ZebrafishMiner: an open source software for interactive evaluation of domain-specific fluorescence in zebrafish

Abstract High-throughput microscopy makes it possible to observe the morphology of zebrafish on large scale to quantify genetic, toxic or drug effects. The image acquisition is done by automated microscopy, images are evaluated automatically by image processing pipelines, tailored specifically to the requirements of the scientific question. The transfer of such algorithms to other projects, however, is complex due to missing guidelines and lack of mathematical or programming knowledge. In this work, we implement an image processing pipeline for automatic fluorescence quantification in user-defined domains of zebrafish embryos and larvae of different age. The pipeline is capable of detecting embryos and larvae in image stacks and quantifying domain activity. To make this protocol available to the community, we developed an open source software package called „ZebrafishMiner“ which guides the user through all steps of the processing pipeline and makes the algorithms available and easy to handle. We implemented all routines in an MATLAB-based graphical user interface (GUI) that gives the user control over all image processing parameters. The software is shipped with a manual of 30 pages and three tutorial datasets, which guide the user through the manual step by step. It can be downloaded at https://sourceforge.net/projects/scixminer/.</jats:p

Junctional adhesion molecule (JAM)-C deficient C57BL/6 mice develop a severe hydrocephalus

The junctional adhesion molecule (JAM)-C is a widely expressed adhesion molecule regulating cell adhesion, cell polarity and inflammation. JAM-C expression and function in the central nervous system (CNS) has been poorly characterized to date. Here we show that JAM-C−/− mice backcrossed onto the C57BL/6 genetic background developed a severe hydrocephalus. An in depth immunohistochemical study revealed specific immunostaining for JAM-C in vascular endothelial cells in the CNS parenchyma, the meninges and in the choroid plexus of healthy C57BL/6 mice. Additional JAM-C immunostaining was detected on ependymal cells lining the ventricles and on choroid plexus epithelial cells. Despite the presence of hemorrhages in the brains of JAM-C−/− mice, our study demonstrates that development of the hydrocephalus was not due to a vascular function of JAM-C as endothelial re-expression of JAM-C failed to rescue the hydrocephalus phenotype of JAM-C−/− C57BL/6 mice. Evaluation of cerebrospinal fluid (CSF) circulation within the ventricular system of JAM-C−/− mice excluded occlusion of the cerebral aqueduct as the cause of hydrocephalus development but showed the acquisition of a block or reduction of CSF drainage from the lateral to the 3rd ventricle in JAM-C−/− C57BL/6 mice. Taken together, our study suggests that JAM-C−/− C57BL/6 mice model the important role for JAM-C in brain development and CSF homeostasis as recently observed in humans with a loss-of-function mutation in JAM-C

Влияние асфальтенов, смол и парафинов на реологические свойства нефтей различных месторождений

Аномальность в поведении нефтей некоторых месторождений является следствием наличия в них сложных структурных единиц, придающие таким нефтям специфические реологические свойства и заметно отличающие их от обычных жидкостей. Изучение поведения аномальных нефтей является актуальной проблемой нефтяной отрасли, так как это путь к повышению эффективности эксплуатации скважин, поскольку при разработки месторождений такого типа нефтей эксплуатации осложняется проявлением аномалий вязкости и подвижности нефти, образованием АСПО и высоковязких эмульсий в призабойной зоне пласта. Основная цель работы - разработка научно-технологических способов регулирования реологических свойств высоковязких нефтей с неньютоновскими свойствами для оптимизации процессов добычи и транспорта по трубопроводам.Learning of the behavior of anomalous oils is an urgent problem in the oil industry, because it is the way to increase the efficiency of well operation. Indeed, development of deposits of this type of oil is complicated by the manifestation of viscosity anomalies and oil mobility due to the formation of AFS and high-viscosity emulsions in the bottomhole formation zone. The urgency of the problem is growing because of the share of hard-to-recover oil has grown substantially over the past decade in the structure of Russian reserves. The main objective of this paper - development of scientific and technological methods for regulating the rheological properties of high-viscosity oils with non-Newtonian properties for optimization of production and transport processes through pipelines

Evaluating chiral symmetry restoration through the use of sum rules

We pursue the idea of assessing chiral restoration via in-medium modifications of hadronic spectral functions of chiral partners. The usefulness of sum rules in this endeavor is illustrated, focusing on the vector and axial-vector channels. We first present an update on constructing quantitative results for pertinent vacuum spectral functions. These spectral functions serve as a basis upon which the in-medium spectral functions can be constructed. A striking feature of our analysis of the vacuum spectral functions is the need to include excited resonances, dictated by satisfying the Weinberg-type sum rules. This includes excited states in both the vector and axial-vector channels. Preliminary results for the finite temperature vector spectral function are presented. Based on a rho spectral function tested in dilepton data which develops a shoulder at low energies, we find that the rho' peak flattens off. The flattening may be a sign of chiral restoration, though a study of the finite temperature axial-vector spectral function remains to be carried out.Comment: 9 pages, conference proceedings from Resonance Workshop at UT Austin, March 5-7 201

Novel non-heteroarylpyrimidine (HAP) capsid assembly modifiers have a different mode of action from HAPs in vitro

One of the most promising viral targets in current hepatitis B virus (HBV) drug development is the core protein due to its multiple roles in the viral life cycle. Here we investigated the differences in the mode of action and antiviral activity of representatives of six different capsid assembly modifier (CAM) scaffolds: three from the well-characterized scaffolds heteroarylpyrimidine (HAP), sulfamoylbenzamide (SBA), and phenylpropenamide (PPA), and three from novel scaffolds glyoxamide-pyrrolamide (GPA), pyrazolyl-thiazole (PT), and dibenzo-thiazepin-2-one (DBT). The target activity and antiviral efficacy of the different CAMs were tested in biochemical and cellular assays. Analytical size exclusion chromatography and transmission electron microscopy showed that only the HAP compound induced formation of aberrant non-capsid structures (class II mode of action), while the remaining CAMs did not affect capsid gross morphology (class I mode of action). Intracellular lysates from the HepAD38 cell line, inducibly replicating HBV, showed no reduction in the quantities of intracellular core protein or capsid after treatment with SBA, PPA, GPA, PT, or DBT compounds; however HAP-treatment led to a profound decrease in both. Additionally, immunofluorescence staining of compound-treated HepAD38 cells showed that all non-HAP CAMs led to a shift in the equilibrium of HBV core antigen (HBcAg) towards complete cytoplasmic staining, while the HAP induced accumulation of HBcAg aggregates in the nucleus. Our study demonstrates that the novel scaffolds GPA, PT, and DBT exhibit class I modes of action, alike SBA and PPA, whereas HAP remains the only scaffold belonging to class II inhibitors

Sum rule analysis of vector and axial-vector spectral functions with excited states in vacuum

We simultaneously analyze vector and axial-vector spectral functions in vacuum using hadronic models constrained by experimental data and the requirement that Weinberg-type sum rules are satisfied. Upon explicit inclusion of an excited vector state, viz. rho', and the requirement that the perturbative continua are degenerate in vector and axial-vector channels, we deduce the existence of an excited axial-vector resonance state, a1', in order that the Weinberg sum rules are satisfied. The resulting spectral functions are further tested with QCD sum rules.Comment: 11 pages (corrected typos and made paper agree with published version

Maintenance of long-term experiments for unique insights into forest growth dynamics and trends: review and perspectives

In this review, the unique features and facts of long-term experiments are presented. Long-term experimental plots provide information of forest stand dynamics which cannot be derived from forest inventories or small temporary plots. Most comprise unthinned plots which represent the site specific maximum stand density as an unambiguous reference. By measuring the remaining as well as the removed stand, the survey of long-term experiments provides the total production at a given site, which is most relevant for examining the relationship between site conditions and stand productivity on the one hand and between stand density and productivity on the other. Thus, long-term experiments can reveal the site-specific effect of thinning and species mixing on stand structure, production and carbon sequestration. If they cover an entire rotation or even the previous and following generation on a given site, they reveal a species' long-term behaviour and any growth trends caused by environmental changes. Second, we exploit the unique data of European long-term experiments, some of which have been surveyed since 1848. We show the long-term effect of different density regimes on stand dynamics and an essential trade-off between total stand volume production and mean tree size. Long-term experiments reveal that tree species mixing can significantly increase stand density and productivity compared with monospecific stands. Thanks to surveys spanning decades or even a century, we can show the changing long-term-performance of different provenances and acceleration of stand production caused by environmental change, as well as better understand the growth dynamics of natural forests. Without long-term experiments forest science and practice would be not in a position to obtain such findings which are of the utmost relevance for science and practice. Third, we draw conclusions and show perspectives regarding the maintenance and further development of long-term experiments. It would require another 150years to build up a comparable wealth of scientific information, practical knowledge, and teaching and training model examples. Although tempting, long-term experiments should not be sacrificed for cost-cutting measures. Given the global environmental change and the resulting challenges for sustainable management, the network of long-term experiments should rather be extended regarding experimental factors, recorded variables and inter- and transdisciplinary use for science and practice

Photon and dilepton emission rates from high density quark matter

We compute the rates of real and virtual photon (dilepton) emission from dense QCD matter in the color-flavor locked (CFL) phase, focusing on results at moderate densities (3-5 times the nuclear saturation density) and temperatures $T\simeq80$ MeV. We pursue two approaches to evaluate the electromagnetic (e.m.) response of the CFL ground state: (i) a direct evaluation of the photon self energy using quark particle/-hole degrees of freedom, and (ii) a Hidden Local Symmetry (HLS) framework based on generalized mesonic excitations where the $\rho$ meson is introduced as a gauge boson of a local SU(3) color-flavor group. The $\rho$ coupling to generalized two-pion states induces a finite width and allows to address the issue of vector meson dominance (VMD) in the CFL phase. We compare the calculated emissivities (dilepton rates) to those arising from standard hadronic approaches including in-medium effects. For rather large superconducting gaps (several tens of MeV at moderate densities), as suggested by both perturbative and nonperturbative estimates, the dilepton rates from CFL quark matter turn out to be very similar to those obtained in hadronic many-body calculations, especially for invariant masses above $M\simeq0.3$ GeV. A similar observation holds for (real) photon production.Comment: 18 pages, 12 figure