The Space Physics Environment Data Analysis System (SPEDAS)

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.

Why air quality in the Alps remains a matter of concern. The impact of organic pollutants in the alpine area

In the middle of Europe, the Alps form a geographical and meteorological trap for atmospheric pollutants including volatile and semi-volatile organic compounds emitted in the surrounding lowlands. This is due to their barrier effects, high precipitation rates, and low ambient temperatures. Also the pollutants emitted in the cities inside the Alps spread in the region depending on orographic and meteorological conditions. Although a number of studies on the distribution and effect of pollutants in the Alps has been published, comprehensive information on potential hazards, and ways to improve this sensible environment are lacking. This opinion paper is the result of a discussion during the Winterseminar of the AlpsBioCluster project in Munich. It summarizes the current literature and presents some case studies on local pollution sources in the Alps, and the possibility of using biomonitoring techniques to assess critical pollution loads and distributions.

Ruminally undegradable protein content and digestibility for forages using the mobile bag in situ technique

Four experiments were conducted to evaluate RUP content and digestibility for smooth bromegrass, subirrigated meadow, upland native range, and warm-season grasses. Samples were collected from esophageally cannulated cows or ruminally cannulated steers. Forages were ruminally incubated in in situ bags for durations of time based on 75% of total mean retention time, which was based on IVDMD and rate of passage calculations. One-half of the bags were duodenally incubated and excreted in the feces, and NDIN was analyzed on all bags for RUP calculations. Crude protein was numerically greater early in the growing cycle for grasses compared with later as grasses matured (P ≤ 0.32). The RUP was 13.3%, 13.3%, and 19.7% of CP for smooth bromegrass, subirrigated meadow, and upland native range, respectively. These values tended to be lower early in the growth cycle and increased (linear P ≤ 0.13) as forages matured for warm-season grasses and subirrigated meadows. Because both CP and RUP content change throughout the growing season, expressing RUP as a percentage of DM gives more consistent averages compared with RUP as a percentage of CP. Coefficient of variation values for RUP as a percentage of DM averaged 0.21 over all 4 experiments compared with 0.26 for RUP as a percentage of CP. Average RUP as a percentage of DM was 2.03%, 1.53%, and 1.94% for smooth bromegrass, subirrigated meadow, and upland native range, respectively. Total tract indigestible protein (TTIDP) linearly increased with maturity for subirrigated meadow samples (P < 0.01). A quadratic response (P ≤ 0.06) for TTIDP was observed in smooth bromegrass and warm-season grass samples. Digestibility of RUP varied considerably, ranging from 25% to 60%. Subirrigated meadow, native range, and smooth bromegrass samples tended to have linear decreases (P ≤ 0.11) in RUP digestibility throughout the growing season. The amount of digested RUP was fairly consistent across experiments and averages for smooth bromegrass, subirrigated meadow, and upland native range were 0.92%, 0.64%, and 0.49% of DM, respectively. Warm-season grasses in Exp. 2 had greater RUP (4.31% of DM) and amount of RUP digested (2.26% of DM), possibly because of cattle selecting for leadplant that contains more CP than the grasses. Forages can vary in CP, RUP, TTIDP, and RUP digestibility depending on the forage type, year, and time within year, but RUP digestibility is likely less than what previous sources have reported.

Contemporaneous cell spreading and phagocytosis: magneto-resistive real-time monitoring of membrane competing processes

Adhesion and spreading of cells strongly depend on the properties of the underlying surface, which has significant consequences in long-term cell behavior adaption. This relationship is important for the understanding of both biological functions and their bioactivity in disease-related applications. Employing our magnetic lab-on-a-chip system, we present magnetoresistive-based real-time and label-free detection of cellular phagocytosis behavior during their spreading process on particle-immobilized sensor surfaces. Cell spreading experiments carried out on particle-free and particle-modified surfaces reveal a delay in spreading rate after an elapsed time of about 2.2h for particle-modified surfaces due to contemporaneous cell membrane loss by particle phagocytosis. Our associated magnetoresistive measurements show a high uptake rate at early stages of cell spreading, which decreases steadily until it reaches saturation after an average elapsed time of about 100 min. The corresponding cellular average uptake rate during the entire cell spreading process accounts for three particles per minute. This result represents a four times higher phagocytosis efficiency compared to uptake experiments carried out for confluently grown cells, in which case cell spreading is already finished and, thus, excluded. Furthermore, other dynamic cell-surface interactions at nano-scale level such as cell migration or the dynamics of cell attachment and detachment are also addressable by our magnetic lab-on-a-chip approach.

Magnetoresistive-based real-time cell phagocytosis monitoring

The uptake of large particles by cells (phagocytosis) is an important factor in cell biology and also plays a major role in biomedical applications. So far, most methods for determining the phagocytic properties rely on cell-culture incubation and end-point detection schemes. Here, we present a lab-on-a-chip system for real-time monitoring of magnetic particle uptake by human fibroblast (NHDF) cells. It is based on recording the time evolution of the average position and distribution of magnetic particles during phagocytosis by giant-magnetoresistive (GMR) type sensors. We employ particles with a mean diameter of 1.2 μm and characterize their phagocytosis-relevant properties. Our experiments at physiological conditions reveal a cellular uptake rate of 45 particles per hour and show that phagocytosis reaches saturation after an average uptake time of 27.7h. Moreover, reference phagocytosis experiments at 4°C are carried out to mimic environmental or disease related inhibition of the phagocytic behavior, and our measurements clearly show that we are able to distinguish between cell-membrane adherent and phagocytosed magnetic particles. Besides the demonstrated real-time monitoring of phagocytosis mechanisms, additional nano-biointerface studies can be realized, including on-chip cell adhesion/spreading as well as cell migration, attachment and detachment dynamics. This versatility shows the potential of our approach for providing a multifunctional platform for on-chip cell analysis.

Artificial cilia of magnetically tagged polymer nanowires for biomimetic mechanosensing

Polymeric nanowires of polypyrrole have been implemented as artificial cilia on giant-magneto-resistive multilayer sensors for a biomimetic sensing approach. The arrays were tagged with a magnetic material, the stray field of which changes relative to the underlying sensor as a consequence of mechanical stimuli which are delivered by a piezoactuator. The principle resembles balance sensing in mammals. Measurements of the sensor output voltage suggest a proof of concept at frequencies of around 190 kHz and a tag thickness of ∼300 nm. Characterization was performed by scanning electron microscopy and magnetic force microscopy. Micromagnetic and finite-element simulations were conducted to assess basic sensing aspects.

What is needed for a sunscreen to provide complete protection

Human skin is increasingly exposed to sunlight. In order to achieve complete protection against the cumulative detrimental effects from sun exposure, topical strategies must shield against the range of solar wavelengths that can damage the skin. Importantly, the harm sustained by the skin is not limited to that caused by the ultraviolet (UV) portion of the light spectrum, but also includes the adverse effects inflicted by near infrared energy. Consequently, in an attempt to provide the necessary broad spectrum coverage, innovative research continues through the exploration of new compounds and novel combinations of chemical and physical UV filters with molecules that are capable of interfering with and/or preventing the deleterious effects of infrared A (IRA) radiation. Existing examples of infrared-protective active agents include mitochondrially targeted antioxidants of synthetic or natural origin.

Prevention of infrared-A radiation mediated detrimental effects in human skin

Photoaging and skin damage that is caused by solar radiation is well known. We have recently learned that within the solar spectrum this damage not only results from ultraviolet (UV) radiation, but also from longer wavelengths, in particular near infrared radiation. Accordingly, infrared radiation (IR) has been shown to alter the collagen equilibrium of the dermal extracellular matrix in at least 2 ways: (1) by leading to an increased expression of the collagen degrading enzyme matrixmetalloproteinase-1 while (2) decreasing the de novo synthesis of the collagen itself. Infrared-A (IRA) radiation exposure, therefore, induces similar biological effects to UV, but the underlying mechanisms are substantially different. IRA acts via the mitochondria and therefore protection from IR requires alternative strategies.

The Effect of Processed Water on Constitutive and Ultraviolet-A-Radiation-Induced Level of Mitochondrial DNA Mutations in Human Dermal Fibroblasts

The integrity of the mitochondrial genome is of crucial importance for the cellular energy metabolism, and increased mutation rates are causally related to premature ageing. We demonstrate that replacement of normal deionized water with processed water in cell culture medium decreases the constitutive levels of the most frequent large-scale deletion of the mitochondrial genome in human dermal fibroblasts. In addition the presence of processed water also prevented the generation of the common deletion which was induced in these cells by repetitive UVA irradiation (3 x 8 J/cm(2) daily). Thus, processed water appears to protect the mitochondrial genome and may thus exert anti-oxidative and anti-ageing effects.