Academiskt försök, til en physico-oeconomisk beskrifning öfwer Hwittis sokn, i Björneborgs län : ... under ... Pehr Adrian Gadds inseende, såsom et academiskt snille-prof utgifwit och förswaradt, den 26. Maji, 1759. Af Ephraim Carenius, satacundensis.

Dedicated to: Carl Fredrich Mennander, Nils Idman, Michaël Forselius, Jacob Fårskål, Anders Berendt Gadd, Georg Haveman, Catharina Tackou, née Morin, Jacob Carenius.

Providing Discourse Services for Researchers in a Repository Setting

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Targeted Annotation of Scientific Literature and Data Resources in Invenio Digital Libraries

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

The Human Communication Science Virtual Lab (HCS vLab): A repository microclimate in a rapidly evolving research-ecosystem

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

The effects of mutated cationic amino acid transporter y+LAT1 at the cellular and systemic level

y+LAT1 is a transmembrane protein that, together with the 4F2hc cell surface antigen, forms a transporter for cationic amino acids in the basolateral plasma membrane of epithelial cells. It is mainly expressed in the kidney and small intestine, and to a lesser extent in other tissues, such as the placenta and immunoactive cells. Mutations in y+LAT1 lead to a defect of the y+LAT1/4F2hc transporter, which impairs intestinal absorbance and renal reabsorbance of lysine, arginine and ornithine, causing lysinuric protein intolerance (LPI), a rare, recessively inherited aminoaciduria with severe multi-organ complications. This thesis examines the consequences of the LPI-causing mutations on two levels, the transporter structure and the Finnish patients’ gene expression profiles. Using fluorescence resonance energy transfer (FRET) confocal microscopy, optimised for this work, the subunit dimerisation was discovered to be a primary phenomenon occurring regardless of mutations in y+LAT1. In flow cytometric and confocal microscopic FRET analyses, the y+LAT1 molecules exhibit a strong tendency for homodimerisation both in the presence and absence of 4F2hc, suggesting a heterotetramer for the transporter’s functional form. Gene expression analysis of the Finnish patients, clinically variable but homogenic for the LPI-causing mutation in SLC7A7, revealed 926 differentially-expressed genes and a disturbance of the amino acid homeostasis affecting several transporters. However, despite the expression changes in individual patients, no overall compensatory effect of y+LAT2, the sister y+L transporter, was detected. The functional annotations of the altered genes included biological processes such as inflammatory response, immune system processes and apoptosis, indicating a strong immunological involvement for LPI.

Characterisation of Cladonia rangiferina transcriptome and genome, and the effects of dehydration and rehydration on its gene expression

Lichens are symbiotic organisms, which consist of the fungal partner and the photosynthetic partner, which can be either an alga or a cyanobacterium. In some lichen species the symbiosis is tripartite, where the relationship includes both an alga and a cyanobacterium alongside the primary symbiont, fungus. The lichen symbiosis is an evolutionarily old adaptation to life on land and many extant fungal species have evolved from lichenised ancestors. Lichens inhabit a wide range of habitats and are capable of living in harsh environments and on nutrient poor substrates, such as bare rocks, often enduring frequent cycles of drying and wetting. Most lichen species are desiccation tolerant, and they can survive long periods of dehydration, but can rapidly resume photosynthesis upon rehydration. The molecular mechanisms behind lichen desiccation tolerance are still largely uncharacterised and little information is available for any lichen species at the genomic or transcriptomic level. The emergence of the high-throughput next generation sequencing (NGS) technologies and the subsequent decrease in the cost of sequencing new genomes and transcriptomes has enabled non-model organism research on the whole genome level. In this doctoral work the transcriptome and genome of the grey reindeer lichen, Cladonia rangiferina, were sequenced, de novo assembled and characterised using NGS and traditional expressed sequence tag (EST) technologies. RNA extraction methods were optimised to improve the yield and quality of RNA extracted from lichen tissue. The effects of rehydration and desiccation on C. rangiferina gene expression on whole transcriptome level were studied and the most differentially expressed genes were identified. The secondary metabolites present in C. rangiferina decreased the quality – integrity, optical characteristics and utility for sensitive molecular biological applications – of the extracted RNA requiring an optimised RNA extraction method for isolating sufficient quantities of high-quality RNA from lichen tissue in a time- and cost-efficient manner. The de novo assembly of the transcriptome of C. rangiferina was used to produce a set of contiguous unigene sequences that were used to investigate the biological functions and pathways active in a hydrated lichen thallus. The de novo assembly of the genome yielded an assembly containing mostly genes derived from the fungal partner. The assembly was of sufficient quality, in size similar to other lichen-forming fungal genomes and included most of the core eukaryotic genes. Differences in gene expression were detected in all studied stages of desiccation and rehydration, but the largest changes occurred during the early stages of rehydration. The most differentially expressed genes did not have any annotations, making them potentially lichen-specific genes, but several genes known to participate in environmental stress tolerance in other organisms were also identified as differentially expressed.

Canticum canticorum cum glossa ordinaria.

F. 1-42. "Incipiunt Cantica Canticorum. osculetur me osculo oris suis...-... hinnuloque cervorum super montes aromatum". F. A, note émargée à l'encre brune ; f. 42-42v. notes et maximes de la même main (additions du XIVe siècle).

Postille super Psalterium. Latin 14255

F. 376-377, anciennes gardes, extraits d'oeuvres juridiques.

Recueil de traités hermétiques.

« Traité de Zoroastre (fol. 1) ; secrets, suitte de l'Enchiridion » (fol. 53) ; traité astrologique de Théophraste Paracelse sur « le grand oeuvre » (fol. 75) ; « vertus des simples qui ont simpathie avec les esprits (fol. 81) ; annotations sur le calendrier naturel et magique, perpétuel, comprenant la très profonde contemplation des choses très secrètes et la connoissance de toute la philosophie (fol. 105) ; traité de la science universelle autrement caballe (fol. 129) ; livre des cent cinquante oraisons qu'il faut dire après chaque pseaume de David » (fol. 137).

Feuillet d'une demi-Bible en français ayant appartenu à Jean de Berry

A l'exception des ex-libris et annotations de Jean Flamel, le manuscrit ne contient que la fin du Psautier sur une colonne (f. 4v) : « Sire, delivre nous en l'eure de la mort. / Sire, delivre (a exponctué) nous au jour du jugement ...-.... Sire, oy m'oroison / Et mon cri a toy viengne ». « Dex a qui propre chose est d'avoir merci ...-.... que la grant misericorde de ta pitié nous absoille. Par Crist nostre Seigneur. Ainsi soit il ». « Ci fine le Psautier en françois ». « Ci doit venir aprés le livre des paraboles Salemon ».

Catalogue sommaire des manuscrits indiens, indo-chinois et malayo-polynésiens de la Bibliothèque nationale

Contient les descriptions des manuscrits Indien 1 à 1064, les descriptions des manuscrits indo-chinois 1 à 512, les additions et corrections par Petrus Voorhoeve (1899-1996), 1952, des notices du catalogue sommaire des manuscrits malayo-polynésiens de la Bibliothèque nationale par A. Cabaton, Paris 1912, les descriptions des manuscrits malayo-polynésiens 1-244 par A. Cabaton et celles des manuscrits malayo-polynésiens 245-283, rédigées par Petrus Voorhoeve (1899-1996),

Recueil de pièces relatives à la maison de Béthencourt ; projet d'édition de l'Histoire de la première découverte et conqueste des Canaries, par Jean de Béthencourt, ou Canarien, publiée par Pierre Bergeron.

Contient : Pièces de vers, en latin et en grec, « exachrosticon », etc., en l'honneur de la maison de Béthencourt, et en particulier de Galien de Béthencourt, conseiller au Parlement de Rouen, et de Jean de Béthencourt, roi des Canaries, par « Petrus QUEVILLY, rector ecclesiæ du Bosguerard », « Robertus DENIS », « Michael PLANCHON, advocatus » ; Table des chapitres L à LXXXVII du Canarien de Jean de Béthencourt [chapitres L à XCIII de l'imprimé de 1630] ; Projet de titre pour le Canarien de Jean de Béthencourt, 1625 ; Annotations pour le Canarien de Jean de Béthencourt ; « Suitte des passages des autheurs qui font mention de la conqueste faicte par messire Jehan de Béthencourt, à mettre apprez le miracle de Sainct-Maclou » ; Lettre orig., en espagnol, de « don Mateo de Betancor », 26 mai 1607 (f. 24), — et traduction française (f. 25) ; Lettres orig., en espagnol, de « don Lucas de Betancor », 1613 (f. 28 et 32), — et traduction française (f. 29 et 33) ; « Chartre de l'an 1024, de Richard, duc de Normandie, par laquelle il confirme les privilèges et possessions tenues par le monastère de Fontenelles ou St-Vandrille » (f. 36), — et autres pièces concernant Béthencourt en Normandie et la famille de Béthencourt, 1320-1589 (f. 38)

Papiers et travaux de D. Jacques LE CLERC, sousprieur de la Trinité de Vendôme, relatifs à la musique.

Contient : « Remarques sur l'ouvrage du P. D. Jacques Le Clerc, composé en 1665, et intitulé Méthode facile et accomplie pour apprendre le chant de l'Église sans l'aide d'aucune gamme » ; c'est le traité dont une copie est contenue dans le ms. français 20001, fol. 1-26, et qui se trouve en plusieurs états dans le ms. français 19103, cf. infra ; Lettre de D. « Anselme Thevart » à D. Benoît de Jumilhac, 1667, orig ; Minute d'une lettre de D. Jacques Le Clerc, incomplète ; « Remarques sur les méthodes du chant de l'Église, aoust 1666 » ; « Deux méthodes pour apprendre le plein chant » ; Traités et fragments de traités de musique, de métrique et d'hymnologie, de la main de D. Jacques LE CLERC ; Fragments imprimés d'hymnologie, avec annotations de D. Jacques Le Clerc, petit in-8°, 5 feuillets

御選古文淵鑑Yu xuan gu wen yuan jian.Recueil de textes anciens préparé par ordre impérial.

Contient : période antérieure aux Qin, livres 1 à 8 ; dynastie des Qin, livre 9 ; dynastie des Han, livres 10 à 20 ; période des Trois Royaumes, livres 21 et 22 ; dynastie des Jin, livres 23 et 24 ; dynastie des Song, livre 25 ; dynasties des Qi, Liang, Chen, livre 26 ; dynastie des Wei septentrionaux, livre 27 ; dynasties des Qi septentrionaux, Zhou septentrionaux, Sui, livre 28 ; dynastie des Tang, livres 29 à 40 ; période des Cinq Dynasties, livre 41 ; dynastie des Song, livres 42 à 64