Direction-of-Arrival Estimation via Sparse Bayesian Learning Exploiting Hierarchical Priors with Low Complexity.

For direction-of-arrival (DOA) estimation problems in a sparse domain, sparse Bayesian learning (SBL) is highly favored by researchers owing to its excellent estimation performance. However, traditional SBL-based methods always assign Gaussian priors to parameters to be solved, leading to moderate sparse signal recovery (SSR) effects. The reason is Gaussian priors play a similar role to l2 regularization in sparsity constraint. Therefore, numerous methods are developed by adopting hierarchical priors that are used to perform better than Gaussian priors. However, these methods are in straitened circumstances when multiple measurement vector (MMV) data are adopted. On this basis, a block-sparse SBL method (named BSBL) is developed to handle DOA estimation problems in MMV models. The novelty of BSBL is the combination of hierarchical priors and block-sparse model originating from MMV data. Therefore, on the one hand, BSBL transfers the MMV model to a block-sparse model by vectorization so that Bayesian learning is directly performed, regardless of the prior independent assumption of different measurement vectors and the inconvenience caused by the solution of matrix form. On the other hand, BSBL inherited the advantage of hierarchical priors for better SSR ability. Despite the benefit, BSBL still has the disadvantage of relatively large computation complexity caused by high dimensional matrix operations. In view of this, two operations are implemented for low complexity. One is reducing the matrix dimension of BSBL by approximation, generating a method named BSBL-APPR, and the other is embedding the generalized approximate message passing (GAMB) technique into BSBL so as to decompose matrix operations into vector or scale operations, named BSBL-GAMP. Moreover, BSBL is able to suppress temporal correlation and handle wideband sources easily. Extensive simulation results are presented to prove the superiority of BSBL over other state-of-the-art algorithms.

Identification of factors impacting on the transmission and mortality of COVID-19.

This paper proposes a dynamic infectious disease model for COVID-19 daily counts data and estimate the model using the Langevinized EnKF algorithm, which is scalable for large-scale spatio-temporal data, converges to the right filtering distribution, and is thus suitable for performing statistical inference and quantifying uncertainty for the underlying dynamic system. Under the framework of the proposed dynamic infectious disease model, we tested the impact of temperature, precipitation, state emergency order and stay home order on the spread of COVID-19 based on the United States county-wise daily counts data. Our numerical results show that warm and humid weather can significantly slow the spread of COVID-19, and the state emergency and stay home orders also help to slow it. This finding provides guidance and support to future policies or acts for mitigating the community transmission and lowering the mortality rate of COVID-19.

The use of remote Femto Second technology in the preparation of black silicon material and optical devices.

The research aims to study the application of remote Femto Second (FS) technology in black silicon material preparation and optical devices. Based on the principle and characteristic research of FS technology, the interaction between FS and silicon is adopted to propose a scheme for preparing black silicon material through experiments. Moreover, the experimental parameters are optimized. Then, the scheme of using the FS for etching polymer optical power splitter as a new technical means is proposed. In addition, while ensuring processing accuracy, the appropriate process parameters of laser etching photoresist are obtained. The results show that the performance of black silicon prepared with SF6 as the background gas is greatly improved in the 400-2200nm range. However, the performance of black silicon samples with the two-layer structure etched at different laser energy densities has little difference. Black silicon with a Se+Si two-layer film structure has the best optical absorption performance in the infrared range of 1100nm-2200nm. Besides, the optical absorption rate is the highest when the laser scanning rate is 0.5mm/s. In the band of >1100nm, when the maximum laser energy density is 6.5kJ/m2, the overall absorption of the etched sample is the worst. The absorption rate is the best when the laser energy density is 3.9kJ/m2. It suggests that the proper parameter selection greatly impacts the quality of the final laser-etched sample.

Molecular dynamics simulation of solidification epitaxial growth in a nanoscale molten pool.

In the hot working process, the liquid metal part formed by the heat source on the workpiece is known as molten pool. Since the solidification process of the molten pool determines the mechanical properties of the structure after hot working, the molten pool solidification under the condition of rapid solidification has attracted the attention of researchers. In thisstudy, to understand the influence of the microstructure and morphology of the base metal on the solidification of the molten pool, a simulation system of epitaxial growth during the solidification of the molten pool is established based on molecular dynamics (MD), and the details of the epitaxial growth of the molten pool solidification are dynamically monitored. The results show that the nano molten pool produces two atomic layers of pre-melting on the base metal before solidification, and then, the molten pool continues to grow with the exposed and ordered atoms of the base metal as the nuclei. The transformation process of the final obtained solidification morphology is consistent with the results observed by in situ TEM experiments. These phenomena reveal the mutual guidance between the molten pool and the base metal during the solidification of the molten pool as well as the genetic effect of the parent metal on the crystallization of the molten pool. In addition, the crystal growth of molten pool solidification follows the growth pattern of directional solidification, from equiaxed to columnar, but the average grain size of each zone is smaller than that of directional solidification. Even the nucleation rate and dislocation density are an order of magnitude higher than in directional solidification. Therefore, the simulation results lay a foundation for the in-depth study of the molten pool solidification process at the atomic scale.

GmWAK1, Novel Wall-Associated Protein Kinase, Positively Regulates Response of Soybean to Phytophthora sojae Infection.

Phytophthora root rot is a destructive soybean disease worldwide, which is caused by the oomycete pathogen Phytophthora sojae (P. sojae). Wall-associated protein kinase (WAK) genes, a family of the receptor-like protein kinase (RLK) genes, play important roles in the plant signaling pathways that regulate stress responses and pathogen resistance. In our study, we found a putative Glycine max wall-associated protein kinase, GmWAK1, which we identified by soybean GmLHP1 RNA-sequencing. The expression of GmWAK1 was significantly increased by P. sojae and salicylic acid (SA). Overexpression of GmWAK1 in soybean significantly improved resistance to P. sojae, and the levels of phenylalanine ammonia-lyase (PAL), SA, and SA-biosynthesis-related genes were markedly higher than in the wild-type (WT) soybean. The activities of enzymatic superoxide dismutase (SOD) and peroxidase (POD) antioxidants in GmWAK1-overexpressing (OE) plants were significantly higher than those in in WT plants treated with P. sojae; reactive oxygen species (ROS) and hydrogen peroxide (H2O2) accumulation was considerably lower in GmWAK1-OE after P. sojae infection. GmWAK1 interacted with annexin-like protein RJ, GmANNRJ4, which improved resistance to P. sojae and increased intracellular free-calcium accumulation. In GmANNRJ4-OE transgenic soybean, the calmodulin-dependent kinase gene GmMPK6 and several pathogenesis-related (PR) genes were constitutively activated. Collectively, these results indicated that GmWAK1 interacts with GmANNRJ4, and GmWAK1 plays a positive role in soybean resistance to P. sojae via a process that might be dependent on SA and involved in alleviating damage caused by oxidative stress.

What I Say Means What I Do: Risk Concerns and Mobile Application-Selection Behaviors.

OBJECTIVE: The goal of this study was to examine the relation between users' reported risk concerns and their choice behaviors in a mobile application (app) selection task. BACKGROUND: Human users are typically regarded as the weakest link in cybersecurity and privacy protection; however, it is possible to leverage the users' predilections to increase security. There have been mixed results on the relation between users' self-reported privacy concerns and their behaviors. METHOD: In three experiments, the timing of self-reported risk concerns was either a few weeks before the app-selection task (pre-screen), immediately before it (pre-task), or immediately after it (post-task). We also varied the availability and placement of clear definitions and quizzes to ensure users' understanding of the risk categories. RESULTS: The post-task report significantly predicted the app-selection behaviors, consistent with prior findings. The pre-screen report was largely inconsistent with the reports implemented around the time of the task, indicating that participants' risk concerns may not be stable over time and across contexts. Moreover, the pre-task report strongly predicted the app-selection behaviors only when elaborated definitions and quizzes were placed before the pre-task question, indicating the importance of clear understanding of the risk categories. CONCLUSION: Self-reported risk concerns may be unstable over time and across contexts. When explained with clear definitions, self-reported risk concerns obtained immediately before or after the app-selection task significantly predicted app-selection behaviors. APPLICATION: We discuss implications for including personalized risk concerns during app selection that enable comparison of alternative mobile apps.

Time-course transcriptome profiling revealed the specific expression patterns of MADS-box genes associated with the distinct developmental processes between winter and spring wheat.

The shoot apex is a region where new cells are produced and elongate. The developmental state of the wheat shoot apex under low temperature affects its cold resistance. In this study, the morphology of shoot apex before overwintering was characterized for 24 wheat line with different winter and spring characteristics. Our research showed that the shoot apex of autumn-sown spring wheat lines reached the temperature sensitive double-ridge stage before overwintering, whereas shoot apex of winter wheat lines are found in temperature-insensitive vegetative or elongation stages. In order to explore how gene expression is associated with shoot apex differentiation in winter and spring wheat, we used strand-specific RNA sequencing to profile the gene expression patterns at four time-points between 14 after germination and 45 days after germination in the winter wheat cultivar Dongnongdongmai No. 1 (DM1) and in the spring wheat cultivar China Spring (CS). We identified 11,848 differentially expressed genes between the two cultivars. Most up-regulated genes in CS were involved in energy metabolism and transport during the seedling stage, whereas up-regulated genes in DM1 were involved in protein and DNA synthesis. MADS-box genes affect plant growth and development. In this study, MADS-boxes with differential expression between CS and DM1 were screened and evolutionary tree analysis was conducted. During all sampling periods, CS highly expressed MADS-box genes that induce flowering promotion genes such as VRN1, VRT and AG, while lowly expressed MADS-box genes that induce flowering-inhibiting homologous genes such as SVP. TaVRN1 composition in DM1 and CS was vrn-A1, vrn-B1, and Vrn-D1b. Analysis of the sequence of TaVRN1 (TraesCS5A01G391700) from DM1 and CS revealed 5 SNP differences in the promoter regions and 3 SNP deletions in the intron regions. The expression levels of cold resistant genes in DM1 were significantly higher than those in CS at seedling stage (neither DM1 nor CS experienced cold in this study), including CBF, cold induced protein,acid desaturase and proline rich proteins. Additionally, the expression levels of auxin-related genes were significantly higher in CS than those in DM1 at 45 days after germination. Our study identified candidate genes associated with the process of differentiation of the shoot apex in winter and spring wheat at the seedling stage and also raised an internal stress tolerance model for winter wheat to endogenously anticipate the coming stressful conditions in winter.

Federation in genomics pipelines: techniques and challenges.

Federation is a popular concept in building distributed cyberinfrastructures, whereby computational resources are provided by multiple organizations through a unified portal, decreasing the complexity of moving data back and forth among multiple organizations. Federation has been used in bioinformatics only to a limited extent, namely, federation of datastores, e.g. SBGrid Consortium for structural biology and Gene Expression Omnibus (GEO) for functional genomics. Here, we posit that it is important to federate both computational resources (CPU, GPU, FPGA, etc.) and datastores to support popular bioinformatics portals, with fast-increasing data volumes and increasing processing requirements. A prime example, and one that we discuss here, is in genomics and metagenomics. It is critical that the processing of the data be done without having to transport the data across large network distances. We exemplify our design and development through our experience with metagenomics-RAST (MG-RAST), the most popular metagenomics analysis pipeline. Currently, it is hosted completely at Argonne National Laboratory. However, through a recently started collaborative National Institutes of Health project, we are taking steps toward federating this infrastructure. Being a widely used resource, we have to move toward federation without disrupting 50 K annual users. In this article, we describe the computational tools that will be useful for federating a bioinformatics infrastructure and the open research challenges that we see in federating such infrastructures. It is hoped that our manuscript can serve to spur greater federation of bioinformatics infrastructures by showing the steps involved, and thus, allow them to scale to support larger user bases.

Embedding Training Within Warnings Improves Skills of Identifying Phishing Webpages.

OBJECTIVE: Evaluate the effectiveness of training embedded within security warnings to identify phishing webpages. BACKGROUND: More than 20 million malware and phishing warnings are shown to users of Google Safe Browsing every week. Substantial click-through rate is still evident, and a common issue reported is that users lack understanding of the warnings. Nevertheless, each warning provides an opportunity to train users about phishing and how to avoid phishing attacks. METHOD: To test use of phishing-warning instances as opportunities to train users' phishing webpage detection skills, we conducted an online experiment contrasting the effectiveness of the current Chrome phishing warning with two training-embedded warning interfaces. The experiment consisted of three phases. In Phase 1, participants made login decisions on 10 webpages with the aid of warning. After a distracting task, participants made legitimacy judgments for 10 different login webpages without warnings in Phase 2. To test the long-term effect of the training, participants were invited back a week later to participate in Phase 3, which was conducted similarly as Phase 2. RESULTS: Participants differentiated legitimate and fraudulent webpages better than chance. Performance was similar for all interfaces in Phase 1 for which the warning aid was present. However, training-embedded interfaces provided better protection than the Chrome phishing warning on both subsequent phases. CONCLUSION: Embedded training is a complementary strategy to compensate for lack of phishing webpage detection skill when phishing warning is absent. APPLICATION: Potential applications include development of training-embedded warnings to enable security training at scale.

Display of major risk categories for android apps.

Communicating cybersecurity risks to mobile-device users is essential. However, existing means of conveying the risks through detailed permission lists are ineffective. Risk indexes that convey overall risk are effective at influencing app-selection decisions, but many users want more information. We examined how users assess the risks associated with downloading applications on the Android platform by comparing various graphical formats of intermediate-level risk displays containing three risk categories: personal privacy; monetary loss; device stability. Bar-graph and table formats were compared, as were vertical and horizontal displays. Participants performed app risk-rating (Experiment 1) and app-selection (Experiments 2 and 3) tasks for hypothetical apps with risk scores on each of the categories. They also specified which risk category was of most concern to them. Increased risk scores in each category led to higher rated risk and lower app-selection rate which matched with self-reported risk concerns. Bar-graphs were more time-efficient and yielded higher risk-ratings than tables, although the two formats did not differ in the app-selection task. Moreover, horizontal bar-graphs yielded faster responses than vertical bar-graphs. The results indicate that the intermediate-level risk display was effective in conveying risk-category information, especially with horizontal bar-graphs, and personalized design of this display based on users' risk concerns is potentially useful. (PsycINFO Database Record

The bHLH transcription factor GmPIB1 facilitates resistance to Phytophthora sojae in Glycine max.

Phytophthora sojae Kaufmann and Gerdemann causes Phytophthora root rot, a destructive soybean disease worldwide. A basic helix-loop-helix (bHLH) transcription factor is thought to be involved in the response to P. sojae infection in soybean, as revealed by RNA sequencing (RNA-seq). However, the molecular mechanism underlying this response is currently unclear. Here, we explored the function and underlying mechanisms of a bHLH transcription factor in soybean, designated GmPIB1 (P. sojae-inducible bHLH transcription factor), during host responses to P. sojae. GmPIB1 was significantly induced by P. sojae in the resistant soybean cultivar 'L77-1863'. Analysis of transgenic soybean hairy roots with elevated or reduced expression of GmPIB1 demonstrated that GmPIB1 enhances resistance to P. sojae and reduces reactive oxygen species (ROS) accumulation. Quantitative reverse transcription PCR and chromatin immunoprecipitation-quantitative PCR assays revealed that GmPIB1 binds directly to the promoter of GmSPOD1 and represses its expression; this gene encodes a key enzyme in ROS production. Moreover, transgenic soybean hairy roots with GmSPOD1 silencing through RNA interference exhibited improved resistance to P. sojae and reduced ROS generation. These findings suggest that GmPIB1 enhances resistance to P. sojae by repressing the expression of GmSPOD1.

Phenylalanine ammonia-lyase2.1 contributes to the soybean response towards Phytophthora sojae infection.

Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.] caused by Phytophthora sojae is a destructive disease worldwide. Phenylalanine ammonia-lyase (PAL) is one of the most extensively studied enzymes related to plant responses to biotic and abiotic stresses. However, the molecular mechanism of PAL in soybean in response to P. sojae is largely unclear. Here, we characterize a novel member of the soybean PAL gene family, GmPAL2.1, which is significantly induced by P. sojae. Overexpression and RNA interference analysis demonstrates that GmPAL2.1 enhances resistance to P. sojae in transgenic soybean plants. In addition, the PAL activity in GmPAL2.1-OX transgenic soybean is significantly higher than that of non-transgenic plants after infection with P. sojae, while that in GmPAL2.1-RNAi soybean plants is lower. Further analyses show that the daidzein, genistein and salicylic acid (SA) levels and the relative content of glyceollins are markedly increased in GmPAL2.1-OX transgenic soybean. Taken together, these results suggest the important role of GmPAL2.1 functioning as a positive regulator in the soybean response to P. sojae infection, possibly by enhancing the content of glyceollins, daidzein, genistein and SA.

A Novel Soybean Dirigent Gene GmDIR22 Contributes to Promotion of Lignan Biosynthesis and Enhances Resistance to Phytophthora sojae.

Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae is a destructive disease of soybean worldwide. Plant dirigent proteins (DIR) are proposed to have roles in biosynthesis of either lignan or lignin-like molecules, and are important for defense responses, secondary metabolism, and pathogen resistance. In the present work, a novel DIR gene expressed sequence tag is identified as up-regulated in the highly resistant soybean cultivar 'Suinong 10' inoculated with P. sojae. The full length cDNA is isolated using rapid amplification of cDNA ends, and designated GmDIR22 (GenBank accession no. HQ_993047). The full length GmDIR22 is 789 bp and contains a 567 bp open reading frame encoding a polypeptide of 188 amino acids. The sequence analysis indicated that GmDIR22 contains a conserved dirigent domain at amino acid residues 43-187. The quantitative real-time reverse transcription PCR demonstrated that soybean GmDIR22 mRNA is expressed most highly in stems, followed by roots and leaves. The treatments with stresses demonstrated that GmDIR22 is significantly induced by P. sojae and gibberellic acid (GA3), and also responds to salicylic acid, methyl jasmonic acid, and abscisic acid. The GmDIR22 is targeted to the cytomembrane when transiently expressed in Arabidopsis protoplasts. Moreover, The GmDIR22 recombinant protein purified from Escherichia coli could effectively direct E-coniferyl alcohol coupling into lignan (+)-pinoresinol. Accordingly, the overexpression of GmDIR22 in transgenic soybean increased total lignan accumulation. Moreover, the lignan extracts from GmDIR22 transgenic plants effectively inhibits P. sojae hyphal growth. Furthermore, the transgenic overexpression of GmDIR22 in the susceptible soybean cultivar 'Dongnong 50' enhances its resistance to P. sojae. Collectively, these data suggested that the primary role of GmDIR22 is probably involved in the regulation of lignan biosynthesis, and which contributes to resistance to P. sojae.

Is Domain Highlighting Actually Helpful in Identifying Phishing Web Pages?

OBJECTIVE: To evaluate the effectiveness of domain highlighting in helping users identify whether Web pages are legitimate or spurious. BACKGROUND: As a component of the URL, a domain name can be overlooked. Consequently, browsers highlight the domain name to help users identify which Web site they are visiting. Nevertheless, few studies have assessed the effectiveness of domain highlighting, and the only formal study confounded highlighting with instructions to look at the address bar. METHOD: We conducted two phishing detection experiments. Experiment 1 was run online: Participants judged the legitimacy of Web pages in two phases. In Phase 1, participants were to judge the legitimacy based on any information on the Web page, whereas in Phase 2, they were to focus on the address bar. Whether the domain was highlighted was also varied. Experiment 2 was conducted similarly but with participants in a laboratory setting, which allowed tracking of fixations. RESULTS: Participants differentiated the legitimate and fraudulent Web pages better than chance. There was some benefit of attending to the address bar, but domain highlighting did not provide effective protection against phishing attacks. Analysis of eye-gaze fixation measures was in agreement with the task performance, but heat-map results revealed that participants' visual attention was attracted by the highlighted domains. CONCLUSION: Failure to detect many fraudulent Web pages even when the domain was highlighted implies that users lacked knowledge of Web page security cues or how to use those cues. APPLICATION: Potential applications include development of phishing prevention training incorporating domain highlighting with other methods to help users identify phishing Web pages.

Overexpression of Soybean Isoflavone Reductase (GmIFR) Enhances Resistance to Phytophthora sojae in Soybean.

Isoflavone reductase (IFR) is an enzyme involved in the biosynthetic pathway of isoflavonoid phytoalexin in plants. IFRs are unique to the plant kingdom and are considered to have crucial roles in plant response to various biotic and abiotic environmental stresses. Here, we report the characterization of a novel member of the soybean isoflavone reductase gene family GmIFR. Overexpression of GmIFR transgenic soybean exhibited enhanced resistance to Phytophthora sojae. Following stress treatments, GmIFR was significantly induced by P. sojae, ethephon (ET), abscisic acid (placeCityABA), salicylic acid (SA). It is located in the cytoplasm when transiently expressed in soybean protoplasts. The daidzein levels reduced greatly for the seeds of transgenic plants, while the relative content of glyceollins in transgenic plants was significantly higher than that of non-transgenic plants. Furthermore, we found that the relative expression levels of reactive oxygen species (ROS) of transgenic soybean plants were significantly lower than those of non-transgenic plants after incubation with P. sojae, suggesting an important role of GmIFR might function as an antioxidant to reduce ROS in soybean. The enzyme activity assay suggested that GmIFR has isoflavone reductase activity.

Improved production of pristinamycin coupled with an adsorbent resin in fermentation by Streptomyces pristinaespiralis.

Batch fermentation by Streptomyces pristinaespiralis with the addition of adsorbent resins was used to increase the production of pristinamycin. In consideration of the adsorption capacity and the desorption ability, a polymeric resin, JD-1, was finally selected. The maximum production of pristinamycin in Erlenmeyer flasks went up to 1.13 from 0.4 g l(-1), by adding 12% (w/v) resin JD-1 into the culture broth at 20 h after inoculation. In a 3 l bioreactor, pristinamycin fermentation with the addition of 12% (w/v) resin JD-1 at 20 h after inoculation reached 0.8 g l(-1), which was a 1.25-fold increase over fermentation without resin.