DeepNOG: fast and accurate protein orthologous group assignment.

MOTIVATION: Protein orthologous group databases are powerful tools for evolutionary analysis, functional annotation or metabolic pathway modeling across lineages. Sequences are typically assigned to orthologous groups with alignment-based methods, such as profile hidden Markov models, which have become a computational bottleneck. RESULTS: We present DeepNOG, an extremely fast and accurate, alignment-free orthology assignment method based on deep convolutional networks. We compare DeepNOG against state-of-the-art alignment-based (HMMER, DIAMOND) and alignment-free methods (DeepFam) on two orthology databases (COG, eggNOG 5). DeepNOG can be scaled to large orthology databases like eggNOG, for which it outperforms DeepFam in terms of precision and recall by large margins. While alignment-based methods still provide the most accurate assignments among the investigated methods, computing time of DeepNOG is an order of magnitude lower on CPUs. Optional GPU usage further increases throughput massively. A command-line tool enables rapid adoption by users. AVAILABILITYAND IMPLEMENTATION: Source code and packages are freely available at https://github.com/univieCUBE/deepnog. Install the platform-independent Python program with $pip install deepnog. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Filament-Reinforced 3D Printing of Clay.

This research resulted in the development of a method that can be used for filament-reinforced 3D printing of clay. Currently, clay-based elements are mixed with randomly dispersed fibrous materials in order to increase their tensile strength. The advantages of taking this new approach to create filament-reinforced prints are the increased bridging ability while printing, the increased tensile strength of the dried elements, and the achievement of non-catastrophic failure behavior. The research methodology used involves the following steps: (1) evaluating properties of various filament materials with respect to multiple criteria, (2) designing a filament guiding nozzle for co-extrusion, and (3) conducting a comprehensive testing phase for the composite material. This phase involves comparisons of bridging ability, tensile strength evaluations for un-reinforced clay prints and filament-reinforced prints, as well as the successful production of an architectural brick prototype. (4) Finally, the gathered results are subjected to thorough analysis. Compared to conventional 3D printing of clay, the developed method enables a substantial increase in bridging distance during printing by a factor of 460%. This capability facilitates the design of objects characterized by reduced solidity and the attainment of a more open, lightweight, and net-like structure. Further, results show that the average tensile strength of the reinforced sample in a dry state exhibited an enhancement of approximately 15%. The combination of clay's ability to resist compression and the filament's capacity to withstand tension has led to the development of a structural concept in this composite material akin to that of reinforced concrete. This suggests its potential application within the construction industry. Producing the prototype presented in this research would not have been possible with existing 3D printing methods of clay.

Basic Research of Material Properties of Mycelium-Based Composites.

The subject of this research is growing mycelium-based composites and exploring their basic material properties. Since the building industry is responsible for a large amount of annual CO2 emissions, rethinking building materials is an important task for future practices. Using such composites is a carbon-neutral strategy that offers alternatives to conventional building materials. Yet, in order to become competitive, their basic research is still needed. In order to create mycelium-based composites, it was necessary to establish a sterile work environment and develop shaping procedures for objects on a scale of architectural building elements. The composite material exhibited qualities that make it suitable for compression-only structures, temporary assemblies, and acoustic and thermal insulation. The methodology includes evaluating several substrates, focused on beech sawdust, with two mycelium strains (Pleurotus ostreatus and Ganoderma lucidum), density calculations, compression tests, three-point flexural tests and capillary water absorption. The results of this study are presented through graphical and numerical values comparing material and mechanical properties. This study established a database for succeeding investigations and for defining the potentials and limitations of this material. Furthermore, future applications and relevant examinations have been addressed.