-menopausal women are not fully consistent. These meta-analyses did not explore the influence of different study designs on the pooled results on the basis of distinguishing between pre- and post-menopausal women. METHODOLOGY AND PRINCIPAL FINDINGS: We performed a meta-analysis of 35 studies which reported results of association between soy isoflavone intake and breast cancer risk for pre- and/or post-menopausal women, calculated pooled odds ratios and their 95% confidence intervals of pre- and post-menopausal women respectively, and further explored soy isoflavone-breast cancer association on the basis of considering different study regions and designs. Summary results suggested that soy isoflavone intake has a protective effect against breast cancer for both pre- and post-menopausal women. However, they are influenced by study design and region. Pooled ORs of studies carried out in Asian countries suggested that soy isoflavone's protective effect exist in both pre- and post-menopausal women (OR = 0.59, 95%CI: 0.48-0.69 for premenopausal women; OR = 0.59, 95%CI: 0.44-0.74 for postmenopausal women). However, there are some differences between the results pooled from different study designs for women in Asian countries (test for consistency, P = 0.04). Pooled OR of studies on postmenopausal women in Western countries suggested that soy isoflavone intake has a marginally significant protective effect (OR = 0.92; 95%CI: 0.83 ∼ 1.00), but further analyses stratifying by study design found no statistically significant association. CONCLUSIONS: We meta-analyzed more and newer research results, and separated women according to menopausal status to explore soy isoflavone-breast cancer association. We founded that soy isoflavone intake could lower the risk of breast cancer for both pre- and post-menopausal women in Asian countries. However, for women in Western countries, pre- or post-menopausal, there is no evidence to suggest an association between intake of soy isoflavone and breast cancer.

Sensitive pseudobienzyme electrocatalytic DNA biosensor for mercury(II) ion by using the autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification.

Herein, a novel sensitive pseudobienzyme electrocatalytic DNA biosensor was proposed for mercury ion (Hg(2+)) detection by using autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification. Thiol functionalized capture DNA was firstly immobilized on a nano-Au modified glass carbon electrode (GCE). In presence of Hg(2+), the specific coordination between Hg(2+) and T could result in the assembly of primer DNA on the electrode, which successfully triggered the HCR to form the hemin/G-quadruplex DNAzyme nanowires with substantial redox probe thionine (Thi). In the electrolyte of PBS containing NADH, the hemin/G-quadruplex nanowires firstly acted as an NADH oxidase to assist the concomitant formation of H2O2 in the presence of dissolved O2. Then, with the redox probe Thi as electron mediator, the hemin/G-quadruplex nanowires acted as an HRP-mimicking DNAzyme that quickly bioelectrocatalyzed the reduction of produced H2O2, which finally led to a dramatically amplified electrochemical signal. This method has demonstrated a high sensitivity of Hg(2+) detection with the dynamic concentration range spanning from 1.0 ng L(-1) to 10 mg L(-1) Hg(2+) and a detection limit of 0.5 ng L(-1) (2.5 pM) at the 3Sblank level, and it also demonstrated excellent selectivity against other interferential metal ions.

[Effects of Ca2+ on acid tolerance of Medicago sativa and Rhizobium meliloti].

Soil acidity is an important environmental factor hampering the effective symbiotic nitrogen fixation of Rhizobium meliloti and its host plant Medicag sativa. The study on the effects of Ca2 + on the acid tolerance of M. sativa and R. meliloti showed that applying 5 and 10 mmol . L(-1) of Ca2+ could promote the growth of R. meliloti and advance its log growth phase. Under neutral pH condition, applying Ca2+ didn't have any significant effects on root hair deformation, while under low pH condition, Ca2+ demonstrated positive functions. The higher the Ca2+ concentration, the more significantly it affected, indicating that Ca2+ might play an important role in the recognition between R. meliloti and its host plant. Applying Ca2+ under low pH made the nodulation ahead of time and the nodulation rate enhanced. Definite concentration of Ca2+ could increase the number of nodules in the same period, which was more obvious at anaphase stage or under lower pH condition.

[Primary study on acid tolerance mechanism of a wild aciduric Rhizobium strain isolated from Pueraria lobata].

An aciduric Rhizobium strain, named as PR389, was isolated from the nodule of wild Pueraria lobata which grew in yellow soil (pH 4.6) on the Jin-yun Mountain in Bei-bei, Chong-qing city. The isolated strain, which could grow under pH 4.6 distinct from the optimal pH 6.5-7.5 for rhizobium, showed some typical features of aciduric rhizobium. This was also confirmed by the proton flux assay. Compared to the acid-sensitive Rhizobium strain PR21, the cell membrane of PR389 could hold back excessive H entering cell. This feature can protect PR389 from harm of acid. In the test of acid tolerance, the aciduric ability of strain PR389 under low acidic (pH 3.8) was restrained by antibiotic chloramphenicol. It was speculated that special proteins in the cells of PR389 could be induced and synthesized in acidic environment.