Scientific knowledge in the age of computation: explicated, computable and manageable?

With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management (KM):second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli (2014, 2016), Efstathiou (2012, 2016) and Hislop (2013) in our analysis of the use of KM in semantic systems biology. Through an empirical philosophical account of KM-enabled biological research, we argue that KM helps produce new first-order biological knowledge that did not exist before, and which could not have been produced by traditional means. KM work is enabled by conceiving of ‘knowledge’ as an object for computational science: as explicated in the text of biological articles and computable via appropriate data and metadata. However, these founded knowledge concepts enabling computational KM risk focusing on only computationally tractable data as knowledge, underestimating practice-based knowing and its significance in ensuring the validity of ‘manageable’ knowledge as knowledge.; Con el aumento de la publicación y la producción de datos, el conocimiento científico no solo es reconocido como un logro, sino también como un desafío. Las publicaciones y los datos científicos se tratan cada vez más como recursos que deben ser ‘gestionados’ digitalmente. Esto da lugar a la Gestión del Conocimiento científico (Knowledge Management (KM)): labor científica de segundo orden destinada a recopilar, cuidar y movilizar de forma directa el conocimiento disciplinario de primera mano y los datos para proporcionar nuevos conocimientos científicos de primer orden. Seguimos el trabajo de Leonelli (2014, 2016), Efstathiou (2012, 2016) y Hislop (2013) en nuestro análisis del uso de la KM en la biología de sistemas semánticos. A través de una descripción filosófica empírica de la investigación biológica habilitada para KM, argumentamos que KM ayuda a producir un nuevo conocimiento biológico de primer orden que no existía antes y que no podría haber sido producido por medios tradicionales. El trabajo de KM está facultado para concebir el “conocimiento” como un objeto para la ciencia computacional: como algo explicitado en el texto de artículos biológicos y como computable a través de datos y metadatos apropiados. Sin embargo, los conceptos fundados permiten el riesgo computacional de KM de centrarse solo en los datos que se pueden tratar de manera computacional como conocimiento, subestimando el conocimiento basado en la práctica y su importancia para garantizar la validez del conocimiento “manejable” como conocimiento

XHM: A system for detection of potential cross hybridizations in DNA microarrays

BACKGROUND: Microarrays have emerged as the preferred platform for high throughput gene expression analysis. Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability of DNA microarray results. RESULTS: We have developed a tool called XHM (cross hybridization on microarrays) for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays. This is done by comparing the sequences of the probes against an extensive database representing the transcriptome of the organism in question. XHM is available online at . CONCLUSIONS: Using XHM with its user-adjustable parameters will enable scientists to check their lists of differentially expressed genes from microarray experiments for potential cross-hybridizations. This provides information that may be useful in the validation of the microarray results

Understanding Organizational Reforms in the Modern State: Specialization and Integration in Norway and France

This article examines the challenge Norway and France face in coordinating specialized government activities after 10 years of comprehensive reforms. The focus is on the tension between territorial and sectoral specialization and between vertical and horizontal specialization. We describe both sector-specific administrative reforms and more overarching general reforms, looking at similarities and differences in the reorganization choices made by the two countries and also at what drives change. We argue that a combination of factors is required to explain outcomes. These factors include not only home-grown reforms but also sectoral challenges, diffusion and learning from abroad, adaptation to the financial crisis and budget deficit, and choices made by powerful political executives. Sometimes these factors work together and reinforce each other, producing radical reforms; at other times they have a mutually constraining influence, resulting in only minor changes

Understanding Organizational Reforms in the Modern State: Specialization and Integration in Norway and France

This article examines the challenge Norway and France face in coordinating specialized government activities after 10 years of comprehensive reforms. The focus is on the tension between territorial and sectoral specialization and between vertical and horizontal specialization. We describe both sector-specific administrative reforms and more overarching general reforms, looking at similarities and differences in the reorganization choices made by the two countries and also at what drives change. We argue that a combination of factors is required to explain outcomes. These factors include not only home-grown reforms but also sectoral challenges, diffusion and learning from abroad, adaptation to the financial crisis and budget deficit, and choices made by powerful political executives. Sometimes these factors work together and reinforce each other, producing radical reforms; at other times they have a mutually constraining influence, resulting in only minor changes

ExTRI: Extraction of transcription regulation interactions from literature

The regulation of gene transcription by transcription factors is a fundamental biological process, yet the relations between transcription factors (TF) and their target genes (TG) are still only sparsely covered in databases. Text-mining tools can offer broad and complementary solutions to help locate and extract mentions of these biological relationships in articles. We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations. Validation procedures indicated that about half of the candidate sentences contain true TF-TG relationships. Post-processing identified 53,000 high confidence sentences containing TF-TG relationships, with a cross-validation F1-score close to 75%. The resulting collection of TF-TG relationships covers 80% of the relations annotated in existing databases. It adds 11,000 other potential interactions, including relationships for ~100 TFs currently not in public TF-TG relation databases. The high confidence abstract sentences contribute 25,000 literature references not available from other resources and offer a wealth of direct pointers to functional aspects of the TF-TG interactions. Our compiled resource encompassing ExTRI together with publicly available resources delivers literature-derived TF-TG interactions for more than 900 of the 1500–1600 proteins considered to function as specific DNA binding TFs. The obtained result can be used by curators, for network analysis and modelling, for causal reasoning or knowledge graph mining approaches, or serve to benchmark text mining strategies.We thank the participants of the COST Action GREEKC (CA15205) for fruitful discussions during workshops supported by COST (European Cooperation in Science and Technology).Peer ReviewedPostprint (published version

22. juli kommisjonen. Organisering, styring og ansvar [The 22. July Commission. Organization, steering and accountability].

INNLEIING 22. juli 2011 vart Norge ramma av to sjokkerande terroristangrep. Ei bilbombe øydela fleire sentrale regjeringsbygningar i Oslo og 8 personar vart drepne i angrepet. Nokre få timar seinare vart 69 politisk aktive ungdomar frå Arbeiderpartiet si ungdomsorganisasjon massakrert på ein leir på Utøya – like nordvest for Oslo. Dei fleste av dei 69 offera var mellom 15 og 18 år. Terroristen vart arrestert på Utøya same kvelden og vedgjekk straks ugjerningane. Rettsaka vist at han var ein ‘einsam ulv’ som opererte åleine utan å vera tilknytt nokon organisasjon. 24. august 2012 vart han dømt til 21 års forvaring

Miniaturized fluorescent RNA dot blot method for rapid quantitation of gene expression

BACKGROUND: RNA dot blot hybridization is a commonly used technique for gene expression assays. However, membrane based RNA dot/slot blot hybridization is time consuming, requires large amounts of RNA, and is less suited for parallel assays of more than one gene at a time. Here, we describe a glass-slide based miniaturized RNA dot blot (RNA array) procedure for rapid and parallel gene expression analysis using fluorescently labeled probes. RESULTS: RNA arrays were prepared by simple manual spotting of RNA onto amino-silane coated microarray glass slides, and used for two-color fluorescent hybridization with specific probes labeled with Cy3 and 18S ribosomal RNA house-keeping gene probe labeled with Cy5 fluorescent dyes. After hybridization, arrays were scanned on a fluorescent microarray scanner and images analyzed using microarray image analysis software. We demonstrate that this method gives comparable results to Northern blot analysis, and enables high throughput quantification of transcripts from nanogram quantities of total RNA in hundreds of samples. CONCLUSION: RNA array on glass slide and detection by fluorescently labeled probes can be used for rapid and parallel gene expression analysis. The method is particularly well suited for gene expression assays that involve quantitation of many transcripts in large numbers of samples

NON-NATURALLY OCCURRING PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS (PRRSV) AND METHODS OF USING

A non-naturally occurring porcine reproductive and respiratory syndrome virus (PRRSV) is provided herein, and methods of making and using the non-naturally occurring PRRSV also are provided