dataesr/scientific-paragraphs-categorization huggingface dataset:
e PERK activation: variation of phospho-eIF2α, ATF4 and CHOP proteins levels (upper part) by western blotting (n = 2). f Cell mortality during a long term Thapsigargin treatment was assessed by cell cytometry with the Live and Dead Assay. Data are shown as mean ± SEM of two independent experiments and were compared by Student's t test (*p < 0. 05; **p < 0. 01; ***p < 0. 001; ns non significant). UPR gene analysis was performed with RT2 Profiler PCR Array System (Qiagen, Courtaboeuf, France) which contained 84 genes for the UPR pathway (Cat. # PAHS-089Z). To this purpose cells were treated with thapsigargin (250 nM, Sigma Aldrich, Lyon, France) for 1 h, 4 h and 16 h or with DMSO as control. RNAs were collected and extracted as previously described  7. Reverse Transcription was carried out with the RT2 First Strand Kit (Qiagen) following the manufacturer's instructions.
OXPHOS Respirometry experiments were performed at 37 °C in the two glass chambers of an OROBOROS Oxygraph under normoxic conditions. DatLab software (ORO-BOROS INSTRUMENTS, Innsbruck, Austria) was used for real-time data acquisition and analysis. Experiments were carried out according to a previously published protocol  42  with some modifications. In brief, cells were seeded onto T75 culture flasks and culture for 7 days to reach ~80% confluence. Cells were trypsinized, washed with PBS and resuspended in mitochondrial respiration medium (MiR05: 110 mM sucrose, 60 mM K + -lactobionate, 0. 5 mM EGTA, 3 mM MgCl 2 , 20 mM taurine, 10 mM KH 2 PO 4 , 20 mM HEPES, 1 g/L BSA fatty acid free and adjusted to pH 7. 1 with KOH at 37 °C) to obtain a concentration of 3. 0 × 10 6 cells per mL. Subsequently, basal OXPHOS was measured after adding glutamate (10 mM), pyruvate (10 mM), malate (10 mM) and succinate (10 mM).
Cells were then pelleted by centrifugation (1500 rpm, 5 min), the supernatant was discarded and the cells washed once in PBS buffer. Then, cells were labelled by Sytox blue(5 microg/ml) during 10 min at RT in a dark room. Reaction was stopped by placing the tubes in ice before being analysed by Cell cytometer on a Becton Dickinson LSRFortessa X-20 using Kaluza software (Beckman coulter, Villepinte, France).
4 with with an optical resolution of 164 nm). 3D-Structured Illumination Microscopy (SIM) was performed on a Zeiss Elyra Microscope coupled to an optovar 1. 6, ×63 objective and a camera EM CCD Andor SIM. During z-astack acquisitions, 5 rotations were applied. Deconvoluted structured illumination images were generated by Zen software, and images were merged in ImageJ. Triple colocalization was analysed using a Matlab-based custom program. Briefly, fluorescence was first in each channel using local thresholding (Phansalkar method  45  ), and a local 2-D median filter with user-defined neighbourhood size was applied to remove noise. Colocalization was then measured using the Manders split coefficients M1 and M2  46  as such: M1 ¼ P i S1 i;coloc P i S1 i and 2 ¼ P j S2 j;coloc P j S2 j , where S1 i,coloc = S1 i if S1 i > 0 and S2 i > 0, and S2 j,coloc = S2 j if S2 j > 0 and S1 j > 0.
Whole transcriptome stability Total RNA was extracted from Sh1 and Sc cells cultured in the presence of 8 μg/ml actinomycin D for 0, 3, 6, 9, 12, 24 and 30 h. A TruSeq Stranded mRNA Sample Preparation Kit (Illumina Inc. , SanDiego, California) was used to construct cDNA libraries according to the manufacturer's instructions with a fragmentation time of 2 min at 94 °C. The individual libraries were multiplexed (2pools, 7 libraries/pool) and sequenced on HiSeq2500 Illumina sequencer using a High Output paired end 2*75 bp run (UMR CNRS 8199 platform, Lille). qPCR quantification and QuBit control of the pool was done before cBot clusterization. Minimal number of reads per sample was 114 × 10 6. RNA-Seq reads were aligned to hg19 reference genome using Tophat v2. 0. 12 47. Cufflinks v2. 2. 1 was used to assemble transcripts and derive as Fragments Per Kilobase of exon model per Million mapped reads (FPKM) values with the ucsc hg19 transcriptome as a reference  48, 49.
Expression data among time points were normalised by the geometric mean of several stable transcripts: RPLP0 (NM_001002), PGK1 (NM_000291) and TRAP1 (NM_016292) (Fig. S8 ). FPKM normalisation, decay model assessment and calculation of mRNA half-lives were conducted according to the protocol described in Imamachi et al. 50. Statistical analyses throughout this study were performed with statistical program R 51. To identify the Gene Ontology (GO) terms enriched in our mRNA data set we used the GSEA computational method  50  and two reference gene sets (Hallmark and GO cellular component) from the Molecular Signatures Data base (MSigDB)  52. For the UPR category, GSEA analysis was also performed using AmiGO, an official web-based open-source tool for querying, browsing, and visualising the Gene Ontology and annotations as described by Monoz-Torres  53, 54.
Statistical analyses For each kind of experiment (WB, qPCR and enzymatic complex activities) n = 3 biological replicates were carried unless otherwise mentionned in the text. All statistical analyses were performed with the GraphPad Prism software version 6. 05. Data are expressed as mean ± SEM unless otherwise mentionned. Data between 2 groups were compared using Student's t-test with Welch correction. Multiple data sets were compared by one-way ANOVA. Frequencies were compared using the Khi2 test. Differences were considered significant if p values ≤0. 05. *p < 0. 05, **p < 0. 01, ***p < 0. 001 and NS is non significant.
Acknowledgements We thank  Drs O. Pluquet ,  F. Zerimech ,  J. Kluza  for helpful discussions,  Ms M-P. Ducourouble  for laboratory management,  Rémi Le Borgne  ( ImagoSeine ) for cell monolayer sample preparation for TEM,  Nathalie Jouy  and  Véronique Dhennin  for facility access. High-resolution 3D-SIM was performed in the  ImagoSeine microscopy facility (Institut Jacques Monod, IJM, Paris ). Mass spectrometry analyses were carried out at the Proteomic facility of the  IJM (Paris). This work was supported by academic fundings from  Inserm ,  Université de Lille ,  CHU de Lille  and by the  Ligue Nationale contre le Cancer, comité de la Somme  (grant to PP) and comité du Nord (grant to IVS); by grants from  "Initiatives d'excellence" (Idex   ANR-11-IDEX-0005-02 ) - Labex « Who Am I? »  ( ANR-11-LABX-0071 ) (to D.
D. ), the  Groupama Foundation -Research Prize for Rare Diseases  (to D. D. ), the  Human Frontier Science Program  ( RGP0038/2018 ), from  Contrat de Plan Etat Région  (CPER Cancer 2007-2013 (to I. v. S. )). The UMR CNRS 8199 platform, (Lille, France) which belongs to the ' Federation de Recherche' 3508 Labex EGID (European Genomics Institute for Diabetes ;  ANR-10-LABX-46 ) was supported by the  ANR   Equipex 2010 session  ( ANR-10-EQPX-07-01 ; ' LIGAN-PM ').
SARS-CoV-2 Isolation and Characterization in Vero E6 Cells and HAE The complete genome sequence of the isolated SARS-CoV-2 virus was deposited in the GISAID EpiCoVTM database under the reference BetaCoV/France/IDF0571/2020 (accession ID EPI_ISL_411218). Phylogenetic analysis confirmed that the isolated virus is representative of the currently circulating strains. 12 e characterized the replicative capacities of this viral strain in Vero E6 cells at different multiplicities of infection (MOIs) (Figure  1A ) using both classic infectious titer determination in cell culture (TCID50) and molecular semiquantitative methods, the latter based on ORF1b-nsp14-specific primers and probes designed by the School of Public Health at the University of Hong Kong. This double approach was facilitated by the appearance of a clearly observable characteristic cytopathic effect from 48 hpi (Figure  1B ) and enabled the validation of a large interval (range 1-8 log10(TCID50)) with high correlation (R 2  0.
These treatments are usually based on limited clinical or preclinical data. Remdesivir (GS-5734) is a prodrug of an adenosine nucleotide analog with demonstrated broad antiviral activity against several RNA viruses in different preclinical models. 24 Remdesivir has recently shown very promising results in animal models for the treatment of different coronaviruses, including MERS-CoV,  25  as well as one in vitro study against SARS-CoV-2. 26 Various clinical trials on the use of remdesivir for the treatment of patients with COVID-19 have already started in China and the United States. Diltiazem is a voltage-gated Ca 2+ channel antagonist commonly used as an antihypertensive for the control of angina pectoris and cardiac arrhythmia. 27 In a recent study, we repurposed diltiazem as an effective host-directed influenza inhibitor due to its thus far undescribed capacity of inducing the IFN antiviral response, particularly IFN-1b and type III IFNs (Figure  S2 ),  8  henceforth prompting an ongoing Phase IIb clinical trial to assess the efficacy of diltiazem-oseltamivir bitherapy in patients with severe influenza (FLUNEXT TRIAL PHRC #15-0442, NCT03212716).
Data and code availability The complete genome sequence of the isolated SARS-CoV-2 is available at the GISAID EpiCoVTM database under the reference BetaCoV/France/IDF0571/2020 (accession ID EPI_ISL_411218). Original data have been deposited to Mendeley Data: http://dx. doi. org/10. 17632/cxs7xwjpfj. 1. Source data for Figures  1  and 4  are available from the corresponding author upon request.
Virus The SARS-CoV-2 strain used in this study was isolated from a 47 y-o female patient enrolled in a French clinical cohort assessing patients with COVID-19 (NCT04262921). This study was conducted according to the declaration of Helsinki and received approval from local ethics commission. The viral strain was sequenced with Illumina MiSeq and deposited in the GISAID EpiCoVTM database under the reference BetaCoV/France/IDF0571/2020 (accession ID EPI_ISL_411218).
NanoString gene expression analysis After on-column mRNA extraction, gene expression levels were evaluated using two customized NanoString nCounter Gene Expression Panels: ''immune response'' (96 genes) and ''type III IFNs'' (12 genes). Data processing and normalization were performed with nSolver analysis software (version 4. 0, NanoString technologies) and results are expressed in fold change induction compared to the mock condition. Heatmap and Principal Component Analysis (PCA) were produced using Genomics Suite 7 (Partek, St Louis, MO, USA).
Transmission electron microscopy Infected nasal and bronchial HAE were fixed with 2% glutaraldehyde (EMS) in 0. 1 M sodium cacodylate (pH 7. 4) buffer at room temperature for 30 min. After washing three times in 0. 2 M sodium cacodylate buffer, cell cultures were post-fixed with 2% osmium tetroxide (EMS) at room temperature for 1 h and deshydrated in a graded series of ethanol at room temperature and embedded in Epon. After polymerization, ultrathin sections (100 nm) were cut on a UCT (Leica) ultramicrotome and collected on 200 mesh grids. Sections were stained with uranyl acetate and lead citrate before observations on a Jeol 1400JEM (Tokyo, Japan) transmission electron microscope, equipped with an Orius 600 camera and Digital Micrograph Software (Gatan).
ACKNOWLEDGMENTS The authors want to acknowledge  Denis Ressnikoff  and the  CIQLE team (UniversiteClaude Bernard Lyon 1)  for their technical assistance with electron microscopy image acquisition and analysis, as well as  Dr. Guy Boivin  for his critical reading of the manuscript. This study was funded by  INSERM REACTing (REsearch & ACtion emergING infectious diseases) ,  CNRS , and Merieux research grants. The sponsors had no role in study design, collection, analysis and interpretation of data, manuscript writing, or in the decision to submit the article for publication.
Secondary Data This empirical section aims to illustrate the implications of a convexification strategy using secondary data that were previously used by  Atkinson and Dorfman (2009)  to evaluate the performance of an unbalanced panel of Chilean hydroelectric power plants. These data are publicly available on the data repository of the Journal of Applied Econometrics. 6 This sample comprises monthly data on M = 3 inputs and N = 1 output for 21 Chilean hydroelectric power plants over the period from April 1986 to December 1997. There are 7 dam plants and 14 run-of-river (ROR) plants in this sample. The three inputs are labor (in thousands of workers), capital (in real pesos), and water (in cubic meters). The single output is electricity generated (in gigawatt hours). More details regarding these data is found in  Atkinson and Dorfman (2009)  and  Atkinson and Halabí (2005).
(f) Statistical uncertainties of the fit: these represent statistical uncertainties in the fit both from the experimental data and from the simulations. (g) Model uncertainties: described above. The total errors for each transition are given by the quadratic sum of errors (a)-(g). Care must be taken when taking an average or a difference of the transition frequencies. Here we assume that error (b), the wavemeter offset, introduces a common offset to all the data series. The other errors are assumed to be uncorrelated across the dataset. The resulting combined uncertainty for the transition frequencies of antihydrogen is 39 MHz or 16 ppb (Fig. 4 , average value). We expect that virtually all of the uncertainties can be considerably reduced in the near future owing to increased statistics and improved control of the systematics.
Acknowledgements This work was supported by: the  European Research Council  through  its Advanced Grant  programme (J. S. H. );  CNPq ,  FAPERJ ,  RENAFAE (Brazil) ;  NSERC, ALPHA-g/ CRUCS CFI ,  NRC/TRIUMF, EHPDS/EHDRS (Canada) ;  FNU (Nice Centre) ,  Carlsberg Foundation (Denmark) ;  ISF (Israel) ;  STFC ,  EPSRC , the  Royal Society  and the  Leverhulme Trust (UK) ;  DOE, NSF (USA) ; and  VR (Sweden). We are grateful for the efforts of the CERN AD team, without which these experiments could not have taken place. We thank  P. Djuricanin  ( University of British Columbia ) for extensive help with the laser system and calibrations. We thank  J. Tonoli  and the CERN staff, as well as  T. Mittertreiner  and the  UBC  staff, for extensive, time-critical help with machining and electrical works.
Zapałowicz's names of new taxa, published in each of the various forms of the Conspectus, meet the conditions of the International Code of Nomenclature (ICN) for valid and effective publication (Art. 29, 30 of ICN; Turland et al. 2018 ). Zapałowicz's new names also meet the conditions for valid publication (Art. 32 of ICN;  Turland et al. 2018 ); all are accompanied by Latin (rarely also French, exceptionally Polish) descriptions and/or diagnoses. Due to the multiple and mostly redundant instances of publication of Zapałowicz's work, however, there is chaos in the citations of the correct place of publication of his names in the taxonomic literature, including in  Stafleu and Cowan (1988) , authoritative online botanical nomenclature databases of taxon names and nomenclatural acts (International Plant Names Index (IPNI), Tropicos (Missouri Botanical Garden 2019)), as well as in the primary literature  (Mitka and Starmühler 2000; Optasyuk and Shevera 2011; Ziman et al.
Additionally, we reviewed the following library collections: Ernst Mayr Library of the Museum of Comparative Zoology at Harvard University, Smithsonian Libraries and the LuEsther T. Mertz Library of the New York Botanical Garden  (the Bulletin, Vols. 1904 -1909 , 1911 -1914 ; digital copies accessed via the Biodiversity Heritage Library (BHL, biodiversitylibrary. org), September 2019). We consulted additional libraries in several countries for the presence in their depositories of wrappers (i. e. temporary covers usually disposed of by the binders) of the fascicles of the Rozprawy from volumes 4B-14B. We follow journal abbreviations provided in the database BPH Online (Hunt Institute for Botanical Documentation 2019). If a title is given in two languages, the second title is preceded by a dash (-).
Updates to the International Plant Names Index (IPNI) database The IPNI database provides nomenclatural information (spelling, author, types and first place and date of publication) for the scientific names of vascular plants. However, not all information concerning Zapałowicz's names is accurate in its current version. Entries of Zapałowicz's names at species rank (including hybrids) in IPNI are corrected here and the hope is expressed that the current inventory may be useful for fixing them. A search of names in IPNI brought to light more than one hundred plant names for species and hybrids described by Zapałowicz (IPNI 2019) (for details, see Table  1 ). Amongst these records, we have identified 14 duplicate IPNI entries that are records of the same names with two different bibliographic citations.
They probably derived from more than one of the three original source databases (Index Kewensis, the Gray Card Index and the Australian Plant Names Index) that had been combined in the late 1990s to create IPNI  (Croft et al. 1999). It seems that the deduplication process conducted by the IPNI team in early 2016  (Nic Lughadha et al. 2016)  was not fully successful, especially in cases when we deal with multiple data sources for Zapałowicz's names. After our processing of the mentioned IPNI entries, we obtained 98 names at species rank (including hybrids). We have searched for their first place and date of publication. Two names, Rorippa × wimmeri Zapał. and Viola berdaui Zapał. , omitted in IPNI, are added by us. One name, Viola × roxolanica attributed to Zapałowicz, must be deleted. This taxon was described by Błocki (Deutsche Bot.
Monatsschr. 5: 147. 1887) at species rank, then Zapałowicz transferred it to a hybrid category. Therefore, it must be cited as Viola × roxolanica Błocki (pro sp. ). In total, we obtained 99 names at species rank (including hybrids), attributed to Zapałowicz, including one combination (Rumex carpaticus (Zapał. ) Zapał. ). Most of these names, 94 out of 99, are attributed to the Conspectus. Corrections are here provided for more than 60% of the respective IPNI entries. We have checked their name spelling (four corrections), authorships (three corrections), associated bibliographical details (63 corrections) and journal names (or their abbreviations; for details, see Table  1 ). Table  1. The inventory of bibliographic data covering Zapałowicz's names of species and hybrids in the International Plant Names Index (IPNI) database.
Species and nothospecies names, authorship and place of their publications were corrected, where necessary, according to the rules of the Shenzen Code  (Turland & al. in Regnum Veg. 159. 2018). Major source corrections are indicated by the word "yes". The list of taxa names with associated basic bibliographical details was extracted on 10 July 2019 from the IPNI database. Duplicated names are marked for deletion. national de l'Académie des Sciences de Cracovie. Classe des Sciences  Mathématiques et Naturelles 1907 (4): 253-254 (in French and Latin). 10. Zapałowicz H (1907 [10 Aug. 1907] ) Krytyczny przegląd roślinności Galicyi. Część X. -Revue critique de la flore de la Galiciae (X partie). Bulletin International de l'Académie des Sciences de Cracovie. Classe des Sciences  Mathématiques et Naturelles 1907 (6): 631-632 (in French and Latin).
Acknowledgements This study was financed from the statutory fund of the  W. Szafer Institute of Botany of the Polish Academy of Sciences. The research is a contribution to the ongoing catalogue of type specimens of vascular plants deposited in KRAM ( W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland ). Part of data was obtained from the  OZwRCIN  Project, co-realised by the Institute in the years 2018-2021, implemented by the Operational Programme Digital Poland for 2014-2020, co-financed by the  European Original Development Fund. Special thanks go to  Dr. Jeffery M. Saarela  ( Canadian Museum of Nature, Ottawa ) and an anonymous Reviewer for thorough and insightful remarks and suggestions on the manuscript. The authors are grateful to the staff of the  British Library  for checking and scanning for them the volume wrappers of the Rozprawy.
Research Data Compared to other countries, very little information is available on Mauritania and we had to combine different databases to get information. The secondary data for the first part of the study was obtained from the Survey of Household Living Conditions (EPCV 2014) implemented by the National Statistics Office (Office National de la Statistique, ONS) for 2014. The survey is the result of a partnership between the ONS, the Ministry of Economic Development, the World Bank, and Afristat. For consumer lending, we had data for 2014 with a sample of 9557 people indicating their access to credit and some demographic and geographical variables. The descriptive statistics are available in Table  A1. The second set of data that was used for financial inclusion came from the Global Financial Inclusion Database (Findex)  (Demirgüç-Kunt et al.
Case Description: Background to Financial System in Mauritania The Mauritanian financial system is composed of 14 commercial banks, two specialized financial institutions, 17 insurance companies, 112 registered MFIs, and more than 145 informal MFIs and government programs. Even though the development of the financial system for the past 15 years was impressive, it only covers 22. 9% of the population, according to the Global Financial Inclusion Database  (Demirgüç-Kunt et al. 2018). Data for 2014 from the ONS indicate that access to credit was only 6. 93% in urban areas and 1. 32% in rural areas, as shown in Figure  1. The figure also shows that some people may have a bank account but access to credit is denied. dummy coefficients, a unit difference in i x is the difference between membership category i x and membership in the omitted category.
Case Description: Background to Financial System in Mauritania The Mauritanian financial system is composed of 14 commercial banks, two specialized financial institutions, 17 insurance companies, 112 registered MFIs, and more than 145 informal MFIs and government programs. Even though the development of the financial system for the past 15 years was impressive, it only covers 22. 9% of the population, according to the Global Financial Inclusion Database  (Demirgüç-Kunt et al. 2018). Data for 2014 from the ONS indicate that access to credit was only 6. 93% in urban areas and 1. 32% in rural areas, as shown in Figure  1. The figure also shows that some people may have a bank account but access to credit is denied. Commercial banks in Mauritania are largely absent from small cities and towns inside the country.
Access to Credit in Mauritania As stated earlier, we have data for 2014 with a sample of 9557 people indicating their access to credit and some demographic and geographical variables. An analysis of the odds of accessing credit provided the results shown in Table  1. The results in columns (2), (4), and (6) show that some common factors and some different factors explain the access to credit in urban and rural environments. We tested for multicollinearity, as shown in Table  A2. In Mauritania there is no significant difference between men and women for the odds of accessing credit nor is there any difference by being the head of the household. Therefore, Hypothesis 1 is not accepted since gender is not significant. It is often considered that microfinance is for the excluded and we should have expected that unemployed people, those on welfare, or inactive people would have higher odds of getting credit.