Control of ULF Wave Accessibility to the Inner Magnetosphere by the Convection of Plasma Density

During periods of storm activity and enhanced convection, the plasma density in the afternoon sector of the magnetosphere is highly dynamic due to the development of plasmaspheric drainage plume (PDP) structure. This significantly affects the local Alfvén speed and alters the propagation of ULF waves launched from the magnetopause. Therefore, it can be expected that the accessibility of ULF wave power for radiation belt energization is sensitively dependent on the recent history of magnetospheric convection and the stage of development of the PDP. This is investigated using a 3-D model for ULF waves within the magnetosphere in which the plasma density distribution is evolved using an advection model for cold plasma, driven by a (VollandStern) convection electrostatic field (resulting in PDP structure). The wave model includes magnetic field day/night asymmetry and extends to a paraboloid dayside magnetopause, from which ULF waves are launched at various stages during the PDP development. We find that the plume structure significantly alters the field line resonance location, and the turning point for MHD fast waves, introducing strong asymmetry in the ULF wave distribution across the noon meridian. Moreover, the density enhancement within the PDP creates a waveguide or local cavity for MHD fast waves, such that eigenmodes formed allow the penetration of ULF wave power to much lower L within the plume than outside, providing an avenue for electron energization

Machine Learning to Automate Network Segregation for Enhanced Security in Industry 4.0

The heavy reliance of Industry 4.0 on emerging communication technologies, notably Industrial Internet-of-Things (IIoT) and Machine-Type Communications (MTC), and the increasing exposure of these traditionally isolated infrastructures to the Internet, are tremendously increasing the attack surface. Network segregation is a viable solution to address this problem. It essentially splits the network into several logical groups (subnetworks) and enforces adequate security policy on each segment, e.g., restricting unnecessary intergroup communications or controlling the access. However, existing segregation techniques primarily depend on manual configurations, which renders them inefficient for cyber-physical production systems because they are highly complex and heterogeneous environments with massive number of communicating machines. In this paper, we incorporate machine learning to automate network segregation, by efficiently classifying network end-devices into several groups through examining the traffic patterns that they generate. For performance evaluation, we analysed the data collected from a large segment of Infineon’s network in the context of the EU funded ECSEL-JU project “SemI40”. In particular, we applied feature selection and trained several supervised learning algorithms. Test results, using 10-fold cross validation, revealed that the algorithms generalise very well and achieve an accuracy up to 99.4%

Electron Dispersion and Parallel Electron Beam Observed Near the Separatrix

The separatrix region is the region between the separatrix and the reconnection jet. Due to the E×B drift and velocity filter effect in which high‐energy particles with high parallel speed can be seen prior to low‐energy particles along the field line, electrons are separated from ions. The electron dynamics in this region is of interest; however it has not been studied in detail, because of the insufficient resolution of plasma data. We present a slow separatrix crossing event observed by Magnetospheric Multiscale (MMS) satellite constellation on 1 January 2016, from the magnetosheath side with high‐resolution burst mode data. The electron edge and ion edge are clearly distinguished in the separatrix region. Two types of electron dispersion, one with a short duration (~0.3 s) and the other with a longer duration (~13 s) were detected between the electron and ion edges. The rapid dispersion (with small time scale) is mainly in the parallel direction, which might originate from a thin layer with non‐frozen‐in electrons close to the separatrix. The gradual (long time scale) dispersion is seen from parallel to perpendicular directions, which comes from the E×B drift of a curved D‐shape distribution of electrons. The width of the electron diffusion region on the magnetosheath side is estimated based on MMS observation. The observation also reveals an unexpected parallel electron beam outside of the electron edge. Wave‐particle interaction or parallel potential in the inflow region may be responsible for the generation of this electron population

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release

Unusual Location of the Geotail Magnetopause Near Lunar Orbit: A Case Study

The Earth's magnetopause is highly variable in location and shape and is modulated by solar wind conditions. On 8 March 2012, the ARTEMIS probes were located near the tail current sheet when an interplanetary shock arrived under northward interplanetary magnetic field conditions and recorded an abrupt tail compression at ∼(‐60, 0, ‐5) RE in Geocentric Solar Ecliptic coordinate in the deep magnetotail. Approximately 10 minutes later, the probes crossed the magnetopause many times within an hour after the oblique interplanetary shock passed by. The solar wind velocity vector downstream from the shock was not directed along the Sun‐Earth line but had a significant Y component. We propose that the compressed tail was pushed aside by the appreciable solar wind flow in the Y direction. Using a virtual spacecraft in a global magnetohydrodynamic (MHD) simulation, we reproduce the sequence of magnetopause crossings in the X‐Y plane observed by ARTEMIS under oblique shock conditions, demonstrating that the compressed magnetopause is sharply deflected at lunar distances in response to the shock and solar wind VY effects. The results from two different global MHD simulations show that the shocked magnetotail at lunar distances is mainly controlled by the solar wind direction with a timescale of about a quarter hour, which appears to be consistent with the windsock effect. The results also provide some references for investigating interactions between the solar wind/magnetosheath and lunar nearside surface during full moon time intervals, which should not happen in general

Profiling of the Tetraspanin CD151 Web and Conspiracy of CD151/Integrin β1 Complex in the Progression of Hepatocellular Carcinoma

Tetraspanin CD151 has been implicated in metastasis through forming complexes with different molecular partners. In this study, we mapped tetraspanin web proteins centered on CD151, in order to explore the role of CD151 complexes in the progression of hepatocellular carcinoma (HCC). Immunoprecipitation was used to isolate tetraspanin complexes from HCCLM3 cells using a CD151 antibody, and associated proteins were identified by mass spectrometry. The interaction of CD151 and its molecular partners, and their roles in invasiveness and metastasis of HCC cells were assayed through disruption of the CD151 network. Finally, the clinical implication of CD151 complexes in HCC patients was also examined. In this study, we identified 58 proteins, characterized the tetraspanin CD151 web, and chose integrin β1 as a main partner to further investigate. When the CD151/integrin β1 complex in HCC cells was disrupted, migration, invasiveness, secretion of matrix metalloproteinase 9, and metastasis were markedly influenced. However, both CD151 and integrin β1 expression were untouched. HCC patients with high expression of CD151/integrin β1 complex had the poorest prognosis of the whole cohort of patients. Together, our data show that CD151 acts as an important player in the progression of HCC in an integrin β1-dependent manner

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers

Seed systems smallholder farmers use

Seed can be an important entry point for promoting productivity, nutrition and resilience among smallholder farmers. While investments have primarily focused on strengthening the formal sector, this article documents the degree to which the informal sector remains the core for seed acquisition, especially in Africa. Conclusions drawn from a uniquely comprehensive data set, 9660 observations across six countries and covering 40 crops, show that farmers access 90.2 % of their seed from informal systems with 50.9 % of that deriving from local markets. Further, 55 % of seed is paid for by cash, indicating that smallholders are already making important investments in this arena. Targeted interventions are proposed for rendering formal and informal seed sector more smallholder-responsive and for scaling up positive impacts

Low Level of Low-Density Lipoprotein Receptor-Related Protein 1 Predicts an Unfavorable Prognosis of Hepatocellular Carcinoma after Curative Resection

BACKGROUND: Low-density lipoprotein receptor-related protein 1 (LRP1) is a multifunctional receptor involved in receptor-mediated endocytosis and cell signaling. The aim of this study was to elucidate the expression and mechanism of LRP1 in hepatocellular carcinoma (HCC). METHODS: LRP1 expression in 4 HCC cell lines and 40 HCC samples was detected. After interruption of LRP1 expression in a HCC cell line either with specific lentiviral-mediated shRNA LRP1 or in the presence of the LRP1-specific chaperone, receptor-associated protein (RAP), the role of LRP1 in the migration and invasion of HCC cells was assessed in vivo and in vitro, and the expression of matrix metalloproteinase (MMP) 9 in cells and the bioactivity of MMP9 in the supernatant were assayed. The expression and prognostic value of LRP1 were investigated in 327 HCC specimens. RESULTS: Low LRP1 expression was associated with poor HCC prognosis, with low expression independently related to shortened overall survival and increased tumor recurrence rate. Expression of LRP1 in non-recurrent HCC samples was significantly higher than that in early recurrent samples. LRP1 expression in HCC cell lines was inversely correlated with their metastatic potential. After inhibition of LRP1, low-metastatic SMCC-7721 cells showed enhanced migration and invasion and increased expression and bioactivity of MMP9. Correlation analysis showed a negative correlation between LRP1 and MMP9 expression in HCC patients. The prognostic value of LRP1 expression was validated in the independent data set. CONCLUSIONS: LRP1 modulated the level of MMP9 and low level of LRP1 expression was associated with aggressiveness and invasiveness in HCCs. LRP1 offered a possible strategy for tumor molecular therapy

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

Metatranscriptomes generated by pyrosequencing hold significant potential for describing functional processes in complex microbial communities. Meeting this potential requires protocols that maximize mRNA recovery by reducing the relative abundance of ribosomal RNA, as well as systematic comparisons to identify methodological artifacts and test for reproducibility across data sets. Here, we implement a protocol for subtractive hybridization of bacterial rRNA (16S and 23S) that uses sample-specific probes and is applicable across diverse environmental samples. To test this method, rRNA-subtracted and unsubtracted transcriptomes were sequenced (454 FLX technology) from bacterioplankton communities at two depths in the oligotrophic open ocean, yielding 10 data sets representing ~350 Mbp. Subtractive hybridization reduced bacterial rRNA transcript abundance by 40–58%, increasing recovery of non-rRNA sequences up to fourfold (from 12% to 20% of total sequences to 40–49%). In testing this method, we established criteria for detecting sequences replicated artificially via pyrosequencing errors and identified such replicates as a significant component (6–39%) of total pyrosequencing reads. Following replicate removal, statistical comparisons of reference genes (identified via BLASTX to NCBI-nr) between technical replicates and between rRNA-subtracted and unsubtracted samples showed low levels of differential transcript abundance (<0.2% of reference genes). However, gene overlap between data sets was remarkably low, with no two data sets (including duplicate runs from the same pyrosequencing library template) sharing greater than 17% of unique reference genes. These results indicate that pyrosequencing captures a small subset of total mRNA diversity and underscores the importance of reliable rRNA subtraction procedures to enhance sequencing coverage across the functional transcript pool.Agouron InstituteGordon and Betty Moore FoundationUnited States. Dept. of Energy. Office of ScienceNational Science Foundation (U.S.) (NSF Science and Technology Center Award EF0424599