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We present an algorithm for the optimization of a class of finite-element integration loop nests. This algorithm, which exploits fundamental mathematical properties of finite-element operators, is proven to achieve a locally optimal operation count. In specified circumstances the optimum achieved is global. Extensive numerical experiments demonstrate significant performance improvements over the state of the art in finite-element code generation in almost all cases. This validates the effectiveness of the algorithm presented here and illustrates its limitations.

Background The falling cost of next-generation sequencing technology has allowed deep sequencing across related species and of individuals within species. Whole genome assemblies from these data remain high time- and resource-consuming computational tasks, particularly if best solutions are sought using different assembly strategies and parameter sets. However, in many cases, the underlying research questions are not genome-wide but rather target specific genes or sets of genes. We describe a novel assembly tool, SRAssembler, that efficiently assembles only contigs containing potential homologs of a gene or protein query, thus enabling gene-specific genome studies over large numbers of short read samples. Results We demonstrate the functionality of SRAssembler with examples largely drawn from plant genomics. The workflow implements a recursive strategy by which relevant reads are successively pulled from the input sets based on overlapping significant matches, resulting in virtual chromosome walking. The typical workflow behavior is illustrated with assembly of simulated reads. Applications to real data show that SRAssembler produces homologous contigs of equivalent quality to whole genome assemblies. Settings can be chosen to not only assemble presumed orthologs but also paralogous gene loci in distinct contigs. A key application is assembly of the same locus in many individuals from population genome data, which provides assessment of structural variation beyond what can be inferred from read mapping to a reference genome alone. SRAssembler can be used on modest computing resources or used in parallel on high performance computing clusters (most easily by invoking a dedicated Singularity image). Conclusions SRAssembler offers an efficient tool to complement whole genome assembly software. It can be used to solve gene-specific research questions based on large genomic read samples from multiple sources and would be an expedient choice when whole genome assembly from the reads is either not feasible, too costly, or unnecessary. The program can also aid decision making on the depth of sequencing in an ongoing novel genome sequencing project or with respect to ultimate whole genome assembly strategies. Electronic supplementary material The online version of this article (10.1186/s12859-019-2949-4) contains supplementary material, which is available to authorized users.

The article discusses the functioning of the local government in Ukraine and Poland. Special emphasis is placed on making use of Polish experiences when carrying out reforms of self-government in Ukraine. Стаття присвячена аналізу розвитку місцевого самоврядування в Україні та Польщі. Особливу увагу приділено використанню польського досвіду у цій сфері для реформування українського місцевого самоврядування.

The article discusses the verv law in Kievan Rus as a historical type of Ukrainian customary law. In particular, law-making function of old Ukrainian territorial communities (vervs) is dealt with. The influence of the verv law on the substance of the body of laws «Ruska Pravda» is examined. Стаття присвячена праву та самоврядуванню територіальних громад в Київській Русі. Досліджено правотворчі функції цих територіальних громад (вервів) та вплив вервного права на зміст законодавчого збірника «Руська правда». Проаналізовано напрямки правового регулювання суспільних відносин за вервним правом.

Ciliated protozoa possess cellular axes reflected in the arrangement of their ciliature. Upon transverse fission, daughter cells develop an identical ciliary pattern, ensuring perpetuation of the cellular phenotype. Experimentally manipulated cells can be induced to form atypical phenotypes, capable of intraclonal propagation and regeneration after encystment. One such phenotype in the ciliate Tetmemena pustulata (formerly Stylonychia pustulata) is the mirror-imaged doublet. These cells possess two distinct sets of ciliature, juxtaposed on the surfaces in mirror image symmetry, with a common anterior–posterior axis. We have examined whether individual ciliary components of Tetmemena mirror-image doublets are mirror imaged. Ultrastructural analysis indicates that despite global mirror imaging of the ciliature, detailed organization of the membranelles is reversed in the mirror-image oral apparatus (OA), such that the ciliary effective stroke propels food away from the OA. Assembly of compound ciliary structures of both OAs starts out identically, but as the structures associated with the mirror-image OA continue to form, the new set of membranelles undergoes a 180° planar rotation on the ventral surface relative to the same structures in the typical OA. The overall symmetry of the OA thus appears to be separable from the more localized assembly of individual basal bodies. True mirror imagery of the membranelles would require new enantiomorphic forms of the individual ciliary components, particularly the basal bodies, which is never observed. These observations suggest a mechanistic hypothesis with implications for the development of left–right asymmetry not only in ciliates, but perhaps also in development of left–right asymmetry in general.