Desingularization of vortices for the Euler equation

We study the existence of stationary classical solutions of the incompressible Euler equation in the plane that approximate singular stationnary solutions of this equation. The construction is performed by studying the asymptotics of equation -\eps^2 \Delta u^\eps=(u^\eps-q-\frac{\kappa}{2\pi} \log \frac{1}{\eps})_+^p with Dirichlet boundary conditions and $q$ a given function. We also study the desingularization of pairs of vortices by minimal energy nodal solutions and the desingularization of rotating vortices.Comment: 40 page

Simulations of galactic dynamos

We review our current understanding of galactic dynamo theory, paying particular attention to numerical simulations both of the mean-field equations and the original three-dimensional equations relevant to describing the magnetic field evolution for a turbulent flow. We emphasize the theoretical difficulties in explaining non-axisymmetric magnetic fields in galaxies and discuss the observational basis for such results in terms of rotation measure analysis. Next, we discuss nonlinear theory, the role of magnetic helicity conservation and magnetic helicity fluxes. This leads to the possibility that galactic magnetic fields may be bi-helical, with opposite signs of helicity and large and small length scales. We discuss their observational signatures and close by discussing the possibilities of explaining the origin of primordial magnetic fields.Comment: 28 pages, 15 figure, to appear in Lecture Notes in Physics "Magnetic fields in diffuse media", Eds. E. de Gouveia Dal Pino and A. Lazaria

Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

Identification of CD8+ cytotoxic T lymphocyte (CTL) epitopes has traditionally relied upon testing of overlapping peptide libraries for their reactivity with T cells in vitro. Here, we pursued deep ligand sequencing (DLS) as an alternative method of directly identifying those ligands that are epitopes presented to CTLs by the class I human leukocyte antigens (HLA) of infected cells. Soluble class I HLA-A*11:01 (sHLA) was gathered from HIV-1 NL4-3-infected human CD4+ SUP-T1 cells. HLA-A*11:01 harvested from infected cells was immunoaffinity purified and acid boiled to release heavy and light chains from peptide ligands that were then recovered by size-exclusion filtration. The ligands were first fractionated by high-pH high-pressure liquid chromatography and then subjected to separation by nano-liquid chromatography (nano-LC)–mass spectrometry (MS) at low pH. Approximately 10 million ions were selected for sequencing by tandem mass spectrometry (MS/MS). HLA-A*11:01 ligand sequences were determined with PEAKS software and confirmed by comparison to spectra generated from synthetic peptides. DLS identified 42 viral ligands presented by HLA-A*11:01, and 37 of these were previously undetected. These data demonstrate that (i) HIV-1 Gag and Nef are extensively sampled, (ii) ligand length variants are prevalent, particularly within Gag and Nef hot spots where ligand sequences overlap, (iii) noncanonical ligands are T cell reactive, and (iv) HIV-1 ligands are derived from de novo synthesis rather than endocytic sampling. Next-generation immunotherapies must factor these nascent HIV-1 ligand length variants and the finding that CTL-reactive epitopes may be absent during infection of CD4+ T cells into strategies designed to enhance T cell immunity

Theory and Applications of Non-Relativistic and Relativistic Turbulent Reconnection

Realistic astrophysical environments are turbulent due to the extremely high Reynolds numbers. Therefore, the theories of reconnection intended for describing astrophysical reconnection should not ignore the effects of turbulence on magnetic reconnection. Turbulence is known to change the nature of many physical processes dramatically and in this review we claim that magnetic reconnection is not an exception. We stress that not only astrophysical turbulence is ubiquitous, but also magnetic reconnection itself induces turbulence. Thus turbulence must be accounted for in any realistic astrophysical reconnection setup. We argue that due to the similarities of MHD turbulence in relativistic and non-relativistic cases the theory of magnetic reconnection developed for the non-relativistic case can be extended to the relativistic case and we provide numerical simulations that support this conjecture. We also provide quantitative comparisons of the theoretical predictions and results of numerical experiments, including the situations when turbulent reconnection is self-driven, i.e. the turbulence in the system is generated by the reconnection process itself. We show how turbulent reconnection entails the violation of magnetic flux freezing, the conclusion that has really far reaching consequences for many realistically turbulent astrophysical environments. In addition, we consider observational testing of turbulent reconnection as well as numerous implications of the theory. The former includes the Sun and solar wind reconnection, while the latter include the process of reconnection diffusion induced by turbulent reconnection, the acceleration of energetic particles, bursts of turbulent reconnection related to black hole sources as well as gamma ray bursts. Finally, we explain why turbulent reconnection cannot be explained by turbulent resistivity or derived through the mean field approach.Comment: 66 pages, 24 figures, a chapter of the book "Magnetic Reconnection - Concepts and Applications", editors W. Gonzalez, E. N. Parke

High-resolution x-ray imaging for microbiology at the Advanced Photon Source

Exciting new applications of high-resolution x-ray imaging have emerged recently due to major advances in high-brilliance synchrotrons sources and high-performance zone plate optics. Imaging with submicron resolution is now routine with hard x-rays: the authors have demonstrated 150 run in the 6--10 keV range with x-ray microscopes at the Advanced Photon Source (APS), a third-generation synchrotrons radiation facility. This has fueled interest in using x-ray imaging in applications ranging from the biomedical, environmental, and materials science fields to the microelectronics industry. One important application they have pursued at the APS is a study of the microbiology of bacteria and their associated extracellular material (biofilms) using fluorescence microanalysis. No microscopy techniques were previously available with sufficient resolution to study live bacteria ({approx}1 {micro}m x 4 {micro}m in size) and biofilms in their natural hydrated state with better than part-per-million elemental sensitivity and the capability of determining g chemical speciation. In vivo x-ray imaging minimizes artifacts due to sample fixation, drying, and staining. This provides key insights into the transport of metal contaminants by bacteria in the environment and potential new designs for remediation and sequestration strategies

Digital Gene Expression Profiling by 5′-End Sequencing of cDNAs during Reprogramming in the Moss Physcomitrella patens

Stem cells self-renew and repeatedly produce differentiated cells during development and growth. The differentiated cells can be converted into stem cells in some metazoans and land plants with appropriate treatments. After leaves of the moss Physcomitrella patens are excised, leaf cells reenter the cell cycle and commence tip growth, which is characteristic of stem cells called chloronema apical cells. To understand the underlying molecular mechanisms, a digital gene expression profiling method using mRNA 5′-end tags (5′-DGE) was established. The 5′-DGE method produced reproducible data with a dynamic range of four orders that correlated well with qRT-PCR measurements. After the excision of leaves, the expression levels of 11% of the transcripts changed significantly within 6 h. Genes involved in stress responses and proteolysis were induced and those involved in metabolism, including photosynthesis, were reduced. The later processes of reprogramming involved photosynthesis recovery and higher macromolecule biosynthesis, including of RNA and proteins. Auxin and cytokinin signaling pathways, which are activated during stem cell formation via callus in flowering plants, are also activated during reprogramming in P. patens, although no exogenous phytohormone is applied in the moss system, suggesting that an intrinsic phytohormone regulatory system may be used in the moss

Evolution and environment of the eastern linear pottery culture: A case study in the site of Polgár-Piócási-Dűlő

A salvage excavation preceding a major investment project was conducted in 2006–2007, during which associated settlement features of a Middle Neolithic, Eastern Linear Pottery Culture (Alföld Linearbandkeramik – ALBK) were uncovered in an area called Piócási-dűlő on the eastern outskirts of Polgár. The features of the ALBK settlement date from two periods. The cluster of multi-functional pits yielding a rich assortment of finds, the handful of post-holes and an unusual ritual well found in the southern part of the investigated area formed one unit from the earliest phase of the Middle Neolithic (ALBK I). The settlement’s other occupation can be assigned to the late phase of the Middle Neolithic (ALBK IV). Five houseplans representing the remains of timber-framed buildings outlined a distinct area with three multi-functional pits. Associated with the above features were 8 burials. The preliminary archaeobotanical results from Polgár–Piócási-dűlő are based on the plant material found within the sediments of 11 archaeological structures, which mainly represent pits and a welI. It can be stated that the natural environment offered habitats in which oak trees dominated in the local vegetation, forming floodplain forests and wooded steppes. They also provided food in the form of fruits and formed an optimal habitat for domestic animals. Arable fields were probably also established in the vicinity of the settlements, suggested by findings of macroscopic plant remains that represented cultivated species. In both settlement phases lithic production activities are manifested both by the local on-site lithic production and – most importantly – by the presence of imported, mainly mesolocal, raw materials that point to contacts with deposit areas, or off-site preliminary working of obsidian and limnoquartzites. The kit of harvesting tools and a large number of grinding stones – especially in the younger phase – for the preparation of plant food suggest a major role of plant cultivation

Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells

Human immunodeficiency virus (HIV) persists indefinitely in individuals with HIV who receive antiretroviral therapy (ART) owing to a reservoir of latently infected cells that contain replication-competent virus1–4. Here, to better understand the mechanisms responsible for latency persistence and reversal, we used the interleukin-15 superagonist N-803 in conjunction with the depletion of CD8+ lymphocytes in ART-treated macaques infected with simian immunodeficiency virus (SIV). Although N-803 alone did not reactivate virus production, its administration after the depletion of CD8+ lymphocytes in conjunction with ART treatment induced robust and persistent reactivation of the virus in vivo. We found viraemia of more than 60 copies per ml in all macaques (n = 14; 100%) and in 41 out of a total of 56 samples (73.2%) that were collected each week after N-803 administration. Notably, concordant results were obtained in ART-treated HIV-infected humanized mice. In addition, we observed that co-culture with CD8+ T cells blocked the in vitro latency-reversing effect of N-803 on primary human CD4+ T cells that were latently infected with HIV. These results advance our understanding of the mechanisms responsible for latency reversal and lentivirus reactivation during ART-suppressed infection