dataesr/scientific-paragraphs-categorization huggingface dataset:
Non-additive gene expression in the F 1 under control conditions Analyses of gene expression data from the 13HP02 experiment, which included a well-watered control treatment (FTSW = 1. 0), resulted in detection of 3,003 genes (FDR < 0. 05) in INEDI with significant expression differences from its parents. For analyses of gene expression patterns potentially associated with heterosis, we focused on the genes exhibiting over-dominant (550 genes) or under-dominant (89 genes) expression levels. The GO enrichment and KEGG pathway mapping results for these genes are listed in Supplementary Table  S2E -F. Overdominant genes were most significantly enriched in Response to chemical (GO:0042221, FDR = 1. 03E-15) in biological process (Fig. 6A ), Cell periphery (GO:0071944, FDR = 5. 58E-3) in cellular component, and reversible chemical reaction related GO terms (Oxidoreductase activity, GO:0016491, FDR = 1.
Relationship between levels of gene expression and alternative splicing We employed sPLS regression to extract correlated information between the gene expression and AS data sets. Output from sPLS includes a set of components and loading vectors similar to that produced by principal components analysis. Using the top 500 DEG and DAS genes, we found a clear distinction between control and drought-stressed samples by sPLS components 1 and 2 with respect to expression and AS patterns, but not between genotypes (Supplementary Figure  S6 ). Furthermore, as seen in Fig. 7A , the first component from DEG is highly correlated (Pearson's correlation coefficient = 0. 87) to DAS. When we combine the two datasets, we see greater discrimination between genotypes within the drought treatment, particularly for INEDI (orange dots) (Fig.
7A ). This suggests that a combination of transcriptional and posttranscriptional information may provide a better explanation of how INEDI's unique responses are established than analyzing each dataset separately. We also tested for correlations between differential expression under drought and AS frequency, which are displayed by circosPlot in Fig. 7B. When we compare DEG to DAS with the same genes, the majority (65%) of correlations were negative (Fig. 7C ). This indicates that stress responsive gene expression is largely negatively correlated with AS frequency, implying that AS often acts to reinforce expression responses (discussed above).
Acknowledgements Funding was provided by  Genome BC  and  Genome Canada  ( LSARP2014-223SUN ), the  French National Research Agency  ( SUNRISE/ANR-11-BTBR-0005 ), the  Midi-Pyrénées Region , the  European Fund for Regional Development , the  French Fund for Competitiveness Clusters  ( OLEOSOL  project), the  NSF Division of Environmental Biology  ( DEB-1745197 ), the  USDA National Institue of Food and Agriculture  ( 2008-35300-19263 ), and the  NSF   Plant Genome Research Program  ( DBI-0820451  and  DBI-1444522 ). We thank  Dan Ebert  for assistance with phenotyping.
The number of new publications doubled already in the 1920s. A second wave of new journals came after 1945, and this wave remained at a high level for four decades with almost a hundred new publications every decade. In 8 BILDI was founded in 1980 as a card catalogue by Josef Oesch (Old Testament), Friedrich Mohr (Old Testament) and Konrad Huber (New Testament). In 1984, the computing department of the University of Innsbruck provided a relational database, which was replaced in 1987 by the STAR database. Under the long-standing leadership of the chief editor of the Elenchus of Biblica, Robert Althann, SJ, there was a collaboration from the 1990s on with the Bible Institute in Rome, which mainly provided the metadata of book reviews to BILDI. I thank Prof. Dr. Josef Oesch and Dr. Mira Stare for their information on the first years of BILDI.
This problem is reflected in the fact that libraries have to pay significant amounts of money to buy additional metadata of inferior quality on articles from commercial suppliers in order to supply them in their own catalogues to their users. Journals and yearbooks were a natural place for subject-related bibliographies, as well as important review journals such as the Theologische Revue and the Theologisches Literaturblatt (along with its predecessors) in the German-speaking world. Editors were academic experts in their own fields of interest, and because of their knowledge of the sources and subjects of research, they were well-equipped to sift through and comment on the literature being published. Parallel to the rise of academic literature, important traditional bibliographies emerged in the first quarter of the 20th century in certain areas of theology, often as an addendum to the academic articles of a given issue or volume.
These indices were produced with the help of the computing centre of the university from the first issue on. The creators of the ZID were proud to announce: "The indexes will be fed on-line into a monitor, which is directly connected with the Centre for Data Processing at the University of Tübingen. The printing of the indexes is done by plotter; the reproduction of minuscule and majuscule letters is now possible through new software". 52 A new time was about to begin! 3 Digital Transition: From the Zeitschrifteninhaltsdienst Theologie to the Index Theologicus Before the computer era, improvements in bibliographic tools were only possible in a very limited fashion: for years, progress meant steadily expanding the canon of processed journals as well as offering new indices and dividing the existing ones into more specific categories.
A new era really began when both the production and the presentation of the issues could be accomplished on the computer. The American Theological Library Association (ATLA) was the first to offer its products online in the mid-1980s,54 then distributed them soon after in the form of CD-ROMs, and now the ATLA Religion Database (RDB) has been published online on EBSCO for the at the 'Philosophisches Institut' of the University of Düsseldorf," but the decision was made in 1979 "that THEODOK should become the department managing the academic information fields of theology and religious studies at the UB Tübingen. "60 The project of a theological information and documentation centre ('Theologische Informations-und Dokumentationsstelle' , or THEODOK) was funded starting in June 1979 as a preliminary project for the FIS/FIZ 14.
Negotiations between the university of Tübingen and the ministry of science and art in Baden-Württemberg in order to secure further financing for THEODOK failed as well; since the DFG was unable to take on the financing, it withdrew its financial support for the IOB. Only the "information services of the theological department which were funded with the help of the DFG and its own revenue," including the Zeitschrifteninhaltsdienst Theologie (ZID), could be continued. 63 A few tasks for THEODOK could be completed and even published later. 64 But they had no influence on future As a result, the focus was put on the continuation of established services, and the technical development of the ZID was relegated to the background. In August 1986, the UB Tübingen started cataloguing with the help of electronic data processing in the database of the 'Library Association of South-Western Germany' (Südwestdeutscher Bibliotheksverbund or SWB), in which all monographs of the specialised academic collections were entered.
66 However, new methods had to be designed for the cataloguing of articles and the presentation of the ZID. The new head of the theological department at the UB Tübingen, Hilger Weisweiler,67 came to the following conclusion: "Two decades after the foundation of the ZID, its basic conception had lost none of its importance and relevance, but the rapid development of data processing technology made the production procedure and the presentation of information on literature [in the ZID] look antiquated. "68 The technical renewal came with the allegroC software developed since the 1980s by the university library in Braunschweig. Preparations for a new ZID database on the basis of allegroC began in 1992, the database was parameterised in 1994 and a first version was made available to the public in 1995.
The ZID database was then offered on two 3. 5-inch floppy disks which could be installed on PCs with the DOS operating system for the price of 350 DM. At the same time, the canon of processed journals was revised and expanded from 420 to over 500 journals. The database The ZID continued to be offered in a print version, but thanks to allegroC, the old production procedure could be dropped. All records were now entered in the database and then imported and processed in a program called TUSTEP,71 which was developed in Tübingen, and which provided the means to have "an appealing layout, [the ability to] display subject headings in the document, but especially a continuous numbering of the documents displayed, which led to a precise access to the index. "72 Another innovation was that Bible passages were now indexed at the level of verses instead of chapters.
This may not seem much, but this feature laid the foundations for IxTheo's present search system for Bible passages, which is based on a modern algorithm and is unique in the whole world. A few desiderata remained nonetheless: Because of staff limits, not all desirable journals could be included in the bibliography, nor was it possible to undertake a complete subject indexing of the contents. 73 But in 1996, subject indexing based on the RSWK74 was introduced thanks to the personal efforts of the staff, and in 1997, the German Bishops' Conference started funding subject indexing and classification with an impressive annual grant, which has continued to this day. From 1997 on, the database was offered as "a CD-ROM on the MS-DOS operating system, and from July of 1999 on also in a Windows version"75 and updated twice a year.
In the meantime, the technical capabilities were so widespread and had attained such a level of development that the printed version could cease to be published at the turn of the millennium. In the beginning, the database was sold by the UB Tübingen itself, but from 2002 to 2006, it was commercialised by the publishing house Mohr Siebeck. 76 For this reason, the name of the bibliography was changed from the Zeitschrifteninhaltsdienst Theologie to the Index Theologicus. However, the goal of a wider distribution through a cooperation with a well-known publishing house was not fulfilled. The commercialisation of the CD-ROM proved to be too much of a burden and was only possible at certain intervals of time. Both problems undermined the unique selling point of IxTheo, which was to always provide information on the most recently published journal articles.
The New IxTheo: Cooperation and Open Access With its release as an open-access database in 2007, IxTheo reached a new milestone in its history. IxTheo was now unique among theological bibliographies which also covered the whole spectrum of theology and religious studies, not because it was an online database, but because it could be accessed free of charge by everyone. This fundamental decision was well ahead of its time back then and constituted the basis for a strategic reorientation. In July of 2011, I took over the leadership of IxTheo and the department managing it and I developed seven guidelines for the reorientation of IxTheo: 1. An independent and modern Internet presence: IxTheo should not disappear through integration in a larger database of a library association, but rather become the central research location for the academic community.
6. Cooperation with capable partners from church and state libraries: IxTheo cannot do everything on its own. There are large and important collections in other libraries, and a cooperation would bring added value to the user community. 7. Cooperation with editors and publishing houses: Content providers should be asked for their contribution in order to have more metadata on offer and to be able to develop new services such as a full text search on the contents owned by publishers. 77 This plan was presented and discussed in 2013 at the 'Katholischer Fakultätentag' (Sankt Augustin) and the 'Evangelischer Fakultätentag' (Heidelberg). 78 Part of the plan was to develop IxTheo further with feedback from the academic community. This is why the Catholic and Protestant faculties of theology of the university of Tübingen were asked to become co-publishers of IxTheo.
In order to realise the main objectives described above, it was necessary to reorganise the department, which had been working as librarians in a traditional way, to introduce new production methods, to develop collaborative capabilities at the technical and organisational levels and to come up with a new plan to deal with the metadata being produced. An effective collaboration with other libraries was only possible if the metadata were not stored anymore in the stand-alone Allegro-database, but rather in the larger database of a library association. As theological monographs purchased at the UB Tübingen had been catalogued in the database of the 'Südwestdeutscher Bibliotheksverbund' (SWB, the Library Association of South-west Germany) since 1986, the idea to migrate the metadata of articles to this database seemed to suggest itself.
A special selection program made it possible to immediately reuse all theologically relevant titles which had been catalogued by other libraries in the common database. The data is now supplied on a daily basis by the common database, it is processed79 and loaded in a SOLR index and then used and displayed in a new discovery system80 which is independent from the library association. When the website was released in July 2016, over 1 million titles were available right away, thus doubling the number of referenced titles in comparison with the old IxTheo (ZID). As a central hub, the new IxTheo now allows users to search for monographs, articles and databases in one search environment -before, the user had to search through three independent databases -as well as giving a direct access to full texts depending on copyright and licensing conditions.
81 These transformations, which were funded by the German Research Council (DFG) through the funding programme for 'Fachinformationsdienste' (FID, specialised information services)82 and were evaluated and followed with great attention by the academic community, constituted the prerequisites for all further developments of IxTheo to this day: the implementation of modern search capabilities for Biblical 18th century;84 the cooperation with/integration of specialised bibliographies in Biblical exegesis,85 church history,86 canon law,87 and patristics88 in IxTheo. In addition to the integration of new sources and types of literature and media, the number of theologically relevant journals indexed in IxTheo rose in a continuous fashion from around 600 to well over a thousand. 89 New production procedures made this possible: The tables of contents of print journals are now transformed into structured metadata (Marc21) through a semi-automatic procedure implemented by ImageWare, a software company from Bonn, Germany.
For this purpose, our own metadata first had to be brought together at a central location, the common database of the SWB, and the tools necessary for formal and subject indexing had to be made available to our cooperation partners. The most crucial point is the continuous exchange of metadata between different systems. Since metadata are seldom 'finished' at any given point in time, it is not enough to perform an initial trade between cooperation partners; there has to be a regular exchange of corrections and supplements, such as the later standardisation of an author's name or an additional classification or subject indexing. In collaboration with the diocesan and cathedral library of Cologne, an asymmetrical procedure was developed for this purpose: The journals indexed in Cologne for IxTheo are catalogued, corrected and indexed directly in the IxTheo cataloguing tool.
"Zoterotranslators," GitHub, accessed November 8, 2021, https://github. com/ubtue/zotero -translators. Unfortunately, there is no general quality standard among publishing houses for the metadata themselves and their transfer, which is why some publishing houses cannot be involved in this procedure. formal and subject indexing of a source does not necessarily lie in the hand of one of the partners, but can be distributed among partners instead in accordance with issues of practicability. For example, IxTheo uses automatic procedures to catalogue journals which are then indexed with subject headings by a cooperation partner. For the task of subject indexing, a tool called the Digital Assistant (DA-3),93 which is used by several libraries, was developed further in collaboration with the software firm Eurospider to such an extent that article data can now be indexed efficiently with it.
This web-based tool is available free of charge to cooperation partners. The first partnership was struck and implemented with BILDI and KALDI (Innsbruck, Austria) after a meeting I had with Mira Stare, the manager of BILDI, at a conference in May of 2014 near Salzburg. 94 This was followed by cooperation agreements with DaKaR (a database of canon law based in Münster) and the 'Augustinusdatenbank' (database on Augustine) of the 'Zentrum für Augustinusforschung' (centre for research on Augustine, located in Würzburg). The migration of data from Mikado (a missiology database located in Aachen)95 is also planned. While preparing the migration of metadata from these cooperation partners into IxTheo, we expanded our concept of presentation, allowing for specific subsets of metadata to be presented on their own, while keeping all metadata referenced in the central IxTheo database.
It seemed appropriate to provide a special, more focused access to academic subjects such as Biblical studies96 as a major theological discipline, canon law97 and Augustine (from a theological and historical point of view) for the benefit of the academic public interested in them. Since the corresponding subsystems contain only a subject-related subset of IxTheo, they list much fewer titles, which helps researchers save time and focus on their area of interest. In addition to this selection, further functions and facets may be used which are important for the discipline. Larger datasets related to a given discipline can be presented in such subsystems in addition to the representation in IxTheo, whereas the effort and expense required to build up and maintain such a subsystem may prove to be too much for smaller datasets.
All this must be financed. The pillars of IxTheo's funding are: (1) Basic funding comes from the state of Baden-Württemberg as the funding body of the university library, (2) grants at the federal level come from the German Research Council (DFG) and (3) some funding is provided by the German Bishops' Conference, i. e. the Roman Catholic Church. This funding model allowed the UB Tübingen to carry out the transition of IxTheo to an open access product in 2007 without any complicated financial-organisational transformation. The innovations and international partnerships thus made possible were already described above. In contrast to this, the ATLA Religion Database (RDB) is financed through licensing fees. The main obstacle for a cooperation between IxTheo and ATLA RDB is not academic or scientific, but rather lies in the different financing models used and their corresponding presentation and operating modes which are open access in the one case, and closed access in the other.
5. 2 Integration of New Types of Media IxTheo reacted to the academic community's need to have the ability to search for all scientifically relevant sources at one central hub -and to obtain a direct access to these sources when possible -by expanding the types of media it catalogues. Traditionally, bibliographies would reference monographs, articles and book reviews. However, digitisation brought along new forms of publications which should be present in a modern bibliography: websites from research projects, databases and, recently, academic weblogs and podcasts. The international GLAM108 initiative also has a digital basis: Collections from various cultural memory institutions are linked together using common authority records across all disciplines. GLAM plays an important role in Christian and religious art and in archaeology, but the referencing of archive material or material from an author's estate in a bibliography also constitutes a new development.
Archival databases and further external resources which provide a standardised and Open Access to their data can easily be integrated into IxTheo thanks to the use and integration of  Wikipedia's BEACON109 format. 110 Research data also come increasingly into focus as a type of medium which will play a more important role in bibliographies in the future. Research data per se are nothing new. What is new, however, is that they are systematically gathered, accessible in electronic form, available when possible in a standardised format and stored according to FAIR111 principles. Research data produced in a given project and processed in such a way that the results achieved are comprehensible and reproducible or can be used in other research projects play a much more important role in the natural and social sciences (at the moment) than in the humanities.
The range of data found includes qualitative interviews, images, audio recordings, semantic word studies, texts processed with TEI and databases. 112 This wide range of data is due to the variety of topics and issues discussed in the theological disciplines and in religious studies as well as their strong inter-disciplinary character. Research data in the humanities are not so much tied to the academic discipline concerned as to the type of media used. This is why humanities consortia built within the major German project of a National Research Data Infrastructure,113 which sets up such consortia in order to address common needs with respect to research data management, platforms and repositories, standardisation and classification as well as research tools, are inter-disciplinary and more interested in the nature (i.
A corresponding international initiative was founded under the name OpenCitations,126 which is supported worldwide by well-known universities such as the KU Leuven since 2020. In Germany, various cooperation partners are working on this issue, because such an enormous task can only be fulfilled through national and international partnerships from libraries and data providers. Timotheus Chang-Whae Kim and I formulated an application scenario for citation data in IxTheo for the project Linked Open Citation Database (LOC-DB)127 run by the university library in Mannheim. 128 This constitutes a very large field of activity for a cooperation between larger theological bibliographies, because citation links in older theological literature cannot be easily and automatically processed as in the case of current literature where DOI-to-DOI comparisons are possible.
EB) did not bring any result. However, competition between these three larger bibliographies led to a natural concentration process at the local level. In Chicago, various bibliographies and abstract services such as the ATLA Catholic Periodical and Literature Index were integrated in the ATLA Religion Database (RDB); in Leuven, both printed bibliographies, the Revue d'histoire ecclésias tique (RHE. B) and the Elenchus bibliographicus (ETL. EB), which each had its own web site, were merged to become the Index Religiosus; and in Tübingen, the FID Theologie integrated its database of journal articles as well as its monographs and other sources in the new Index Theologicus. These databases grew significantly and by leaps and bounds in the process and now offer much more comprehensive search capabilities to the current academic generation than to earlier ones.