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This study is an empirical inquiry into the re-election of elected assembly members and investigates whether incumbents' general participation in legislative sessions is a determinant of the outcome of their re-election efforts. This study measures legislative participation based on the amount of speech on the plenary session floor during the immediately preceding term, which is tabulated from published local assembly transcripts. The data for the analysis come from 41 prefecture assemblies in Japan that held elections on the same day in April 2015. This sample enables us to test whether legislative participation has a positive electoral impact across different localities. The empirical analysis of the re-election outcomes of elected officials suggests that floor speech is a factor contributing to electoral success for assembly members. In addition, this speech effect diminishes as incumbents accumulate terms, and it is the first term legislators who benefit most from the positive re-election effect of speech. [ABSTRACT FROM AUTHOR]

Abstract Background Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. Results We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. Conclusions MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.

In this paper, the author analyzes the institution of recall of a mayor in the legal system of the Republika Srpska by critically examining the provisions of two legislative acts: The Election Act of Republika Srpska and the Local Self-government Act of Republika Srpska. The institution of recall has a serious democratic potential because it is an instrument enabling political control of mayors by citizens. However, the current legal solutions in Republika Srpska limit this potential because they do not encourage citizens to use this instrument of political control, which is not the case with political parties. Given the fact that the decision on initiating the recall procedure depends on a local assembly, recall has very often been used as a tool for political confrontation between a local assembly and a mayor, while the citizens have remained a second-class political subject. The Election Act of Republika Srpska does not contain adequate provisions on the protection of rights of citizens and political subjects during the recall procedure. In fact, this issue is relatively unregulated or underregulated. The Local Self-government Act of Republika Srpska protects a local assembly which triggers an unsuccessful recall procedure since there is no legal guarantee that such a local assembly would be dissolved. The author proposes different solutions which should improve the regulation of this legal institute and reduce the possibility of turning it into a tool for political manipulation.

Background: Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. Results: We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. Conclusions: MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package. [ABSTRACT FROM AUTHOR]

Abstract 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.

With the rapid development of short-read sequencing technologies, many population-scale resequencing studies have been carried out to study the associations between human genome variants and various phenotypes in recent years. Variant calling is one of the core bioinformatics tasks in such studies to comprehensively discover genomic variants in sequenced samples. Many efforts have been made to develop short read-based variant calling approaches; however, state-of-the-art tools are still computationally expensive. Meanwhile, cutting-edge genomics studies also have higher requirements on the yields of variant calling. Herein, we propose Partial-Order Alignment-based single nucleotide polymorphism (SNV) and Indel caller (Psi-caller), a lightweight variant calling algorithm that simultaneously achieves high performance and yield. Mainly, Psi-caller recognizes and divides the candidate variant site into three categories according to the complexity and location of the signatures and employs various methods including binomial model, partial-order alignment, and de Bruijn graph-based local assembly to handle various categories of candidate variant sites to call and genotype SNVs/Indels, respectively. Benchmarks on simulated and real short-read sequencing data sets demonstrate that Psi-caller is times faster than state-of-the-art tools with higher or equal sensitivity and accuracy. It has the potential to well handle large-scale data sets in cutting-edge genomics studies.

This paper aims to clarify how teachers’ expertise is discussed in local assemblies. As observed in discussions about teacher expertise, there has been critical opinion about the professional duty of teachers. The local assembly councilor is an elected officer similar to the mayor. This means that they are answerable to citizens in the local government. The local assembly is based on local autonomy law, and so the assembly councilor must be chosen by election. Accordingly, the municipal councilor’s election ward operates in a multimember constituent electoral system for the whole municipality. Under this electoral system, it is necessary for complaints to be made about any differences by candidates with similar claims, and it should also be pointed out that this limits the possibility of collaboration after the election. Significantly, it is notable that differences of opinion are less likely to occur regarding educational policies. With this in mind, this paper considers how teacher expertise was discussed focusing on the assembly of the city designated by ordinance. The city designated by ordinance holds the authority to manage its own teacher personnel. This approach is the most suitable for observation. Specifically, 14 cities designated by ordinance were accessed in the webbased Hansard House of Assembly, and their extracted discussions on the expertise of teachers were used in this research. As a result, it is suggested that there are few remarks about teachers, and there are few discussions on their expertise. In the aforementioned analysis of Hansard, it is also observed that when there were cases of a teacher involved in an accident at the time, the remarks then increased, and the number of remarks increased or decreased according to the level of interest of individual councilors. Furthermore, some councilors appear to have deepened their expert knowledge on education and ask questions requiring a level of expertise. Although it is thought that high-level professional remarks are the result of actions based on some profits, this finding should not be seen as negative. One reason for consideration is that procuring democratic legitimacy for educational policy demands intervention from highly knowledgeable councilors. [ABSTRACT FROM AUTHOR]

Aim: The interaction of land use with local versus regional processes driving biological homogenization (β‐diversity loss) is poorly understood. We explored: (a) stream β‐diversity responses to land cover (forest versus agriculture) in terms of physicochemistry and physicochemical heterogeneity; (b) whether these responses were constrained by the regional species pool, i.e. γ‐diversity, or local assembly processes through local (α) diversity; (c) whether local assembly operated through the regional species abundance distribution (SAD) or intraspecific spatial aggregation; and (d) the dependence on body size, dispersal capacity and trophic level (producer versus consumer). Location: USA, Canada and France. Time period: 1993–2012. Major taxa studied: Stream diatoms, insects and fish. Methods: We analysed six datasets totalling 1,225 stream samples. We compared diversity responses to eutrophication and physicochemical heterogeneity in forested versus agricultural streams with regression methods. Null models quantified the contribution of local assembly to β‐diversity (β‐deviance, βDEV) for both types of land covers and partitioned it into fractions explained by the regional SAD (βSAD) versus aggregation (βAGG). Results: Eutrophication explained homogenization and more uneven regional SADs across groups, but local and regional biodiversity responses differed across taxa. The βDEV was insensitive to land use. The βSAD largely exceeded βAGG and was higher in agriculture. Main conclusions: Eutrophication but not physicochemical heterogeneity of agricultural streams underlay β‐diversity loss in diatoms, insects and fish. Agriculture did not constrain the magnitude of local versus regional effects on β‐diversity but controlled the local assembly mechanisms. Although the SAD fraction dominated in both land covers, it increased further in agriculture at the expense of aggregation. Notably, the regional SADs were more uneven in agriculture, exhibiting excess common species or stronger dominance. Diatoms and insects diverged from fish in terms of biodiversity, SAD shape and βDEV patterns, suggesting an overriding role of body size and/or dispersal capacity compared with trophic position. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The ability to detect the genetic variations between two individuals is an essential component for genetic studies. In these studies, obtaining the genome sequence of both individuals is the first step toward variation detection problem. The emergence of high-throughput sequencing (HTS) technology has made DNA sequencing practical, and is widely used by diagnosticians to increase their knowledge about the casual factor in genetic related diseases. As HTS advances, more data are generated every day than the amount that scientists can process. Genome assembly is one of the existing methods to tackle the variation detection problem. The de Bruijn graph formulation of the assembly problem is widely used in the field. Furthermore, it is the only method which can assemble any genome in linear time. However, it requires an enormous amount of memory in order to assemble any mammalian size genome. The high demands of sequencing more individuals and the urge to assemble them are the driving forces for a memory efficient assembler. In this work, we propose a novel method which builds the de Bruijn graph while consuming lower memory. Moreover, our proposed method can reduce the memory usage by 37% compared to the existing methods. In addition, we used a real data set (chromosome 17 of A/J strain) to illustrate the performance of our method. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

Given the increasing cost-competiveness of renewable energy (RE) technologies, competitive auction schemes have increasingly been adopted in recent years across various developed and developing countries. Local content requirements (LCRs) are frequently used as part of RE auction schemes to promote local industrial development. In this paper, we present a review of the literature on the effectiveness of LCRs in fostering local industrial development across various developing countries focusing on South Africa, Brazil, India and China. Specifically, this paper analyses the effectiveness of LCRs in promoting the establishment of local manufacturing facilities of onshore wind turbine and solar PV components in these countries. Further, the paper provides a review of the main determining factors stressed in the literature to account for variations in the effectiveness of LCRs. We have found that the literature generally ascribes importance to the role of LCRs in stimulating local component production in developing countries. However, previous research on the effectiveness of LCRs in establishing local component manufacturing differs across the technologies and the countries analysed. The variation in the effectiveness of LCRs can be explained by a framework that combines the following four determining factors: (i) market size and stability; (ii) policy design and coherence; (iii) the restrictiveness of the LCRs; and (iv) the domestic industrial base. The paper highlights a lack of systematic approaches and rigour in existing research, thus proposing the development of a common framework and set of indicators to assess the efficiency of LCRs. • Review of the use of local content requirements (LCRs) in renewable energy auction schemes in developing countries. • Study of the effects of LCRs in localising production of wind and solar components in South Africa, Brazil, India and China. • Finds that the effectiveness of LCRs in promoting local industrial development differs across countries and technologies. • Determinant factors is suggested to explain the variations in the effectiveness of LCRs across countries and technologies. • Concludes by suggesting more rigour and development of a common methodology in research on LCRs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]