iLDM: An Interoperable Graph-Based Local Dynamic Map

Local dynamic map (LDM) is a key component in the future of autonomous and connected vehicles. An LDM serves as a local database with the necessary tools to have a common reference system for both static data (i.e., map information) and dynamic data (vehicles, pedestrians, etc.). The LDM should have a common and well-defined input system in order to be interoperable across multiple data sources such as sensor detections or V2X communications. In this work, we present an interoperable graph-based LDM (iLDM) using Neo4j as our database engine and OpenLABEL as a common data format. An analysis on data insertion and querying time to the iLDM is reported, including a vehicle discovery service function in order to test the capabilities of our work and a comparative analysis with other LDM implementations showing that our proposed iLDM outperformed in several relevant features, furthering its practical utilisation in advanced driver assistance system development.

Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation

Background Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome. Results In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL). Conclusion The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.

The appositional construction in Bulgarian – Issues, opinions, solutions

The article discusses several solutions that aim to reveal the direction of the dependence between the components of the appositional construction. An emphasis is placed on the analysis of the most amorphous and debatable structural type: common noun + proper noun. One of these solutions concerns the choice of a basic research approach and its consistent and logically sound application, which would aid the correct “distribution” of the syntactic functions of the components in constructions of this structural type. The article draws special attention to the autonymic use of proper nouns. It is based on the premise that the two components of this type of appositional construction can have a common reference, which is a function of their different referential features and that these components contribute – to a varying degree – to the realization of these features.

Influence of 16S rRNA Reference Databases in Amplicon-Based Environmental Microbiome Research

Purpose: The reference databases play a pivotal role in amplicon microbiome research but the sequence content and taxonomic information available in common reference databases differ. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated. Methods: This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference. Results: The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated based on different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by different databases vary significantly (P-value=0.001), irrespective of amplicon regions. Importantly, the study found that the core-microbiome structure in environmental studies could be altered by the reference databases. Conclusion: In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.

A harmonized atlas of mouse spinal cord cell types and their spatial organization

Single-cell RNA sequencing data can unveil the molecular diversity of cell types. Cell type atlases of the mouse spinal cord have been published in recent years but have not been integrated together. Here, we generate an atlas of spinal cell types based on single-cell transcriptomic data, unifying the available datasets into a common reference framework. We report a hierarchical structure of postnatal cell type relationships, with location providing the highest level of organization, then neurotransmitter status, family, and finally, dozens of refined populations. We validate a combinatorial marker code for each neuronal cell type and map their spatial distributions in the adult spinal cord. We also show complex lineage relationships among postnatal cell types. Additionally, we develop an open-source cell type classifier, SeqSeek, to facilitate the standardization of cell type identification. This work provides an integrated view of spinal cell types, their gene expression signatures, and their molecular organization.

Prescribed work, real work, and regulatory strategies for the work organization in an agricultural implement manufacturer

BACKGROUND: The work organization not only comprises the formal structure but also social interactions, which are developed according to its own rules based on variabilities and professional competences. During real work, there are regulatory processes that result in the development of strategies to meet the requirements of the work organization and maintain health status. OBJECTIVE: To understand the regulatory processes involved in work activities and analyze the extent to which the developed strategies are sufficient to protect employees’ integrity and guarantee performance. METHODS: This study was carried out in an agricultural implement manufacturing company, whose qualitative procedures were analyzed by combining activity observations, interviews, and self-confrontation. RESULTS: In view of the interaction of logic, operators comply with some rules to the detriment of others, based on the decision processes of their individual and collective experience. The availability of resources compatible with activity demands increases the possibility of action and competence development. The cost of regulations for less experienced operators is higher, taking into consideration the level of uncertainty resulting from contradictions and variabilities. CONCLUSION: It is necessary to discuss the contradictions manifested in operators’ work routines through interactions between heterogeneous rationalities. From this, it is possible to construct a common reference about the activity and increase the possibilities of action during real work.

The value of genotype-specific reference for transcriptome analyses

High quality transcriptome assembly using short reads from RNA-seq data still heavily relies upon reference-based approaches, of which the primary step is to align RNA-seq reads to a single reference genome of haploid sequence. However, it is increasingly apparent that while different genotypes within a species share core genes, they also contain variable numbers of specific genes that are only present a subset of individuals. Using a common reference may thus lead to a loss of genotype-specific information in the assembled transcript dataset and the generation of erroneous, incomplete or misleading transcriptomics analysis results. With the recent development of pan-genome information in many species, it is important that we understand the limitations of single genotype references for transcriptomics analysis. In this study, we quantitively evaluated the advantages of using genotype-specific reference genomes for transcriptome assembly and analysis using cultivated barley as a model. We mapped barley cultivar Barke RNA-seq reads to the Barke genome and to the cultivar Morex genome (common barley genome reference) to construct a genotype specific Reference Transcript Dataset (sRTD) and a common Reference Transcript Datasets (cRTD), respectively. We compared the two RTDs according to their transcript diversity, transcript sequence and structure similarity and the accuracy they provided for transcript quantification and differential expression analysis. Our evaluation shows that the sRTD has a significantly higher diversity of transcripts and alternative splicing events. Despite using a high-quality reference genome for assembly of the cRTD, we miss ca. 40% transcripts present in the sRTD and cRTD only has ca. 70% true assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression and differential alternative splicing analysis. However, gene level quantification and comparative expression analysis are less affected by the source RTD, which indicates that analysing transcriptomic data at the gene level may be a reasonable compromise when a high-quality genotype-specific reference is not available.

An Ignored Pitfall in Selecting Reference Genes and the Solution with Emphasis on Subtypes and Sex of Thyroid Cancer Patients

Routine tissue specific reference genes are widely used in transcriptomics studies without concerning their target genes, sex of patients, and diseases subtype. We proposed the concept of specific reference genes for each target gene after considering sex of patients and thyroid cancer subtypes. RT-qPCR technique was coupled with expression meta-analysis of samples with different races and ethnicities, in both sexes, and in different thyroid cancer subtypes. Eight common reference genes were evaluated and some of them undoubtedly ruled out. We found that mean and SD values of the genes must be considered carefully before the selection of reference genes. A formula was also developed accordingly and we equipped it with statistical analysis of more than 25000 genes. In conclusion, the reckless selection of reference genes can distort the output and must be prohibited.