Estimation of direct and cross power spectral density of discrete data using the fast Fourier transform

Direct and cross power spectral density estimation of discrete data using fast Fourier transform with digital filter solutio

Central African biomes and forest succession stages derived from modern pollen data and plant functional types

New detailed vegetation reconstructions are proposed in Atlantic Central Africa from a modern pollen data set derived from 199 sites (Cameroon, Gabon and Congo) including 131 new sites. In this study, the concept of plant functional classification is improved with new and more detailed plant functional types (PFTs) and new aggregations of pollen taxa. Using the biomisation method, we reconstructed (1) modern potential biomes and (2) potential succession stages of forest regeneration, a new approach in Atlantic Central African vegetation dynamics and ecosystem functioning reconstruction. When compared to local vegetation, potential biomes are correctly reconstructed (97.5% of the sites) and tropical rain forest (TRFO biome) is well identified from tropical seasonal forest (TSFO biome). When the potential biomes are superimposed on the White's vegetation map, only 76.4% of the sites are correctly reconstructed. But using botanical data, correspondence and cluster analyses, the 43 sites from Congo (Mayombe) evidence more affinities with those of central Gabon and so they can also be considered as correctly reconstructed as TRFO biome and White's map should be revised. In terms of potential succession stages of forest regeneration, the mature forest (TMFO) is well differentiated from the secondary forest (TSFE), but inside this latter group, the young and the pioneer stages are not clearly identified due probably to their low sampling representation. Moreover, linked to their progressive and mosaic character, the boundaries between two forest biomes or two forest stages are not clearly detected and need also a more intensive sampling in such transitions

Transportin 3 Promotes a Nuclear Maturation Step Required for Efficient HIV-1 Integration

The HIV/AIDS pandemic is a major global health threat and understanding the detailed molecular mechanisms of HIV replication is critical for the development of novel therapeutics. To replicate, HIV-1 must access the nucleus of infected cells and integrate into host chromosomes, however little is known about the events occurring post-nuclear entry but before integration. Here we show that the karyopherin Transportin 3 (Tnp3) promotes HIV-1 integration in different cell types. Furthermore Tnp3 binds the viral capsid proteins and tRNAs incorporated into viral particles. Interaction between Tnp3, capsid and tRNAs is stronger in the presence of RanGTP, consistent with the possibility that Tnp3 is an export factor for these substrates. In agreement with this interpretation, we found that Tnp3 exports from the nuclei viral tRNAs in a RanGTP-dependent way. Tnp3 also binds and exports from the nuclei some species of cellular tRNAs with a defective 3'CCA end. Depletion of Tnp3 results in a re-distribution of HIV-1 capsid proteins between nucleus and cytoplasm however HIV-1 bearing the N74D mutation in capsid, which is insensitive to Tnp3 depletion, does not show nucleocytoplasmic redistribution of capsid proteins. We propose that Tnp3 promotes HIV-1 infection by displacing any capsid and tRNA that remain bound to the pre-integration complex after nuclear entry to facilitate integration. The results also provide evidence for a novel tRNA nucleocytoplasmic trafficking pathway in human cells

Principles And Practices Fostering Inclusive Excellence: Lessons From The Howard Hughes Medical Institute’s Capstone Institutions

Best-practices pedagogy in science, technology, engineering, and mathematics (STEM) aims for inclusive excellence that fosters student persistence. This paper describes principles of inclusivity across 11 primarily undergraduate institutions designated as Capstone Awardees in Howard Hughes Medical Institute’s (HHMI) 2012 competition. The Capstones represent a range of institutional missions, student profiles, and geographical locations. Each successfully directed activities toward persistence of STEM students, especially those from traditionally underrepresented groups, through a set of common elements: mentoring programs to build community; research experiences to strengthen scientific skill/identity; attention to quantitative skills; and outreach/bridge programs to broaden the student pool. This paper grounds these program elements in learning theory, emphasizing their essential principles with examples of how they were implemented within institutional contexts. We also describe common assessment approaches that in many cases informed programming and created traction for stakeholder buy-in. The lessons learned from our shared experiences in pursuit of inclusive excellence, including the resources housed on our companion website, can inform others’ efforts to increase access to and persistence in STEM in higher education

LUX -- A Laser-Plasma Driven Undulator Beamline

The LUX beamline is a novel type of laser-plasma accelerator. Building on the joint expertise of the University of Hamburg and DESY the beamline was carefully designed to combine state-of-the-art expertise in laser-plasma acceleration with the latest advances in accelerator technology and beam diagnostics. LUX introduces a paradigm change moving from single-shot demonstration experiments towards available, stable and controllable accelerator operation. Here, we discuss the general design concepts of LUX and present first critical milestones that have recently been achieved, including the generation of electron beams at the repetition rate of up to 5 Hz with energies above 600 MeV and the generation of spontaneous undulator radiation at a wavelength well below 9 nm.Comment: submitte

Gas phase dicyanoacetylene (C4N2) on Titan: New experimental and theoretical spectroscopy results applied to Cassini CIRS data

International audienceDicyanoacetylene has not been observed so far in the gas phase in Titan’s atmosphere but this molecule is still on the list of the detected species, on the basis of the correspondence between a solid phase feature measured at 478 cm−1 in the laboratory and a spectral feature observed by Voyager. In this work, the infrared spectrum of gaseous C4N2 has been investigated to improve our knowledge of the band intensities and the line parameters for this molecule. Results of previously investigated bands have been revised and the intensity of the ν9 band at 107 cm−1, measured for the first time, was found to be the strongest absorption in the whole infrared domain. We have also improved the analysis of the complex rotational and hot band structure of C4N2 in order to obtain the first line lists for both bending modes ν8 and ν9. Using our radiative transfer code including the new line list of the strong ν9 band, we have searched for the signature of C4N2 at 107 cm−1 in the atmosphere of Titan utilizing Titan CIRS far infrared spectra. Despite averaging a large number of CIRS spectra at northern latitudes during the very favorable Titan winter, no gaseous C4N2 could be detected. At the 1-σ level we obtain an abundance upper limit of 5.3 × 10−10 for the limb average which is lower than or comparable to previously inferred values. As a consequence, the absence or very low amount of gaseous C4N2 makes quite puzzling its presence in the solid phase with an abundance compatible with the observed spectral feature at 478 cm−

Nutrient and fecal microbe sources for a eutrophic lake and recommended remediation steps, Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a man-made lake, classified as nutrient-impaired (303d list) by the EPA and State of Kentucky. The lake drains a watershed with residential developments, cattle pasture, modified woodlands, and some industrial/urban usage in the city of Richmond. The principal tributaries are Taylor Fork and Old Town Branch that meet to form the trunk of the lake approximately one mile in length. The upper reaches of Taylor Fork are adjacent to a densely-packed (quarter-acre lots) housing development with septic systems, and its watershed drains some portions of southern Richmond. Old Town Branch drains cattle pasture and residential areas of moderate to large lot size. An intermittent tributary flowing into Pond Cove drains cattle pasture and one small housing development. Fecal material contributes both nutrients and microbes to Wilgreen Lake. Both cattle and human fecal material enter the lake as documented by high fecal microbes counts and DNA tracing techniques. DNA tracing methods are limited by our sampling frequency but show that bovine Bacteroides microbes dominate water samples even at loci where suspected septic effluent enters the lake. The nitrogen isotopic composition (d15N) of lake plankton and algae are broadly consistent with nitrogen input from human fecal material, but results are equivocal. We suspect that large amounts of nutrients do enter the lake through septic groundwater input, however, the strong bovine signal clearly suggests deployment of remediation methods that would limit runoff from pastures adjacent to Wilgreen Lake and within its watershed. Such methods include fencing cattle off from drainages and the lake, and planting vegetative buffers around stream and lake margins. Our data alone cannot justify elimination of septic systems by costly implementation of a sewage treatment system

Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding?

Phenotypic plasticity, the ability of cells to reversibly alter their phenotypes in response to signals, presents a significant clinical challenge to treating solid tumors. Tumor cells utilize phenotypic plasticity to evade therapies, metastasize, and colonize distant organs. As a result, phenotypic plasticity can accelerate tumor progression. A well-studied example of phenotypic plasticity is the bidirectional conversions among epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M) phenotype(s). These conversions can alter a repertoire of cellular traits associated with multiple hallmarks of cancer, such as metabolism, immune evasion, invasion, and metastasis. To tackle the complexity and heterogeneity of these transitions, mathematical models have been developed that seek to capture the experimentally verified molecular mechanisms and act as ‘hypothesis-generating machines’. Here, we discuss how these quantitative mathematical models have helped us explain existing experimental data, guided further experiments, and provided an improved conceptual framework for understanding how multiple intracellular and extracellular signals can drive E/M plasticity at both the single-cell and population levels. We also discuss the implications of this plasticity in driving multiple aggressive facets of tumor progression