Dark‑adaptation in the eyes of a lake and a sea population of opossum shrimp (Mysis relicta): retinoid isomer dynamics, rhodopsin regeneration, and recovery of light sensitivity

We have studied dark-adaptation at three levels in the eyes of the crustaceanMysis relictaover 2-3 weeks after exposing initially dark-adapted animals to strong white light: regeneration of 11-cisretinal through the retinoid cycle (by HPLC), restoration of native rhodopsin in photoreceptor membranes (by MSP), and recovery of eye photosensitivity (by ERG). We compare two model populations ("Sea", S-p, and "Lake", L-p) inhabiting, respectively, a low light and an extremely dark environment. 11-cisretinal reached 60-70% of the pre-exposure levels after 2 weeks in darkness in both populations. The only significant L-p/S(p)difference in the retinoid cycle was that L(p)had much higher levels of retinol, both basal and light-released. In S-p, rhodopsin restoration and eye photoresponse recovery parallelled 11-cisretinal regeneration. In L-p, however, even after 3 weeks only ca. 25% of the rhabdoms studied had incorporated new rhodopsin, and eye photosensitivity showed only incipient recovery from severe depression. The absorbance spectra of the majority of the L(p)rhabdoms stayed constant around 490-500 nm, consistent with metarhodopsin II dominance. We conclude that sensitivity recovery of S(p)eyes was rate-limited by the regeneration of 11-cisretinal, whilst that of L(p)eyes was limited by inertia in photoreceptor membrane turnover.Peer reviewe

Modulational Instability in Equations of KdV Type

It is a matter of experience that nonlinear waves in dispersive media, propagating primarily in one direction, may appear periodic in small space and time scales, but their characteristics --- amplitude, phase, wave number, etc. --- slowly vary in large space and time scales. In the 1970's, Whitham developed an asymptotic (WKB) method to study the effects of small "modulations" on nonlinear periodic wave trains. Since then, there has been a great deal of work aiming at rigorously justifying the predictions from Whitham's formal theory. We discuss recent advances in the mathematical understanding of the dynamics, in particular, the instability of slowly modulated wave trains for nonlinear dispersive equations of KdV type.Comment: 40 pages. To appear in upcoming title in Lecture Notes in Physic

Catalytic Oxidation of Volatile Organic Compounds in Industrial Off-Gases

Processes and apparatuses for catalytic oxidation of VOCs in industrial off-gases are described, including steady state and unsteady state processes, a combined adsorption-catalytic process and an advanced method of ozone induced oxidation for low concentrated exhausts. On the basis of research and development works a series of catalytic incinerators, operating in steady state and unsteady state mode, of various capacity were designed, constructed and tested in the purification of ventilation air and off-gases from VOCs. The principles of operation of different types of catalytic incinerators and possible areas of application are discussed. For VOC concentrations 150-1000 mg/m3 unsteady state catalytic incinerators of KART type should be used, for concentrations 1000-3000 mg/m3 steady state KROT apparatuses are recommended, and for concentrations over 3000 mg/m3 up to 7000 mg/m3 installations TKM-250. It is shown that for the purification of low concentrated gases with the content of organic vapors below 150 mg/m3 adsorptioncatalytic method or catalytic oxidation with ozone in the installation OKA-3000 are most effective. Main kinetic dependencies of the ozone induced oxidation of toluene and acetone over copper oxide catalyst are given and discussed. It is shown that the efficiency of this method of VOCs removal is based on low operation temperature 313-343 K, by contrast to conventional catalytic incineration by air requiring preliminary heating of the gases to 523-573 K. A special consideration is given to adsorptive damping as an efficient method for leveling the VOCs concentrations in the real industrial exhausts directed to the catalytic treatment. The use of adsorptive dampers filled with carbon allows elimination of large deviations of pollutant concentrations in the gas entering the catalyst bed, thus increasing the VOCs removal efficiency from average values. For calculations of adsorptive dampers, an equation describing the profiles of VOC concentrations in gas phase along the length of the adsorbate bed in the damper was derived

Quantum Disorder and Quantum Chaos in Andreev Billiards

We investigate the crossover from the semiclassical to the quantum description of electron energy states in a chaotic metal grain connected to a superconductor. We consider the influence of scattering off point impurities (quantum disorder) and of quantum diffraction (quantum chaos) on the electron density of states. We show that both the quantum disorder and the quantum chaos open a gap near the Fermi energy. The size of the gap is determined by the mean free time in disordered systems and by the Ehrenfest time in clean chaotic systems. Particularly, if both times become infinitely large, the density of states is gapless, and if either of these times becomes shorter than the electron escape time, the density of states is described by random matrix theory. Using the Usadel equation, we also study the density of states in a grain connected to a superconductor by a diffusive contact.Comment: 20 pages, 10 figure

Charge-Dependent Correlations in Relativistic Heavy Ion Collisions and the Chiral Magnetic Effect

We provide a phenomenological analysis of present experimental searches for local parity violation manifested through the Chiral Magnetic Effect. We introduce and discuss the relevant correlation functions used for the measurements. Our analysis of the available data from both RHIC and LHC shows that the present experimental evidence for the Chiral Magnetic Effect is rather ambiguous. We further discuss in some detail various background contributions due to conventional physics, which need to be understood quantitatively in order to draw a definitive conclusion about the existence of local parity violation in heavy ion collisions.Comment: 37 pages, to appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Ye

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

YesGalaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.NIH [U41 HG006620, U24 HG010263, U24 CA231877, U01 CA253481]; US National Science Foundation [1661497, 1758800, 2216612]; computational resources are provided by the Advanced Cyberinfrastructure Coordination Ecosystem (ACCESS-CI), Texas Advanced Computing Center, and the JetStream2 scientific cloud. Funding for open access charge: NIH. ELIXIR IS and Travel grants; EU Horizon Europe [HORIZON-INFRA-2021-EOSC-01-04, 101057388]; EU Horizon Europe under the Biodiversity, Circular Economy and Environment program (REA.B.3, BGE 101059492); German Federal Ministry of Education and Research, BMBF [031 A538A de.NBI-RBC]; Ministry of Science, Research and the Arts Baden-Württemberg (MWK) within the framework of LIBIS/de.NBI Freiburg. Galaxy Australia is supported by the Australian BioCommons which is funded through Australian Government NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons, as well as investment from the Queensland Government RICF program.Please note, contributors are listed in alphabetical order

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

YesGalaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.NIH [U41 HG006620, U24 HG010263, U24 CA231877, U01 CA253481]; US National Science Foundation [1661497, 1758800, 2216612]; computational resources are provided by the Advanced Cyberinfrastructure Coordination Ecosystem (ACCESS-CI), Texas Advanced Computing Center, and the JetStream2 scientific cloud. Funding for open access charge: NIH. ELIXIR IS and Travel grants; EU Horizon Europe [HORIZON-INFRA-2021-EOSC-01-04, 101057388]; EU Horizon Europe under the Biodiversity, Circular Economy and Environment program (REA.B.3, BGE 101059492); German Federal Ministry of Education and Research, BMBF [031 A538A de.NBI-RBC]; Ministry of Science, Research and the Arts Baden-Württemberg (MWK) within the framework of LIBIS/de.NBI Freiburg. Galaxy Australia is supported by the Australian BioCommons which is funded through Australian Government NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons, as well as investment from the Queensland Government RICF program

Japanese quail (Coturnix japonica) as a model of accelerated aging of human retinal processes. Report 1. Assessment of the age RPE lipofuscin accumulation depending on the retinal amount of oxycarotenoids

ABSTRACT Purpose. Using the eyes of quails C. japonic as a model system to evaluate age-related accumulation of lipofuscin granules in the cells of the retinal pigment epithelium depending on the level of oxycarotenoids content in the retina and in the retinal pigment epithelium itself. Material and methods. Assessment of the oxycarotenoids content in the retinas of birds was carried out in the absorption spectra of chloroform-methanol extracts from the tissue of isolated retinas and retinal pigment epithelium. The content of lipofuscin in cells of retinal pigment epithelium was estimated by a morphometric analysis of the fluorescent microscopy microphotographs. Results. It is shown that in the cells of the retinal pigment epithelium of old birds (from 43 weeks and older) the volume contents of lipofuscin is 17 times higher than that in young birds aged 13 weeks. In this case, the old birds (56 weeks) with a low concentration of oxycarotenoids in retina: 1.49 mcg/g. raw weight ±0.09(σ), the volume lipofuscin granule quantity was in one and a half times higher than in the birds with a high content of oxycarotenoids: 3.1 mg/g. raw weight ±0.27(σ). Conclusions. The data obtained with the model animal system — the eyes of C. japonica birds, indicates the dependence of the aging accumulation of lipofuscin in the retinal pigment epithelium cells on the content of oxycarotenoids in the retina and its pigment epithelium

Japanese quail (Coturnix japonica) as the model of human aging retinal processes. Report № 2. Comparative analysis of the composition of retinoids isolated from retinal pigment epithelium of human and Japanese quail eyes

ABSTRACT Purpose. To compare the composition of retinoids of lipofuscin granules (LG) isolated from retinal pigment epithelium (RPE) of human cadaver eyes and Japanese quail. Material and methods. The Japanese quail′s retina and retinal pigment epithelium were chosen as a model of laboratory aging simulation. The evaluation of the amount of quail′s RPE retinoids was done by measuring of the fluorescence spectra and HPLC-analysis of the chloroform- methanol extraction from PRE. Results and conclusions. It has been shown that the spectral characteristics and the relative content of retinoids in lipofuscin granules (LG) isolated from retinal pigment epithelium (RPE) of human cadaver eyes and Japanese quail was very resemblance. These results allowed to consider Japanese quail (Coturnix japonica) as a suitable and enough adequate model of rapid human aging retinal processe