dataesr/scientific-paragraphs-categorization huggingface dataset:
RESULTS AND HYPOTHESIS HG003 Bona Fide sRNAs Based on a computational analysis of our HG003 RNA-seq data (GEO GSE104971), 88 UTRs, 22 antisense RNAs, 24 CDSs, 11 T-boxes, and riboswitches, and 3 toxin-antitoxin systems were annotated among the 527 putative regulatory RNAs found and  Motifs were defined as given by Regprecise  (Novichkov et al. , 2013)  for S. aureus N315 strain. We also search for GraRS, WalKR, and SrrA putative regulations using reported motifs  (Sterba et al. , 2003; Hartig and Jahn, 2012; Nicolas et al. , 2012; Mäder et al. , 2016; Durand et al. , 2017) ; *corresponds to proposed or validated regulations reported elsewhere (discussed in the text) corresponding to motifs that did not pass the stringent E-value chosen or that are upstream of sequences selected for analysis.
No DNA binding site was found for GraRS and WalKR. indexed in the SRD database  (Sassi et al. , 2015). According to the definition given above, we considered a restricted list of 352 putative sRNA candidates to which we adjoined those of Carroll et al. 's and Mäder et al. 's sRNA lists. A gene-finding format (GFF) file including these putative sRNAs was generated (Data Sheet 1) and visually analyzed and compared to HG003 RNAseq profiles using Artemis genome browser  (Rutherford et al. , 2000). In addition, HG001 tiling array profiles were scrutinized for each putative sRNA using the S. aureus expression data browser (http://genome. jouy. inra. fr/cgi-bin/aeb/index. py). From these inspections, we applied the bona fide criteria to compile a curated list of 41 bona fide sRNAs expressed in at least one biological condition in the HG003 strain (Table  1 ).
, 2009). As RsaF and its promoter were not detected in the transcriptome databases, we chose to consider just two transcripts, RsaE and the RsaE/S390 fusion. Also, many previously reported sRNAs are now known to be part of UTRs. One example is Teg49: initially characterized as a bona fide sRNA  (Beaume et al. , 2010) , it is also within the 5 ′ UTR of sarA mRNA, yet Teg49 plays a trans-acting role by modulating sarA expression  (Kim et al. , 2014; Manna et al. , 2017). For two recently proposed sRNAs, S1077 (Figure  S4 ) and S736, which have their own terminators, authors showed that they are both part of longer transcripts that extend downstream of their terminators  (Mäder et al. , 2016)  and are probably cis-acting elements. Alternatively, transcriptional terminator read-through from sRNA genes could generate longer regulatory RNAs.
The 4. 5S RNA, which is the RNA component of the signal recognition particle ribonucleoprotein complex and is not a regulatory RNA was removed from the bona fide sRNA list. Two other sRNAs that interact with proteins, 6S RNA and tmRNA, were kept in the sRNA list as they may have regulatory functions  (Makhlin et al. , 2007; Cavanagh and Wassarman, 2014). Our RNA-seq transcriptome data are similar to those produced by tiling arrays and presented in the S. aureus expression data browser (http://genome. jouy. inra. fr/cgi-bin/aeb/ index. py). Indeed, many bona fide sRNAs listed in Tables 1, 2 are independently detected using these two methodologies. Our transcriptome analysis contains 27 bona fide sRNAs not annotated as such in the Mäder et al. study, although reported elsewhere. Six are located in repeat regions not evaluated by the tiling array method (e.
g. , S627 and S629 Figure  S5 ). Others have either no expression or an expression level that does not fulfill the cut-off selection imposed by the authors (Figure  S6 ). The slight expression differences observed [namely for, srn_0890, Teg147, Teg108 (Figure  S6 ), Sau-85, RsaB, Sau-5949, SprB, Teg122, Teg124, sRNA334, Sau-19 (Figure  S6 ), and sRNA390] could be due to allelic variation of the tcaR regulator between the two sister strains HG001 and HG003 or to specific expression of sRNAs in at least one of the conditions tested only in our dataset (e. g. , heat shock). sRNA Features S. aureus is a low guanine-cytosine (33% GC) content member among Firmicutes. Local variation within the genome of this percentage may reflect DNA acquisition by horizontal transfer  (Garcia-Vallve et al. , 2000).
ACKNOWLEDGMENTS This work has benefited from the facilities and expertise of the high-throughput sequencing platform of I2BC (http://www. i2bc. paris-saclay. fr/). We thank the MIGALE platform,  Pierre Nicolas  (Jouy-en-Josas, France) and  Ulrike Mäder  ( Greifswald University ) for providing useful analyze tools and permission to print website captures;  Alban Ott  for help with Figure 3;  Sandy Gruss  for critical reading of the manuscript,  Annick Jacq , and  Mared Sous  for helpful discussions and warm support.
FUNDING This work was funded by the  Agence Nationale pour la Recherche (ANR)  (grant #  ANR-15-CE12-0003-01  " sRNA-Fit ") and by the  Fondation pour la Recherche Médicale (FRM)  (grant #  DBF20160635724  " Bactéries et champignons face aux antibiotiques et antifongiques "). WL and CM are the recipients of Chinese scholarship council, and fellowships from the  ANR , respectively.
sRNA boundaries are given according to publications and GEO GSE104971 data. The presence of "UCCC" motif proposed by Geissmann et al. is indicated. NB: Northern blot; RT: RT-PCR; 5 ′ -3 ′ : 5 ′ 3 ′ RACE. aMäder et al. , 2016. b Carroll et al. , 2016. c Geissmann et al. , 2009. d Abu-Qatouseh et al. , 2010. e Bohn et al. , 2010. f Lioliou et al. , 2012. g Pichon and Felden, 2005. h Eyraud et al. , 2014. i Novick et al. , 1993. j Marchais et al. , 2010. k Beaume et al. , 2010.
02 and 0. 7 T), applied in the sample plane, parallel to the neutron spin polarization. Reflectivity curves were acquired for the two spin eigenstates (commonly referred to as spin-up and spin-down) of the incoming beam. In this configuration the reflectivity measurement is sensitive to the structural depth profile as well as to the magnetic component parallel to the applied field. In particular the neutron senses the total magnetic induction B(z) as a function of depth within the sample. Model fitting was carried out using the GenX package  [40]  based on an optical transfer matrix approach  [41]  and a differential evolution fitting algorithm. Muon-spin spectroscopy. Transverse-, longitudinal-, and zero-field muon-spin rotation (μ + SR) measurements were carried out using the low-energy muon (LEM) beamline at SμS  [42].
The LEM beamline produces very slow, spin-polarized, positive muons with tunable energies between 0 and 30 keV 174427-2  [43, 44]. Muon-spin spectroscopy is a very sensitive probe of the local (but not element specific) magnetic order. Dynamics can be probed on the microsecond timescale. For the measurements, the samples were glued to a Ni-plated Al sample holder with a small magnetic field applied perpendicular to the surface of the sample. Measurements were made on two Dy:Bi 2 Te 3 films of different Dy concentrations, one of which is equivalent to the one used for XMCD and PNR. All data analysis was carried out using the WIMDA program  [45]. Soft x-ray angle-resolved photoemission spectroscopy. Soft x-ray ARPES measurements were performed at the ADRESS beamline of the Swiss Light Source at the Paul Scherrer Institut, Switzerland  [46].
Biomarkers The Olink Cardiovascular III panel was used to create the biomarker profiles in the two HF phenotypes. This panel comprises 92 cardiovascular disease-related biomarkers, which were selected based on literature searches, disease association in the Coremine database, and in collaboration with experts within the cardiovascular field. Measurement of these 92 biomarkers was performed by Olink Bioscience analysis service (Uppsala, Sweden), using the Proseek® multiplex Inflammatory 96*96 kit. (16)  The Proseek® reagents are based on the Proximity Extension Assay (PEA) technology, which binds 92 oligonucleotide-labeled antibody probe pairs to the target biomarker. For further quantification, real-time PCR was performed. Olink wizard and GenEx software were used for further data analysis.
This work was supported by the  Netherlands Cardiovascular Research Initiative : an initiative with support of the  Dutch Heart Foundation ; Renal Connection to microvascular disease and heart failure with preserved ejection fraction [ CVON2014-11 RECONNECT]  and a grant from the  European Commission  [ FP7-242209-BIOSTAT-CHF; EudraCT 2010-020808-29 ]. IM is supported by a  NHS Education for Scotland/Chief Scientist Office Postdoctoral Clinical Lectureship  ( PCL/17/07 ). D. A. reports grants from  Vifor and Abbott Vascular , and fees for consultancy from  Vifor ,  Bayer ,  Boehringer Ingelheim ,  Brahms ,  Janssen ,  Novartis ,  Servier ,  Stealth Peptides , and  ZS Pharma. K. D. has received honoraria and/or research support from  Medtronic ,  Boston Scientific St Jude, Biotronik and Sorin (device companies) , and  Merck ,  Novartis ,  Amgen ,  Boehringer Ingelheim ,  Astra Zeneca ,  Pfizer ,  Bayer ,  GSK ,  Roche ,  Sanofi ,  Abbott ,  Otsuka ,  Leo ,  Servier , and  Bristol Meyers Squibb  (pharmaceutical companies).
MRI Data Collection Structural data for both studies were acquired at the CERMEP neuroimaging facility in Lyon, France. In Study A (21 HR and 20 LR)  (Eichenlaub et al. , 2014b) , structural MRI were acquired with a T1-weighted MPRAGE sequence (1. 0 mm isotropic resolution) on a 1. 5T Siemens Sonata MR system (Siemens Medical Solutions, Erlangen, Germany). In Study B, structural MRI were acquired with a T1-weighted MPRAGE sequence (0. 9 mm isotropic resolution) on a 3T Siemens Primage MR system (28 HR and 27 LR,  Vallat et al. , 2018b). Out of the 96 subjects, four were excluded based on age or BMI outlier rejection.
Four participants were excluded from further analyses because of a low data quality (one HR and one LR from Study A, one HR and one LR from study B). For the remaining 88 participants, we estimated the total intracranial volume (TIV) to further correct for different head size and volume. Images were then smoothed with an isotropic Gaussian kernel of 6 mm full width at halfmaximum. 1 http://www. neuro. uni-jena. de/cat/.
After recording the control heart activity for 0. 5 min, the tested compounds were applied, and an additional 2 min of heart activity was recorded. The recording of new-isolated heart activity was preceded with 10 min of preincubation with saline A to stabilize the heart rate. The calculation of changes in the heart rate was conducted according to a previously described method  [53] , as the percentage change between the heart activity recorded before and after application. The obtained data were analyzed with LARWA and ANALIZA software (Both programs have been written in 2004 for our Department, Pozna ń, Poland). For each concentration, 5-12 larvae were used.
The chamber was placed on an Olympus SZX12 stereomicroscope that was equipped with a Pixeling 662 camera. Similar to the heart bioassay, the recording was preceded by 10 min of preincubation. Each recording lasted 2 min; after 30 s of control recording, 10 µL of the tested substances was applied through the port with the Hamilton syringe. The obtained data were analyzed with the AnTracker (PreOptic, Warsaw, Poland) software. The changes in the oviduct and hindgut contraction frequency were calculated as the percentage change between the frequencies recorded before and after application of the tested compounds. For each used concentration, 6-13 larvae were used.
Statistical analysis All the data are presented as the mean values ± SEM of n number of replicates. The statistical significance of differences between the control and treatment values was determined using appropriate statistical test: one-way ANOVA Tukey's test, Student's t-test, or, if there was not a normal distribution, the nonparametric Kruskal-Wallis test and Dunn's Multiple Comparison test. The statistical analyses were conducted using GraphPad Prism 5 software (GraphPad Software Inc, Version 5. 01, MacKiev, La Jolla, CA, USA, 1992-2007). Differences were considered to be statistically significant if p ≤ 0.
0. To achieve ligand exchange, the trans chamber was perfused with at least 5 times the chamber volume of the electrophysiology buffer that contains cAMP or cGMP at the concentrations specified in the text. All current signals were acquired with Clampex (V10, Molecular Devices), filtered at 1 kHz with an 8-pole low pass Bessel filter and digitized at 20 kHz with Digidata 1440 A digitizer (Molecular Devices). Data were analyzed in Clampfit (V10, Molecular Devices) where single-channel recordings were idealized with the single-channel search mode The number of channels was estimated directly from the recordings at saturating cAMP and +100 mV, by dividing the largest current amplitude in the recording (where all channels in the bilayer are open at the same time) by the single-channel current amplitude.
Acknowledgements This work was supported in part by  National Institutes of Health  grants ( R01GM124451 ) to C. N. and S. S. Early parts of the work were funded by a  European Research Council (ERC)  Grant (# 310080 ,  MEM-STRUCT-AFM ) to S. S. A. M. was supported by a  Long Term EMBO Fellowship  ( ALTF 1427-2014 ) and a  Marie Curie Action  ( MSCA IF-2014-EF-655157 ).
All images were recorded in super-resolution counting mode using the automated data collection software Serial EM  [25]  with a defocus range of 1. 8 to 3. 4 μm. In the case of the Rea1_ΔAAA2-H2α AMPPNP state a Volta phase plate was used in combination with a target defocus of 0. 5 μm. The irradiated area on the VPP was changed every hour.
Image processing Motion correction and dose-weighting were performed using MotionCor2  [26]. CTF parameters were estimated using Gctf  [27]. Subsequent processing was done using Relion-2. 0 [28]  unless stated otherwise. Micrographs were first manually examined to remove images with significant uncorrected drift, large amount of contamination, a large astigmatism, extreme defocus values (<1. 2 μm or >5 μm), or abnormal Fourier patterns. Micrograph quality evaluation in the case of the Rea1_ΔAAA2-H2α AMPPNP phase plate data set was done according to von Löffelholz et al. [29]. For the Rea1 ADP dataset a small set of particles was manually picked and subjected to reference-free 2D classification. A selection of 2D class averages representing different views of Rea1 was selected, centred using the Relion shift_com function, and used as references for autopicking by Gautomatch (K.
Negative stain sample preparation and data acquisition Rea1 or the Rea1_ΔAAA2-H2α deletion mutant in buffer B without glycerol were diluted to a final concentration of 45 nM. AMPPNP, ATP, or ADP were added to reach a final concentration certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. of 3 mM. Negative-stain electron microscopy was performed on plasma-cleaned carbon film on 400-square-mesh copper grids (Electron Microscopy Sciences). 3 μl sample was applied to the grids that were subsequently stained with 2% (w/v) uranyl acetate. Data collection was done on an FEI tecnai G2 operated at 200kV and equipped with a Gatan Ultrascan 2K*2K CCD camera. Data were collected at 1 μm underfocus, with a pixel size of 3. 629 Å and an estimated dose of 25 electrons / Å 2 during 1 s exposures.
Acknowledgements We gratefully acknowledge  Julio Ortiz  and  Tat Cheung Cheng  for their help during cryoEM data collection. This research was supported by an  ATIP-avenir grant  to H. S. H. S also acknowledges the support of the  MRC Laboratory of Molecular Biology  during the initial stages of the project. This study was supported by the grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de la Recherche  under the  frame program Investissements d'Avenir   ANR-10-IDEX-0002-02. The authors acknowledge the support and the use of resources of the  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INBS-05  and of Instruct-ERIC. We thank  Andrew Carter ,  Patrick Schultz ,  Albert Weixlbaumer ,  Alastair McEwen  and  Sandrine Morlot  for their invaluable comments on the manuscript.
He provided a title for each of these anthologies (based on their source magazine), illustrated many of their covers, and provided a table of contents, handwritten with bibliographic details for each item. The table of contents also includes symbols through which Gibson rated the 'SF content' of the items he collected. We have identified approximately 78 symbols, however Gibson left no key to their exact meaning, even if he did sprinkle his anthologies with marginalia that provide some clues about his approach to classification. To help us make sense of this unusual collection and its vast potential, we began by combining archival and exploratory visualization methods in an intertwined way  (Forlini et al. , 2016; Hinrichs et al. , 2016; Hinrichs et al. , 2018). Working with a subset of 50 digitized anthologies, we produced detailed metadata (including titles, date and place of publication, author name and gender, keywords, and abstracts) from reading more than 1,500 individual items in Special Collections.
In parallel, we developed the Speculative W@nderverse which provides different perspectives on the Gibson anthologies and this underlying metadata through an interlinked visualization (see Figure  2 ). The W@nderverse visualization consists of four interactive and interlinked visual views that showcase the topics present in the SF items through keyword motifs and also in relation to the Gibson symbols, the temporal distribution of SF items, and the large variety of titles and authors included in the anthologies (for more details about the visualization see  Hinrichs et al. , 2016). The W@nderverse thus offers multiple points of entry into the Gibson Anthologies. People may scroll through story titles and access abstracts, or they may select SF items based on a particular range of years by manipulating the timeline.
2012: 13). We consider the W@nderverse a product of our early explorations of the Gibson anthologies. It is a visualization sandcastle that has, through its very limitations, motivated our theoretical explorations of ways to embrace the unique aesthetic and material characteristics of print collections while translating them into digital form. The W@nderverse emphasizes the content-related metadata of the Gibson anthologies, but it only hints at the qualities of this collection of unique print artifacts. While the item list (see Figure  2 , on the right of the interface) provides a glimpse of the anthology covers, this does not effectively convey what the Gibson anthologies may look and feel like (e. g. , their size, weight, and paper material) neither does it allow the navigation of the collection based on aesthetic or material features.
This range of paper types (and their associated price points) is also significant as it highlights the diversity of forms of Victorian periodicals -a diversity that is erased in current digital displays of periodicals  (Mussell, 2016). Making visible raw paper material may also help alert readers to the fact that the appearance of paper will also bear the marks of environmental exposure and age (through things like 'foxing' for example). Once combined with representations of literary content (from metadata manually derived through archival and curatorial work, or computationally derived through text analysis), these visual representations of paper 'feel' can invite readers to explore the broader significance of the Gibson anthologies. By analyzing the content of these early SF stories by paper type, we can begin to tell a more 'textured' history of how literary innovation was tied to changes in paper-making and periodical publishing.
To highlight the crafted nature of the anthologies is to attempt to use the digital medium against the grain, so to speak. The anthologies are the work of one's hands, and as Piper notes 'there is a profound sense of person that comes through the work of one's hands that cannot be fully replicated digitally  ' (2012: 81). However, if we move away from attempting to 'replicate' digitally, we could better imagine ways to evoke or elicit different but nonetheless meaningful related experiences. For example, in the case of the hand-crafted Gibson anthologies, we could invite readers to engage in the kind of performative archiving that Gibson practiced through the work of his hands, and we could do this both on screen and through data physicalization. Tapping into the malleability and versatility of the digital medium we could invite readers to engage with the crafted nature of the anthologies by permitting the disassembling and reassembling of collected pages according to different variables (dates of publication, authors, literary or formal features, etc.
). This would accentuate the scrapbook-like nature of the anthologies and the practice of scrapbooking itself as a form of meaning-making through print artifacts that has migrated into the digital realm through 'the "cut and paste" terminology used by computer programs and applications'  (Grubar Garvey, 2012: 21)  Moving beyond on-screen representations, we could explore digitally-enhanced data physicalization as a means to translate information one gets from handling the anthologies and noting their scrapbook-like nature. This means understanding the ways Gibson himself implicitly re-thought the structure of the book and the page as he deconstructed existing periodicals and, by cutting, pasting, and binding, reconstructed from their individual pages anthologies of his own making. As others have also suggested, we believe that translating print into a digital environment should involve a rethinking of the formal structure of the page and the physical structure of the codex book to take advantage of the fluidity and malleability of the digital medium  (Piper, 2012).
Furthermore, we combined CD4 cell count, mothers' weight loss and HIV-1 disease stage as per WHO classification to create the composite endpoint called 'HIV-1 disease progression'. HIV-1 disease progression was Open Access accelerated when CD4 cell count decreased to <350 cells/ µL, or the HIV-1 infection was assessed by the trial physician at stage 3 or above, or the mothers lost >10% of their weight; otherwise, HIV-1 disease progression was deemed absent or slow. Our main independent variable was EPBF (until week 26 post partum) or any breastfeeding (until week 50 post partum) duration. The data were collected by trained physicians, pharmacists, biologists and counsellors. Seca-brand scales and stadiometers were used to measure the mother's height and weight. Weights were rounded to the nearest 10 g and the height to the nearest millimetre.
These multivariate analyses were run taking all participants together and also as two strata comprising South African mothers (stratum 1) and Burkina Faso, Uganda and Zambia together (stratum 2) because South Africa presented important socioeconomic, cultural and demographic differences compared with the other countries. For continuous variables, the mean values with 95% CI were estimated, and for categorical variables, percentages were used. Associations between variables were tested using the χ 2 test for categorical variables. STATA/SE V. 13. 1 statistical software has been used for the analyses. ethics Prior to enrolment, the mothers signed a written informed consent and assent forms for themselves and their children, respectively. The trial was conducted according to the sponsor (ANRS) ethic charter, Good Clinical Practices and the principles of the Helsinki declaration.