Bsoft: image and molecular processing in electron microscopy

Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages.     

Removal and determination of trimethylsilanol from the landfill gas

The removal and determination of trimethylsilanol (TMSOH) in landfill gas has been studied before and after the special E3000-ITC System. The system works according to principle of temperature swing. The performance of TMSOH and humidity removal was 20% and more than 90%, respectively. The six of active carbons and impinger method were tested on the full-scale landfill in Poland for TMSOH and siloxanes determination. The extraction method and absorption in acetone were used. The concentration of TMSOH and siloxanes were found in range from 23.6 to 29.2 mg/m³ and from 18.0 to 38.9 mg/m³, respectively. The content of TMSOH in biogas originating from landfill was 41% out of all siloxanes. Moreover, the used system is alternative to other existing technique of landfill gas purification.     

Microbial biosignatures in ancient deep-sea hydrothermal sulfides

Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.     

The Impact of Scale,Recycling Boundary,and Type of Waste on Symbiosis and Recycling

Innovative waste recycling through industrial processes such as industrial and urban symbiosis has long been practiced and recently received much attention in the field of industrial ecology, with researchers making efforts to identify key contributing factors to successful industrial symbiosis. By analyzing 88 sample recycling projects in 23 eco‐towns in Japan, this article focuses on the factors of project scale, recycling boundary, and types of waste in relationship to environmental benefits and operational performance. The results showed that larger eco‐towns achieved more savings of virgin materials and higher stability in operation. Large‐scale projects tended to locate closer to the users of recycled products than did small‐scale projects. For treating similar types of waste, projects producing recycled products for special users (e.g., feedstock to a blast furnace for iron production) tended to locate closer to the users than those not producing for special users. The type of waste had a strong effect on the savings of virgin materials and recycling boundaries, while local factors had significant impacts on operational performance. The results also showed that agglomeration did not significantly contribute to the environmental benefits or operational performance of eco‐town projects. Another finding was that national agencies were helpful for facilitating cross‐prefecture transportation and long‐distance transaction of wastes. Implications of the findings are also discussed.     

Assessing the fishing footprint using data integrated from different tracking devices: Issues and opportunities

Different tracking devices are currently used to record the activity of fishing vessels in space and time and to analyse the pattern of fishing effort with respect to sea substrates, resources, or socio-economics factors. Among these devices, the Vessel Monitoring System (VMS) and the Automatic Identification System (AIS) represent the most interesting and fertile data sources for fisheries investigations but an integration of these two sources was never explored. Two large VMS and AIS datasets, covering the activity of the Italian fishing vessels with length-over-all ≥15 m for the whole year 2012, were used to perform the first assessment of the features characterizing each data source, and ultimately the properties of the estimators of ecological indicators of fishing pressure obtained using these data. In this way, a dataset related to five vessels equipped by a third high frequency device (the Fishing Observing System) was used as reference for a comparative analysis of fishing activity as reconstructed by VMS and/or AIS. Moreover, the ecological indicator 5 of fishing pressure as spatial extent of fishing activity (defined within the Data Collection Framework for Fisheries—DCF) was used as a reference to test the separate and integrated usage of VMS and AIS data. Results evidenced important differences in spatial, temporal and fleet coverage between VMS and AIS. Namely, VMS is affected by a lower frequency with respect to AIS but covers a larger portion of the fleet. Furthermore, AIS mainly operates near the harbours, so that offshore activity is underrepresented. The integration of VMS and AIS data, however, allows valorising the strengths and minimizing the limits of each source. In fact, the assessment of the total spatial extent of fishing activities (as captured by the DCF indicator 5) is significantly improved by the integrated usage of VMS and AIS data.