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Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.

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Is Kuhn's notion of exemplar applicable to ongoing biomedical sciences? Many philosophers may be skeptical because Kuhn's cases are mostly from physics and chemistry. However, how do philosophers test the above (non-)applicability directly? We will use examples to illustrate a scientometric approach to the integrated history and philosophy of science (SciHPS) and argue that SciHPS can provide an empirical basis to empirically test and revise a philosophical concept questioned for its applicability to biomedical sciences. This paper will build on Yan, K., M. L. Tsai, and T. R. Huang. [2021. "Improving the Quality of Case-Based Research in the Philosophy of Contemporary Sciences." Synthese 198 (10): 9591–9610. ] heart-rate variability (HRV) case study to examine the biomedical changes within the HRV community from 1970 to 2022. We will investigate how a task force standardises and entrenches methodological standardisations, and argue that some of the task force's methodological standardisations are tool-afforded by an algorithm. These tool-afforded aspects further explain why an HRV method is robustly dominant in the HRV community despite other HRV scholars having developed alternatives to compete with the dominant one. We will then show how to use SciHPS to empirically test and revise the Kuhnian concept of exemplar into a concept of citation-exemplar that better captures the above tool-afforded aspects of standardisations. [ABSTRACT FROM AUTHOR]

An adsorbent obtained by applying orthophosphoric acid to a peat surface was investigated during the refining of used mineral lubricating oil. The degree of regeneration (clarification) of the used oil depended on the adsorbent modification method, i.e., the acid/peat ratio, adsorbent/oil residue mass ratio, and mixing time of the phases. [ABSTRACT FROM AUTHOR]

Democracy begins and ends with the media - according to this worldly recognized sentence, every ordinary Balkan could estimate the democratic perspective of its own country. That is why the effect of the new media (social networks), deserves continuous scientific and research attention, also done in this paper basically through comparative and statistic methods, with specific analysis of the Macedonian case. The media revolution produced largely positive changes in everyday life. But negative effects could not be abstracted: Internet - populism, loss of confidence in the media, fake news and hate speech. Perhaps the first solution that comes to mind is law regulation. But knowing that clear basal of the network services is freedom of speech and expression, any attempt of regulation (objectively or not) is legitimately considered censorship. This paper attempts to answer the question: is it possible journalism to fight fake news through a direct media battle?. [ABSTRACT FROM AUTHOR]

This paper tackles the interoperability problems of enterprise information systems by presenting a distributive model-driven platform for parallel coordination of multiple negotiations in data-intensive collaborative working environments. The proposed model was validated and verified by an industrial application scenario within the European research project H2020 C2NET (Cloud Collaborative Manufacturing Networks). This real scenario developed data-intensive collaborative and cloud-enabled tools that allow the optimisation of the supply network of manufacturing SMEs, proposing a negotiation solution based on a model-driven interoperable decentralised architecture. [ABSTRACT FROM AUTHOR]

The known technical solutions for regeneration of used fuels and oils are generalized. A new extractant based on orthophosphoric acid is studied and a method for extractive cleaning (refining) of waste industrial oils and diesel fuel is proposed. A technological scheme and a laboratory experimental procedure of refining (clarifying) waste petroleum products as a hydrocarbon stock are proposed. [ABSTRACT FROM AUTHOR]

Radio frequency identification (RFID) is a promising technology which can potentially assist in enhancing the efficiency of manufacturing by reorganising and optimising internal operations, such as purchasing, warehousing, management, and distribution of materials in the production, as well as in external supply chain management. RFID makes it possible to identify individual objects in the production automatically and wirelessly, so it has an increasing potential in various applications which can make manufacturing more efficient and productive. This survey provides an insight to the application of RFID technology in the management of manufacturing and supply chain. The survey includes a summary on the main purposes of use and on the main application fields of the technology. In manufacturing, typical application targets of RFID are related to warehouse management, process management, tool management, supply chain management, and life cycle management. In addition, the main users, i.e. those manufacturing branches which have been the primary users of RFID this far, are listed in this survey to reveal the current industrial practice. Furthermore, the current challenges in implementing the technology are discussed, as well as the most potential future manufacturing applications and research directions. The sources used for this study are original peer-reviewed reviews and journal articles, conference papers, and web references. [ABSTRACT FROM AUTHOR]

Background: In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results: The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). Conclusion: Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features. [ABSTRACT FROM AUTHOR]

Background: Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models. Results: The statistical analysis of the results of more than 500 hybridized samples distributed among 12 organs provides an experimental validation for 465 novel genes. The hybridization evidence was confirmed by RT-PCR approaches for 88% of the 465 novel genes. Comparisons with the current annotation show that these novel genes often encode small proteins, with an average size of 137 aa. Our approach has also led to the improvement of pre-existing gene models through both the extension of 16 CDS and the identification of 13 gene models erroneously constituted of two merged CDS. Conclusion: This work is a noticeable step forward in the improvement of the Arabidopsis genome annotation. We increased the number of Arabidopsis validated genes by 465 novel transcribed genes to which we associated several functional annotations such as expression profiles, sequence conservation in plants, cognate transcripts and protein motifs. [ABSTRACT FROM AUTHOR]