Different contributions to space weather and space climate from different big solar active regions

The purpose of this paper is to show that large active regions (ARs) with different magnetic configurations have different contributions to short-term and long-term variations of the Sun. As a case study, the complex $\delta$-type AR 12673 and the simple $\beta$-type AR 12674 are investigated in detail. Since the axial dipole moment at cycle minimum determines the amplitude of the subsequent cycle and space climate, we have assimilated the individual observed magnetic configurations of these two ARs into a surface flux transport model to compare their contributions to the axial dipole moment $D$. We find that AR 12673 has a significant effect on $D$ at the end of the cycle, making it weaker because of the abnormal and complicated magnetic polarities. An initial strongly positive $D$ ends up with a strongly negative value. The flare-poor AR 12674 has a greater contribution to the long-term axial dipole moment than the flare-rich AR 12673. We then carry out a statistical analysis of ARs larger than 800 $\mu$Hem from 1976 to 2017. We use the flare index FI and define an axial dipole moment index DI to quantify the effects of each AR on space weather and space climate, respectively. Whereas the FI has a strong dependence on the magnetic configuration, the DI shows no such dependence. The DI is mainly determined by the latitudinal location and the latitudinal separation of the positive and negative magnetic fluxes of the ARs. Simple ARs have the same possibility as complex ARs to produce big DI values affecting space climate.Comment: 18 pages, 8 figures, Accepted for publication in the Astrophysical Journa

A Taxonomy of Hyperlink Hiding Techniques

Hidden links are designed solely for search engines rather than visitors. To get high search engine rankings, link hiding techniques are usually used for the profitability of black industries, such as illicit game servers, false medical services, illegal gambling, and less attractive high-profit industry, etc. This paper investigates hyperlink hiding techniques on the Web, and gives a detailed taxonomy. We believe the taxonomy can help develop appropriate countermeasures. Study on 5,583,451 Chinese sites' home pages indicate that link hidden techniques are very prevalent on the Web. We also tried to explore the attitude of Google towards link hiding spam by analyzing the PageRank values of relative links. The results show that more should be done to punish the hidden link spam.Comment: 12 pages, 2 figure

Prediction of trans-antisense transcripts in Arabidopsis thaliana

BACKGROUND: Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. Experimental and computational methods have demonstrated the widespread occurrence of NATs in eukaryotes. However, most previous studies only focused on cis-NATs with little attention being paid to NATs that originate in trans. RESULTS: We have performed a genome-wide screen of trans-NATs in Arabidopsis thaliana and identified 1,320 putative trans-NAT pairs. An RNA annealing program predicted that most trans-NATs could form extended double-stranded RNA duplexes with their sense partners. Among trans-NATs with available expression data, more than 85% were found in the same tissue as their sense partners; of these, 67% were found in the same cell as their sense partners at comparable expression levels. For about 60% of Arabidopsis trans-NATs, orthologs of at least one transcript of the pair also had trans-NAT partners in either Populus trichocarpa or Oryza sativa. The observation that 430 transcripts had both putative cis- and trans-NATs implicates multiple regulations by antisense transcripts. The potential roles of trans-NATs in inducing post-transcriptional gene silencing and in regulating alternative splicing were also examined. CONCLUSION: The Arabidopsis transcriptome contains a fairly large number of trans-NATs, whose possible functions include silencing of the corresponding sense transcripts or altering their splicing patterns. The interlaced relationships observed in some cis- and trans-NAT pairs suggest that antisense transcripts could be involved in complex regulatory networks in eukaryotes

Algebraic quantification of an active region's contribution to the solar cycle

The solar dipole moment at cycle minimum is considered to be the most successful precursor for the amplitude of the subsequent cycle. Numerical simulations of the surface flux transport (SFT) model are widely used to effectively predict the dipole moment at cycle minimum. Recently an algebraic method has been proposed to quickly predict the contribution of an active region (AR) to the axial dipole moment at cycle minimum instead of SFT simulations. However, the method assumes a bipolar magnetic region (BMR) configuration of ARs. Actually most ARs are asymmetric in configuration of opposite polarities, or have more complex configurations. Such ARs evolve significantly differently from that of BMR approximations. We propose a generalized algebraic method to describe the axial dipole contribution of an AR with an arbitrary configuration, and evaluate its effectiveness compared to the BMR-based method. We employ mathematical deductions to obtain the generalized method. We compare the results of the generalized method with SFT simulations of observed ARs, artificially created BMRs, and ARs with more complex configurations. We also compare the results with that from the BMR-based method. The generalized method is equivalent to the SFT model, and precisely predicts the ARs' contributions to the dipole moment. The method has a much higher computational efficiency than SFT simulations. Although the BMR-based method has similar computational efficiency as the generalized method, it is only accurate for symmetric bipolar ARs. The BMR-based method systematically overestimates the dipole contributions of asymmetric bipolar ARs, and randomly miscalculate the contributions of more complex ARs. The generalized method provides a quick and precise quantification of an AR's contribution to the solar cycle evolution, which paves the way for the application into the physics-based solar cycle prediction.Comment: 9 pages, 5 figures. Accepted for publication in A&

Studies on cold hardiness of grapevine roots

For 16 grapevine rootstocks, the critical chilling temperatures were determined. There were great differences in cold hardiness among these vines. The cold hardiness öf several newly introduced rootstocks was higher than that of rootstock variety Beta and they showed even multiple resistance. Thus, after further testing experiments, they might become valuable rootstocks in cold regions.There were some differences in cold hardiness among 3 fruiting varieties tested. This finding can be used as reference in formulating winter protection measures for own-rooted grapes.Comparative examination of the methods for testing cold hardiness showed that the combination of electrolytic conductance method with root section culture was simple and reliable for measuring cold hardiness of grape roots, while TTC reduction method, because of its Jack of regularity in test results, was not suitable for this purpose.The characteristics of root structure have certain correlations with cold hardiness: (i) Varieties with higher cold hardiness have smaller hark and ray cells than tender varieties and their tissue structure is more compact. (ii) Vessel diameter is smaller and vessel density is lower in hardy varieties. (iii) Varieties with higher cold h ardiness have a lower percentage of hark and a higher rate of xylem in their roots.Thus, these characteristics of root structure could be used as an additional index in forecasting and screening cold hardiness of grape roots

Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana

BACKGROUND: Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana. RESULTS: We developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice. CONCLUSION: We combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets

BACKGROUND: A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some miRNAs and their time- and tissue-specific expression patterns make experimental miRNA identification difficult. We present here a computational method for genome-wide prediction of Arabidopsis thaliana microRNAs and their target mRNAs. This method uses characteristic features of known plant miRNAs as criteria to search for miRNAs conserved between Arabidopsis and Oryza sativa. Extensive sequence complementarity between miRNAs and their target mRNAs is used to predict miRNA-regulated Arabidopsis transcripts. RESULTS: Our prediction covered 63% of known Arabidopsis miRNAs and identified 83 new miRNAs. Evidence for the expression of 25 predicted miRNAs came from northern blots, their presence in the Arabidopsis Small RNA Project database, and massively parallel signature sequencing (MPSS) data. Putative targets functionally conserved between Arabidopsis and O. sativa were identified for most newly identified miRNAs. Independent microarray data showed that the expression levels of some mRNA targets anti-correlated with the accumulation pattern of their corresponding regulatory miRNAs. The cleavage of three target mRNAs by miRNA binding was validated in 5' RACE experiments. CONCLUSIONS: We identified new plant miRNAs conserved between Arabidopsis and O. sativa and report a wide range of transcripts as potential miRNA targets. Because MPSS data are generated from polyadenylated RNA molecules, our results suggest that at least some miRNA precursors are polyadenylated at certain stages. The broad range of putative miRNA targets indicates that miRNAs participate in the regulation of a variety of biological processes

Species-specific and needle age-related responses of photosynthesis in two Pinus species to long-term exposure to elevated CO2 concentration

There is, so far, no common conclusion about photosynthetic responses of trees to long-term exposure to elevated CO2. Photosynthesis and specific leaf area (SLA) of 1-year-old and current-year needles in Pinus koraiensis and P. sylvestriformis grown in open-top chambers were measured monthly for consecutive two growing seasons (2006, 2007) after 8-9years of CO2 enrichment in northeastern China, to better understand species-specific and needle age-related responses to elevated CO2 (500μmolmol−1CO2). The light-saturated photosynthetic rates (P Nsat) increased in both species at elevated CO2, but the stimulation magnitude varied with species and needle age. Photosynthetic acclimation to elevated CO2, in terms of reduced V cmax (maximum carboxylation rate) and J max (maximum electron transport rate), was found in P. koraiensis but not in P. sylvestriformis. The photosynthetic parameters (V cmax, J max, P Nsat) measured in different-aged needles within each species responded to elevated CO2 similarly, but elevated CO2 resulted in much pronounced variations of those parameters in current-year needles than in 1-year-old needles within each species. This result indicated that needle age affects the magnitude but not the patterns of photosynthetic responses to long-term CO2 enrichment. The present study indicated that different species associated with different physioecological properties responded to elevated CO2 differently. As global change and CO2 enrichment is more or less a gradual rather than an abrupt process, long-term global change experiments with different plant species are still needed to character and better predict the global change effects on terrestrial ecosystem