Oscillations and waves in solar spicules

Since their discovery, spicules have attracted increased attention as energy/mass bridges between the dense and dynamic photosphere and the tenuous hot solar corona. Mechanical energy of photospheric random and coherent motions can be guided by magnetic field lines, spanning from the interior to the upper parts of the solar atmosphere, in the form of waves and oscillations. Since spicules are one of the most pronounced features of the chromosphere, the energy transport they participate in can be traced by the observations of their oscillatory motions. Oscillations in spicules have been observed for a long time. However the recent high-resolutions and high-cadence space and ground based facilities with superb spatial, temporal and spectral capacities brought new aspects in the research of spicule dynamics. Here we review the progress made in imaging and spectroscopic observations of waves and oscillations in spicules. The observations are accompanied by a discussion on theoretical modelling and interpretations of these oscillations. Finally, we embark on the recent developments made on the presence and role of Alfven and kink waves in spicules. We also address the extensive debate made on the Alfven versus kink waves in the context of the explanation of the observed transverse oscillations of spicule axes

Atmospheric muon flux at PeV energies

In the near future the energy region above few hundreds of TeV may really be accessible for measurements of the atmospheric muon spectrum by the IceCube array. Therefore one expects that muon flux uncertainties above 50 TeV, related to a poor knowledge of charm production cross sections and insufficiently examined primary spectra and composition, will be diminished. We give predictions for the very high-energy muon spectrum at sea level, obtained with the three hadronic interaction models, taking into account also the muon contribution due to decays of the charmed hadrons.Comment: 8 pages, 3 figures. The version published in Int. J. Mod. Phys.

Trophic Relationships and Food Supply of Heterotrophic Animals in the Pelagic Ecosystem of the Black Sea

During recent decades, the Black Sea has been affected by many negative factors that strongly changed the condition of its ecosystem. Especially trophic relationships in the Black Sea pelagic system became very vulnerable influencing the food supply, productivity and abundance of many species and populations of this marine basin. Food is one of most important link between biota and its environment. In this monograph, the role and variability of trophodynamic processes that effect the well-being (health) of main heterotrophic components of ecosystem were analysed in detail for a few key species as indicators for estimation of ecosystem condition in whole. These are most significant mass species of the Black Sea pelagic ecosystem. Among copepods this is Calanus euxinus that dominates the mesozooplankton which makes up the fodder base of planktivorous fishes. Among gelatinous these are medusa Aurelia aurita and the alien ctenophores Mnemiopsis leidyi and Beroe ovata which affected strongly mesozooplankton composition. Lastly among fishes the anchovy Engraulis encrasicolus ponticus and sprat Sprattus sprattus phalericus that dominate small pelagic fishery. We considered in this monograph: • Diel feeding behaviour, in situ feeding rate of Calanus euxinus and impact of mesozooplankton on primary production and phytoplankton biomass. • The effect of vertical migrations on energy budget and its components in C. euxinus; metabolic substrates used in catabolic processes under both aerobic and hypoxic conditions, the role of reserve lipids and effect of abiotic factors on individual growth and population structure of this species. • The intensity and efficiency of ingestion and energy transformation in three gelatinous species ( jellyfish Aurelia aurita, ctenophores Mnemiopsis leidyi and Beroe ovata) and their predatory impact on zooplankton community. • Nutritional condition and food supply of anchovy and sprat in the close interaction with natural biotic and abiotic and anthropogenic factors. • Tendencies in this interaction during long time space: since 1960 s till present years. • Estimation of population condition of these species and its long-term change. This monograph is the collective work of Ukrainian and Turkish scientists studying complex hydrobiological problems of the Black Sea. Its aim is to reveal the significance of nutritional factors on the ecology of Black Sea biota, including changes which have already occurred, as well as offering some insight into changes that may happen in the future. Our joint investigations started in the first half of the 1990s, when conditions for the close cooperation of researchers from the two countries were suitable after the collapse of the Soviet era. This spirit continues to the present day. Professor Ümit Unluata, Director of Erdemli Institute of Marine Sciences (Middle East Technical University, Ankara) was of paramount importance in organising and fostering the work undertaken. We would like to devote this monograph to the memory of him, who died so prematurely. We are also grateful to Academician Professor V. N. Eremeev, Director of the Sevastopol Institute of Biology of the Southern Sea (National Academy of Sciences of Ukraine), and to the directors of Erdemli Institute of Marine Sciences (Professor Ilkay Salihoglu, Professor Sukru Besiktepe and Professor Ferit Bingel) who also made significant contributions to the Ukrainian–Turkish collaboration. We are grateful to Dr Bill Parr from the Black Sea Ecosystem Recovery Project for his valuable efforts in improving earlier drafts. All these investigations were carried out within the framework of the following five NATO linkage-grants: • Pelagic animal food supply in the unstable Black Sea environment, • Will the new alien ctenophore Beroe ovata control the plankton community in the Black Sea? • Grazing, growth and production of Calanus euxinus in the Black Sea, • Bioindicators for assessment of Black Sea ecosystem recovery, • Adaptability and vulnerability of marine species in changing environments. And four TUBITAK - NASU joint projects: • Quantification of the recent ctenophore invader Beroe ovata impact in the Black Sea • Monitoring of the Black Sea anchovy and sprat, • Salinity tolerance as a key factor of invasion success of the copepods of Calanus genus into the Sea of Marmara, • Salinity tolerance as a key factor of invasion success of the mesozooplankton species into the Sea of Marmara. We hope that this publication will make a substantial contribution to future studies of the Black Sea ecosystem and offers further understanding of those features regulating biological processes in this unique marine basin

On inconsistency of experimental data on primary nuclei spectra with sea level muon intensity measurements

For the first time a complete set of the most recent direct data on primary cosmic ray spectra is used as input into calculations of muon flux at sea level in wide energy range $E_\mu=1-3\cdot10^5$ GeV. Computations have been performed with the CORSIKA/QGSJET and CORSIKA/VENUS codes. The comparison of the obtained muon intensity with the data of muon experiments shows, that measurements of primary nuclei spectra conform to sea level muon data only up to several tens of GeV and result in essential deficit of muons at higher energies. As it follows from our examination, uncertainties in muon flux measurements and in the description of nuclear cascades development are not suitable to explain this contradiction, and the only remaining factor, leading to this situation, is underestimation of primary light nuclei fluxes. We have considered systematic effects, that may distort the results of the primary cosmic ray measurements with the application of the emulsion chambers. We suggest, that re-examination of these measurements is required with the employment of different hadronic interaction models. Also, in our point of view, it is necessary to perform estimates of possible influence of the fact, that sizable fraction of events, identified as protons, actually are antiprotons. Study of these cosmic ray component begins to attract much attention, but today nothing definite is known for the energies $>40$ GeV. In any case, to realize whether the mentioned, or some other reasons are the sources of disagreement of the data on primaries with the data on muons, the indicated effects should be thoroughly analyzed

SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation

Abstract Cellular differentiation is a complex process where a less specialized cell evolves into a more specialized cell. Despite the increasing research effort, identification of cell-fate determinants (transcription factors (TFs) determining cell fates during differentiation) still remains a challenge, especially when closely related cell types from a common progenitor are considered. Here, we develop SeesawPred, a web application that, based on a gene regulatory network (GRN) model of cell differentiation, can computationally predict cell-fate determinants from transcriptomics data. Unlike previous approaches, it allows the user to upload gene expression data and does not rely on pre-compiled reference data sets, enabling its application to novel differentiation systems. SeesawPred correctly predicted known cell-fate determinants on various cell differentiation examples in both mouse and human, and also performed better compared to state-of-the-art methods. The application is freely available for academic, non-profit use at http://seesaw.lcsb.uni.lu

Network analysis of human glaucomatous optic nerve head astrocytes

<p>Abstract</p> <p>Background</p> <p>Astrocyte activation is a characteristic response to injury in the central nervous system, and can be either neurotoxic or neuroprotective, while the regulation of both roles remains elusive.</p> <p>Methods</p> <p>To decipher the regulatory elements controlling astrocyte-mediated neurotoxicity in glaucoma, we conducted a systems-level functional analysis of gene expression, proteomic and genetic data associated with reactive optic nerve head astrocytes (ONHAs).</p> <p>Results</p> <p>Our reconstruction of the molecular interactions affected by glaucoma revealed multi-domain biological networks controlling activation of ONHAs at the level of intercellular stimuli, intracellular signaling and core effectors. The analysis revealed that synergistic action of the transcription factors AP-1, vitamin D receptor and Nuclear Factor-kappaB in cross-activation of multiple pathways, including inflammatory cytokines, complement, clusterin, ephrins, and multiple metabolic pathways. We found that the products of over two thirds of genes linked to glaucoma by genetic analysis can be functionally interconnected into one epistatic network via experimentally-validated interactions. Finally, we built and analyzed an integrative disease pathology network from a combined set of genes revealed in genetic studies, genes differentially expressed in glaucoma and closely connected genes/proteins in the interactome.</p> <p>Conclusion</p> <p>Our results suggest several key biological network modules that are involved in regulating neurotoxicity of reactive astrocytes in glaucoma, and comprise potential targets for cell-based therapy.</p

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

Introduction: Human epidermal growth factor receptor 2 (HER2)-amplified breast cancer represents a clinically well-defined subgroup due to availability of targeted treatment. However, HER2-amplified tumors have been shown to be heterogeneous at the genomic level by genome-wide microarray analyses, pointing towards a need of further investigations for identification of recurrent copy number alterations and delineation of patterns of allelic imbalance. Methods: High-density whole genome array-based comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) array data from 260 HER2-amplified breast tumors or cell lines, and 346 HER2-negative breast cancers with molecular subtype information were assembled from different repositories. Copy number alteration (CNA), loss-of-heterozygosity (LOH), copy number neutral allelic imbalance (CNN-AI), subclonal CNA and patterns of tumor DNA ploidy were analyzed using bioinformatical methods such as genomic identification of significant targets in cancer (GISTIC) and genome alteration print (GAP). The patterns of tumor ploidy were confirmed in 338 unrelated breast cancers analyzed by DNA flow cytometry with concurrent BAC aCGH and gene expression data. Results: A core set of 36 genomic regions commonly affected by copy number gain or loss was identified by integrating results with a previous study, together comprising > 400 HER2-amplified tumors. While CNN-AI frequency appeared evenly distributed over chromosomes in HER2-amplified tumors, not targeting specific regions and often < 20% in frequency, the occurrence of LOH was strongly associated with regions of copy number loss. HER2-amplified and HER2-negative tumors stratified by molecular subtypes displayed different patterns of LOH and CNN-AI, with basal-like tumors showing highest frequencies followed by HER2-amplified and luminal B cases. Tumor aneuploidy was strongly associated with increasing levels of LOH, CNN-AI, CNAs and occurrence of subclonal copy number events, irrespective of subtype. Finally, SNP data from individual tumors indicated that genomic amplification in general appears as monoallelic, that is, it preferentially targets one parental chromosome in HER2-amplified tumors. Conclusions: We have delineated the genomic landscape of CNAs, amplifications, LOH, and CNN-AI in HER2-amplified breast cancer, but also demonstrated a strong association between different types of genomic aberrations and tumor aneuploidy irrespective of molecular subtype

The Planetary Fourier Spectrometer (PFS) onboard the European Mars Express mission

International audience; The Planetary Fourier Spectrometer (PFS) for the Mars Express mission is an infrared spectrometer optimised for atmospheric studies. This instrument has a short wave (SW) channel that covers the spectral range from 1700 to 8200.0cm-1 (1.2- 5.5mum) and a long-wave (LW) channel that covers 250- 1700cm-1 (5.5- 45mum). Both channels have a uniform spectral resolution of 1.3cm-1. The instrument field of view FOV is about 1.6o (FWHM) for the Short Wavelength channel (SW) and 2.8o (FWHM) for the Long Wavelength channel (LW) which corresponds to a spatial resolution of 7 and 12 km when Mars is observed from an height of 250 km. PFS can provide unique data necessary to improve our knowledge not only of the atmosphere properties but also about mineralogical composition of the surface and the surface-atmosphere interaction. The SW channel uses a PbSe detector cooled to 200-220 K while the LW channel is based on a pyroelectric ( LiTaO3) detector working at room temperature. The intensity of the interferogram is measured every 150 nm of physical mirrors displacement, corresponding to 600 nm optical path difference, by using a laser diode monochromatic light interferogram (a sine wave), whose zero crossings control the double pendulum motion. PFS works primarily around the pericentre of the orbit, only occasionally observing Mars from large distances. Each measurements take 4 s, with a repetition time of 8.5 s. By working roughly 0.6 h around pericentre, a total of 330 measurements per orbit will be acquired 270 looking at Mars and 60 for calibrations. PFS is able to take measurements at all local times, facilitating the retrieval of surface temperatures and atmospheric vertical temperature profiles on both the day and the night side