dataesr/scientific-paragraphs-categorization huggingface dataset:
Distribution of source types Another aspect that can be derived from the database is the distribution of source types during the first four decades in the sixteenth century. As already mentioned, the project does not concentrate on printed polyphonic music, but on all sources containing printed musical notation, regardless of their content. The items are sorted into eight distinct source types (see  Figure I. 3). Calculated solely according to the numbers of titles containing printed music, the largest group-a third of the total number of titles in the database-comprises liturgical books, both Roman Catholic and Protestant. This is not only the most comprehensive group but also the most diverse. The books in this group vary greatly in their content and formats, ranging from large missals, graduals, and antiphoners in folio, to agendas and processionals in quarto, as well as even smaller breviaries and Lutheran church orders.
Early printing techniques Once a printer has decided to publish a certain oeuvre, he (or in some cases she) had to decide how to realise this technically. How was the notation to be printed? Was it worth investing in a specific music font? Was it worth risking multiple runs of the same sheet through the press, or was a single impression less likely to result in misalignment and waste? Our work on the database and the articles presented in this volume shed new light on the technical aspects of printing music in the early sixteenth century. The database provided us with a way of seeing the 'bigger picture': the distribution of the different printing techniques and their development over time, as well as the general trends in printing different kinds of sources containing notation. At the same time, detailed examination of individual publications reminded us time and time again that no development is linear, and that individual printers found many different solutions to the same problem at hand.
38 See Kmetz, 'Closed Market'. were embedded in missals otherwise printed from double impression, as seen in Johann Winterburger's 1510 Vienna edition of the Missale Salisburgense. This composite single-/ multiple-impression technique allowed Winterburger to render chant in two different versions simultaneously: in the regular, ferial form in which the singers performed only the notes printed in black, and in a more elaborate festal form, with optional notes suitable for more important feasts printed in red. 36 Work on the vdm database brought to light another use of this technique. We found several publications from the 1510s onwards that include instructions for the correct enunciation of Latin (and some Greek) texts. In some of these, such as the editions of Johannes Cochlaeus' Grammatica printed by Reinhard Beck at Strasbourg, the printer used musical notation to indicate long and short syllables in verse.
Thus, to give any precise numbers in writing would render this publication incorrect by the time it goes to press. However, it is safe to say that of all publications described in the database only a small percentage (less than 10 per cent) contain polyphonic music. The largest group is, as it is with Lotter, that of liturgical publications (of different denominations), followed by books of music pedagogy, humanist dramas and others. 8 Thus, Lotter's output can be seen as representative of this distribution. Let us take a closer look at his publications. Among his thirty-one liturgical titles we find ten missals, the majority (six) for his own diocese, Meissen. That he printed in the archbishop's rooms in 1520 suggests a good rapport with the ecclesiastical authorities. 9 Additionally, he was also the only printer in Leipzig in this period to print music from moveable type, and was thus the obvious choice as a printer to publish missals, which were commonly printed in that way.
24 he shift (or at least diversification) of Lotter's attention from Leipzig towards Wittenberg indicates a more general change in the centres of printing, for music and more generally. The data from vdm makes this particularly evident, especially in the realms of liturgical and polyphonic music. Comparing the locations where polyphonic music was issued between 1500 and 1540, a shift is noticeable around 1520. Before this time, the main centres for printing polyphony were Augsburg, Mainz, Basle and Cologne. After the beginning of the Reformation, Lutheran cities such as Nuremberg, Frankfurt, Strasbourg and Wittenberg took over. This change is strongly connected to the movements of individual printers. In Wittenberg we can observe how printers originally attracted to the town for its potential in the market of Reformation books later issued other kinds of publications there.
Aside from providing me access to the information they had on the Egenolff music books resident in their wonderful database, and doing it well before their site went live in July 2015, they brought me up to speed on the value and the pitfalls of USTC and VD16. Without their generous support and advice, this article would never have been written. 2 Among the many books that discuss Fust's financial backing of Gutenberg and his press, see Pettegree, The Book,  [29] [30] [31] [32] Kapr, Johann Gutenberg, [156] [157] [158] [159]  and the enthralling novel by Alix Christie, Gutenberg's Apprentice (New York: Harper Collins, 2014) which although a fictional account of Gutenberg and his relationships with Fust and Peter Schöffer is well-grounded in serious research. 3 On Jacob Fugger as a businessman, patron, and financier to the Hapsburg dynasty, see Steinmetz, The Richest Man and Strieder, Jacob Fugger the Rich.
This database (www. ustc. ac. uk, last accessed on 31 January, 2016) allowed me to not only assemble a list of all of Egenolff's publications, but also to sort them by date, language, format, and subject/classification. Moreover, the database enabled me to access remotely digital copies of the Egenolff prints that are available on the World Wide Web. Aside from USTC, I also relied heavily on the German national database sponsored by the Deutsche Forschungsgemeinschaft and the Bayerische Staatsbibliothek: Verzeichnis der im deutschen Sprachbereich erschienenen Drucke des  16. Jahrhunderts (VD 16). Using VD16 (www. vd16. de, last accessed on 31 January, 2016) in tandem with USTC, I was able to check the accuracy of earlier printed catalogues and studies of Egenolff's output. Among the secondary literature in print that still remains enormously useful today, see Benzing, 'Christian Egenolff', and idem, 'Die Drucke Christian Egenolffs'.
Polyphonic music sources in the database vdm Our research project has allowed us to question the traditional narrative because it is not focused primarily on repertoire, but on printed objects bearing legible printed music notation, without taking into account what kind of music they transmit. We knew from the very beginning of our project that we would be working not only with polyphony but also with a variety of 'different' kinds of music: short examples in theory treatises and textbooks, tablatures, monophonic songs, humanist ode-settings and dramatic choruses, as well as chant and congregational hymns for liturgical and devotional purposes. As we compiled the data from the standard bibliographies, it became increasingly clear that these 'different' kinds of music were not outliers but constitute the overwhelming majority of what was published during the period under investigation.
The forty-three polyphonic music books printed in German-speaking lands in the first four decades of the sixteenth century, catalogued in the RISM volumes A/I and B/I, represent only 14 per cent of the total number of editions including printed music. Almost three years later, at the end of the first stage of the project, the number of sources containing musical notation in our database has more than doubled to 695 titles. 3 This massive increase in the number of editions was due to the consultation of older repertoirebased and regional catalogues, secondary literature, systematic search in libraries, and the careful distinguishing of editions that had been bundled together into one single title in earlier bibliographies. (Some new editions with musical notation came up by chance, for example when they were bound together with books that were already registered, which we recorded in situ.
The musicological community has never spent much interest nor money on producing a catalogue of printed liturgical books containing music, and hence neglects a large part of the production of the sixteenth century (as well as for later times). A prominent exception is the database RELICS, hosted by the University of Michigan. 5 It is still the best place to start with a study of Renaissance liturgical printed books, although based only on volunteer contributions by scholars who mainly work in major research libraries in the United States. However, since this database includes holdings from only a few European libraries, with some additional data supplemented from published bibliographies and library catalogues (such as the fundamental catalogue of Weale, Bibliographia liturgica, and Amiet, Missels et bréviaires imprimés), it can make no claim to completeness.
Moreover, music is not in the focus of this database (nor is it of the catalogues by Weale and Amiet), so that 6 When one searches 'music' as a keyword, one also gets titles with the description 'no music'. Moreover, it depends on the person who entered the data whether there is information on the presence of music at all. 7 In vdm we count 26 editions, RISM A/I gives 12 editions. The author Megel is already mentioned in the 1498 edition (vdm 73), fol. b3 r. POLYPHONIC MUSIC IN EARLY GERMAN PRINT 247 it is difficult to develop a search routine for titles that contain music. 6 The best way to find new liturgical books containing music is still to go to libraries and check all available items there. Due to this lamentable research situation, one can be sure that there are still many more unknown editions hidden in the stacks.
All numbers given in the following tables are based on the status of the data in vdm from 21 December 2015. See the current version of the database on our homepage: www. vdm. sbg. ac. at. 4 For the classification of the sources types see the Introduction in this volume. 5 http://quod. lib. umich. edu/r/relics/ 246 ANDREA LINDMAYR-BRANDL.
The vdm database lists folding charts in Gregor Reisch, Margarita philosophica (Strasbourg: Johann Grüninger, 1515), vdm 490, and Johannes Frosch, Rerum musicarum (Strasbourg: Peter Schöffer the Younger and Matthias Apiarius, 1535), vdm 564 and 637. For a sample of sixteenth-to seventeenth-century examples, cf. Owens, 'You Can Tell a Book by Its Cover', esp. 362-or 364, including: Monochordum.
University of Vienna  and is an active member of several academic institutions and organisations. She directs two research projects: one on the critical edition of works by  Gaspar van Weerbeke , the other the project Early music printing in German-speaking lands. King's  College, London, UK. She completed her undergraduate and Master's degrees in Vienna (including a term at  New York University ), followed by a PhD on the dissemination of Italian sacred music in German-speaking lands in early modern Europe at the  University of Cambridge  (2012). She then took up a post-doctoral position at the  University of Salzburg , working on the project and database Music printing in German-speaking lands. Her current research project, entitled  Owners and Users of Early Music Books , is funded by a  Leverhulme Early Career Fellowship.
She then took up a post-doctoral position at the  University of Salzburg , working on the project and database Early music printing in German-speaking lands, before  University of Vienna  and is an active member of several academic institutions and organisations. Currently she directs two research projects: one on the critical edition of works by  Gaspar van Weerbeke , the other the project Early music printing in German-speaking lands. Grantley McDonald is a postdoctoral researcher and lecturer in musicology at the  University of Vienna , where he directs the FWF research project The court chapel of Maximilian I: between art and politics. He holds doctoral degrees in musicology (Melbourne, 2002) and history (Leiden, 2011). Grantley has been awarded fellowships at the  Herzog August Bibliothek (Wolfenbüttel), Centre d'Études Supérieures de la Renaissance (Tours), KU Leuven, Trinity College Dublin , and the  University of Salzburg , where he worked on the  FWF  project.
3 All numbers given in the following tables are based on the status of the data in vdm from 21 December 2015. See the current version of the database on our homepage: www. vdm. sbg. ac. at. 4 For the classification of the sources types see the Introduction in this volume. 5 http://quod. lib. umich. edu/r/relics/ 246 ANDREA LINDMAYR-BRANDL.
2 The vdm database lists folding charts in Gregor Reisch, Margarita philosophica (Strasbourg: Johann Grüninger, 1515), vdm 490, and Johannes Frosch, Rerum musicarum (Strasbourg: Peter Schöffer the Younger and Matthias Apiarius, 1535), vdm 564 and 637. For a sample of sixteenth-to seventeenth-century examples, cf. Owens, 'You Can Tell a Book by Its Cover', esp. 362-or 364, including: Monochordum. Regula musica ([c. 1550], D-Mbs 2 Mus. pr. 156-11, urn:nbn:de:bvb:12-bsb00090648-3); Sigmund Salminger, Gradatio, sive scala principiorum artis musicae (Augsburg: Philipp Ulhard, [c. 1545]; D-Mbs 2 Mus. pr. 156-1/8, urn:nbn:de:bvb:12-bsb00090645-6), vdm 1183. Only one example is listed in Deutsche illustrierte Flugblätter, vol. 3, Nr. 160, 312.
Patients Lung transplant recipients were recruited from September 2009 to October 2013 within the multicentre Cohort of Lung Transplantation (COLT) cohort (NCT00980967). The local ethical committee (Comité de Protection des Personnes Ouest 1-Tours, 2009-A00036-51) approved the study, and all participants provided written informed consent. Inclusion criterion was at least 3 years of follow-up unless the diagnosis of BOS was made before (Figure  S1  in Supplementary Material). The eligible patients (n = 688) were phenotyped by a blind adjudication committee as described previously  (21, 22) , based on pulmonary function tests and chest imaging according to ISHLT/ ERS/ATS guidelines  (3, 23). Assessed pulmonary tests were performed before the transplantation, the day of the transplantation, 1 and 6 months after the transplantation and every 6 months thereafter up to 3 years posttransplantation.
gene expression Microarray analysis Total RNA (100 ng) were labeled using the Two-Color Agilent Low Input Quick Amp Labeling Kit and hybridized on SurePrint G3 Human Gene Expression v3 8 × 60K Microarrays following the manufacturer's instructions (Agilent Technologies). Data extraction of median feature intensity was performed with Feature Extraction software v10. 7 (Agilent Technologies). To remove signal intensity bias between each array, median feature intensities were normalized with the lowess (locally weighted scatter plot smoothing) method, then spots for which half the samples exhibited a signal less than the mean of all median signals were removed. Correction between two microarray hybridization batches was performed on the 28,867 remaining spots with the Combat algorithm  (24)  available through the R package sva  (25).
These normalized microarray data were deposited in the Gene Expression Ominbus database (accession number GSE94557). Mean expression levels for the spots targeting the same genes were assessed, resulting in 16,128 unique genes. In the BOS PRED group, the closest time point from transplantation was selected in cases of several samples per patient, so that no patient duplicate was included. Genes with low variation (i. e. , variance <0. 2), and thus considered as invariants, were excluded, resulting in 6,581 analyzed genes. For the identification of differential genes, linear modeling with empirical Bayes statistical procedure was performed, comparing the STA group and each group of interest, using the limma package in R. Genes with p < 5% and fold change (FC) >1. 5 were considered as differentially expressed.
The biological significance of selected genes was assessed using GOminer software. Only gene ontology (GO) categories enriched with a false discovery rate (FDR) <10% and with at least five represented genes were selected. The cell type source of differential genes was  evaluated using the web tool Enrichr  (26). Relative estimation of cell abundances using gene expression data was performed through the CIBERSORT software  (27) , and gene set enrichment analysis (GSEA) was performed to highlight relevant biological processes using curated gene sets from the Molecular Signatures Database (1,000 permutations and FDR threshold of 25%)  (28).
statistical analysis Non-parametric Kruskal-Wallis tests with Dunn's ad hoc pairwise comparisons, Mann-Whitney tests, ROC curves, log-ranked survival analyses, and Fisher's exact test for categorical variables were performed using GraphPad Prism v. 6 (GraphPad Software, La Jolla, CA, USA). Time-to-event analysis was performed using Cox proportional analysis between gene expression and time to BOS with the R survival package (Coxph function, R software v. 3. 3. 2).
We demonstrated that the method could well highlight phenomena already described in the response of cells to irradiation. Interestingly, the work suggested that endothelial cells may display an inflamed phenotype throughout RT, with possible effects on the vasculature of both normal tissues and tumors. Here, we wanted to go deeper into the use of this dataset by a bioinformatics analysis of differentially expressed gene clusters. This new study has sought to establish a novel method to cluster time periods of statistically differentially expressed genes determined by our previous method of GPs and the Bayesian likelihood ratio test. This new method has been applied to our previously published dataset of real-time qPCR measurements of the transcriptional profiles of human umbilical vascular endothelial cell (HUVEC) genes following irradiation at 2 Gy.
Dataset We used the dataset we generated and published previously  [7]. This dataset corresponds to real-time qPCR measurements of the transcriptional profiles of 301 human umbilical vascular endothelial cell (HUVEC) genes following irradiation at 2 Gy. Briefly, in the previous study, transcriptional profiles of 301 genes of HUVECs were measured with real-time qPCR under control conditions and with a single irradiation dose of 2 Gy (case) at 0 h with measurements T obs at 12 h, 1, 2, 3, 4, 7, 14 and 21 days. Gene expression assays were performed using a panel of premade TaqMan low-density array gene signature (angiogenesis, inflammation, apoptosis, immune response and protein kinase) (Applied Biosystems). Experiments were performed in triplicate for each time point of the time course. GPR models were learned for each gene under both conditions over prediction time points T ? that cover smoothly days 0 to 24  [7].
As usually done in the multivariate case, each TF profile was normalized by dividing the values of each function by their standard error to account for differences in degrees of magnitude among the TF time variation functions. The functional principal component scores (FPCS) were calculated using the Matlab package PACE  [45]  and the FPCS number included in the hierarchical complete-linkage algorithm was selected according to the percentage of explained variance (here 95%), which is a usual criterion in FPCA.
Pathway analysis of differentially expressed genes Pathway and sub-network enrichment analyses were performed using the web version of the software Pathway Studio (Mammalian, ChemEffect, DiseaseFX, version 11. 2. 5. 9, updated Oct 22, 2016) from Elsevier  [46]. Names and expression ratio values of the differentially expressed genes and associated TFs were imported into the Pathway Studio. The data input was queried against the Pathway Studio knowledge base for biological interactions. Proteins mapped to the knowledge base were used to build protein networks. Interaction networks were added that included "radiation" as a treatment.
Analyses were conducted according to the procedure previously described in detail  [47]. Data Assist software (Applied Biosystems) was used to determine fold changes, with fixed criteria: a maximum allowable Ct value at 37 was fixed and maximum Ct values were not included in calculations. Normalization was performed using a global normalization method on a per sample basis  [48]. Experiments were performed in triplicate for each time point of the time course. Data are given as means ± SD. Student's t-test p-values were adjusted using the Benjamini-Hochberg false discovery rate method using Data Assist software, and an adjusted p-value less than 0. 05 was applied to select statistically differentially expressed genes.
Simulated data First, we employed simulated clustering data-generated by GP models-to analyze which kernel is best, and which clustering method is best. Afterwards, we simply employed the OVL kernel and outlier-resistant spectral method to real data. We generated simulated clusters by generating 50 GPs N ðm i ; S i Þ, i = 1,. ,50 where m i $ N ð0; s m f K l m Þ S i ¼ s S 2 f K l S with s m f $ Gam 4; 1 = 4 ð Þ s S f $ Gam 2; 1 = 2 ð Þ l m $ Gam 4; 3 = 2 ð Þ l S $ Gam 4; 3 = 2 ð Þ and where K l is a Gaussian kernel with length scale l. Hence, each simulated cluster is represented as a GP whose mean is a sample from another GP, and whose covariance is a kernel matrix defined by a sigma f and l parameters sampled from Gamma distributions. We sampled 300 time series from these 50 GP clusters, while also sampling 100 independent time series, which represent outliers.
[7]. Temporal profiles of gene expression were then clustered with the new method presented in this paper, and regulatory motif sites were searched using the MotifMap system to propose putative TFs responsible for the expression of these genes. Finally, the data were analyzed using Pathway Studio software to explore network interactions and molecular pathways and to allow biological perspectives. https://doi. org/10. 1371/journal. pone. 0204960. g001 However the outlier-resistant variant has higher precision, as expected, while having a lower recall. For biological studies, trading of the recall for higher precision is in general beneficial to reduce the number of false positives. Hence, we chose the spectral k-means-as our clustering method of choice for the real clustering experiments.
Gene expression temporal clustering We clustered the gene expression curves by the OVL kernel and the spectral clustering. We constructed the different curves and clustered the gene expression curves by the proposed methods. We retrieved a set of temporal clusters corresponding to similar profiles. We clustered both difference curves as well as the irradiated curves. As an application, we used the dataset we generated and published previously  [7]. This dataset corresponds to real-time qPCR measurements of the transcriptional profiles of 301 HUVEC genes following irradiation at 2 Gy. In the present work, the published dataset was used to cluster the gene expression curves by the proposed new OVL kernel and the spectral clustering method, which had never been done before. The 301 gene expression profiles were obtained from the GP models computed earlier  [7].