dataesr/scientific-paragraphs-categorization huggingface dataset:
Occurrence of AKI was associated with both shortand long-term risk of mortality in different settings  (1). Furthermore, there was increasing evidence that AKI is associated with a risk of cardiovascular events  (3, 20). Recently, Go et al. (21)  explored the association between AKI and the risk of cardiovascular events during the year following hospital discharge. Using a large database with propensity score matching, they observed that AKI was a risk factor for heart failure during the year following discharge. Such cardiovascular consequences of AKI may be causal (at least partially) in the poor outcomes of the injury. In this study, we explored the association between AKI and circulating expression of Gal-3 and cardiac injury in critically ill patients. We observed that patients who presented with AKI during ICU stay and survived had higher plasma Gal-3 levels at discharge, along with high plasma levels of biomarkers of cardiac injury and failure.
We examined a large and unique data set of feather traits from known-age individuals of the short-lived, long-distance migratory Sand Martin (Riparia riparia). Intense sampling over 17 consecutive years has captured many known age individuals repeatedly so our data enables both longitudinal (e. g. , the same individuals producing different feathers as they grow older) and cross-sectional (e. g. , younger vs older individuals) investigation into the role of plasticity and natural selection on feather morphology. We hypothesise that improved feather quality, measured as feather size, mass, rachis width and bending stiffness all enhance survivorship. We therefore predict that older birds will have better quality feathers  [13]  compared to their younger counterparts, or even the same individuals when younger, resulting in differences in feather quality when comparing analyses of longitudinal and cross-sectional data.
Field data and feather collection Birds were captured at breeding colonies in mist nets along the Tisza River  [38]. A total of 129,179 individuals were captured by TSz and teams between 1995 and 2011, of which 12,225 were subsequently recaptured. Field teams plucked the second outermost tail feather (T5) from both sides of selected adult individuals that had moulted in Africa, and for which age and nest were known. Our resultant sample comprises 12,260 pairs of feathers harvested between 1995 and 2011, and includes those collected in consecutive years from the same individuals. The analyses presented here are therefore based on the subset of feathers from 148 birds that met the following criteria. The birds were of known age (i. e. , first ringed as nestlings or juveniles), and with tail feathers that were collected in two different years between 1995 and 2011.
Feathers from 31 additional individuals aged between four and seven, or older, were also considered, even though specimens from previous years were unavailable (179 birds in total). Sex and biometric data (i. e. , wing length, tail length, body mass, keel, and tarsus length) were also measured. The return rate of individuals whose feathers had been removed was compared with a control group that was captured simultaneously, but that did not have their feathers removed. Feather sampling had no significant effect on return rate between 1995 and 2011 in either sex; the return rate of males was 10. 5% (244/2,329) and 9. 7% (491/5,070) in sampled and control birds, respectively (χ 2 = 1. 119, df = 1, P = 0. 296), while in females the return rate was 9. 0% (215/2,385), and 8. 7% (627/7,202) (χ 2 = 0.
01 days (SD = 20. 213, n = 151), compared to worn, 83. 65 days (SD = 15. 236, n = 176). The mean difference between these data is 12. 63 days (SE = 2. 006, t = -6. 298, df = 275. 731, P < 0. 001). Rachis width, the distance between the outside edges of the dorsoventral walls, was measured to the nearest 0. 01 mm across the umbilicus superior (i. e. , at the base of the feather vane) using digital Vernier callipers (Powerfix Z11155). Growth bar widths were measured from digital photos taken with a Canon 7D camera in a dark room with shallow angle lighting  [41] ; we measured the width and position of all visible growth bars from the base of the vane to the feather tip  [22]  using ImageJ  [40]. The width of a growth bar is the distance between the proximal edges of two adjacent dark bands. Results from a random subset of our complete data show that measurements of feather length, mass, and rachis width are highly repeatable  [42]  (i.
Thus, using all visible individual growth bars, we calculated mean GBW for each feather. Repeatability of this measure was significant (R = 0. 645, SE = 0. 094, F 39,40 = 4. 815, P < 0. 001) for a randomly selected subset of feathers. We measured the dorsoventral bending stiffness of feathers using a Zwick 005 testing machine  [6, 43]. In total, 327 feathers were cantilevered 1 cm from the base (calamus) and loaded at 2 mm/min, 38 mm from the rachis base (two-thirds mean sampled feather length) until 6 mm displacement  [43]. In total, ca. 3,900 data points were recorded for each feather, which allowed us to estimate bending stiffness as the slope from the initial, linear phase of a load-displacement curve. These bending stiffness measurements were highly repeatable and significant (R = 0. 993, SE = 0.
Acknowledgments We are grateful for field work assistance from  Zs. Nagy ,  Z. D. Szabo, B. Habarics ,  D. Icso ,  A. Pelenczei , as well as numerous volunteers from  MME/BirdLife Hungary  and students of the University of Nyı ´regyhaza. We also thank  E. Molnar  for laboratory assistance and the  Nyı ´regyhazi Local Chapter of MME/BirdLife Hungary  for providing infrastructure and resources for field and laboratory studies. This manuscript benefitted from the valuable comments and much appreciated comments of three anonymous reviewers; we thank them for their contribution and support.
Study design and data collection procedure This was a qualitative exploratory study. A semi-structured interview guide created by the first author (Athanase Millogo) was used to conduct one-on-one in-depth interviews with each study participant. The interview guide consisted of five major topics that were used to initiate the discussions and probing was used to explore the issues further. The interviews were designed to assess general perception of epilepsy, cultural beliefs and practices toward epilepsy and PWE, and knowledge about the link between human epilepsy and porcine cysticercosis. All interviews were conducted by one of the coauthors (Alida Da). The guide was pilot tested in a different village before its use. All interviews were recorded using a voice recorder. The interviews were tape-recorded in local languages (Moore or Lyele) depending on the setting and lasted from 20 to 40 min.
Data analysis The tape-recorded interview scripts were transcribed in Microsoft Word and translated from the local languages into French and English and back translated in Moore or Lyele to insure the accuracy of the translations. The translations were made by interpreter using Moore or Lyele as native language and able to translate from French to Moore or Lyele. Data were analyzed by three independent analysts (Alida Da, Athanase Millogo, Helena A. Ngowi) using N-VIVO version 1. 1, note-based analysis, and MAXQDA, respectively. The reason for having three independent analysts was for triangulation to verify the conclusions reached. Data were coded by assigning same codes in passages or quotations with similar concepts. The codes were then quantified to identify thematic ideas for each aspect investigated.
Acknowledgments We would like to express our gratitude to  Chantal Millogo  for collecting the data and  Léopold Bado  for the translation and back translation from French to Lyele. Special thanks to  Dr. L. Raphaël Nébié  and  Elie Sawadogo  and to all the members of the three villages for their warm welcome and their active participation to the study. This study was funded by the  National Institute for Neurological Disorders and Stroke (NINDS)  and the  Fogarty International Center (FIC)  of the  US National Institutes of Health (Epidemiology and Burden of Neurocysticercosis in Burkina Faso)  ( R21 NS055353 ) as part of the Brain Disorders in the Developing World:  Research Across the Life Span (BRAIN) grant program. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Calcium flux assessment in Tregs and ECs by time-lapse videomicroscopy Adherent ECs were labeled with Fura-2 calcium indicator (Thermo Fisher Scientific) at 7. 5 mM in Hanks balanced salt solution medium containing calcium (Thermo Fisher) for 1 hour at RT. Cells were seeded in m-slide 8-well (ibidi, #80826; Martinsried, Germany) plate in Hanks balanced salt solution supplemented with 1% FCS, and measurements of fura-2 fluorescence at 340 and 380 nm were obtained using a widefield Leica DMI 6000B microscope (Micro-PICell core facilities, SFR Institut de Recherche en Sant é, Nantes, France) for 15 minutes. Calcium flux was quantified by the ratio 340 nm (free calcium)/380 nm (bound calcium) intensity in all individual cells tracked over time by Icy Software (created by the Quantitative Image Analysis Unit at Institut Pasteur, Paris, France).
Acknowledgments The authors thank  Megan Levings  for providing the CAR constructs and critical reading of the manuscript. The authors thank  Steven Nedellec  and  Philippe Hulin  and the microscopic facility  MicroPICell SFR Bonamy in Nantes  for their technical expertise and assistance in cell imaging experiments. The authors thank  P. Gu  érif,  I. Guihard , and  A. Fleury  from the  CHU of Nantes  for their help. This work was partially funded by  Labex "Immunotherapy, Graft, Oncology" (IGO)  project (no. ANR-11-LABX-0016-01 ) and TxCell S. A. This work was realized in the context of the  Institut Hospitalo-Universitaire (IHU)- Cesti  project ( ANR-10-IBHU-005 ). Labex IGO and  IHU-Cesti projects are part of the "Investissements d'Avenir" French Government program  managed by the  ANR.
Microarray Analysis Transcriptome analysis was carried out on the Affymetrix HGU133plus 2. 0 platform (Affymetrix, Santa Clara, CA, United States) in biological replicates as described before  (Pichler et al. , 2008; Kress et al. , 2010). Briefly, the transcriptome of Taxexpressing Tesi cells was compared to that of Tesi/Tet cells, where Tax expression was repressed. Further, the HTLV-1 in vitrotransformed cell line (MT-2) was compared to postmitotic CD4 + T lymphocytes. The microarray data have been deposited in NCBI's Gene Expression Omnibus  (Edgar et al. , 2002)  and are accessible at www. ncbi. nlm. nih. gov/geo and GEO Series accession numbers are GSE10508 and GSE17718. Quantitative Real-Time RT-PCR (qPCR) and RT-PCR Total cellular RNA from transfected cells or untransfected cell lines was isolated (NucleoSpin R RNA, Macherey Nagel, Düren, Germany) and reversely transcribed to cDNA by applying random hexamer primers and Superscript TM II Reverse Transcriptase (both Thermo Fisher Scientific, Waltham, MA, United States) according to the manufacturers' instructions.
Every experiment was independently performed at least three times and relative copy numbers (rcn) were calculated by normalization of respective transcript levels on those of β-actin. Total RNA from HTLV-1-infected patients and uninfected controls was prepared from whole cells using Trizol (Invitrogen, Thermo Fisher Scientific) as previously described  (Terol et al. , 2017). After reverse transcription (RT) using 5x All-In-One RT MasterMix (ABM, Vancouver, BC, Canada), the abundance of transcripts was assessed by qPCR analysis using the SYBR green PCR master mix (Roche Diagnostics) and gene-specific primer sets. Data were analyzed using LightCycler R 480 Software (Roche Diagnostics). Primers for COL4A1 (qHsaCID0010223) and COL4A2 (qHsaCED0044576) and the housekeeping gene HPRT-1 (qHsaCID0016375) were from BioRad (Hercules, CA, United States).
Cells were washed three times and incubated with secondary antibodies antimouse Alexa Fluor R 488 and anti-rabbit Alexa Fluor R 647 (both Life Technologies GmbH) in blocking solution (45 min, 37 • C) one after the other with three washing steps in between. Finally, samples were covered with ProLong TM Gold Antifade Mountant with DAPI (Life Technologies GmbH) according to the manufacturer's instructions. Images were acquired using a Leica TCS SP5 confocal laser scanning microscope equipped with a 63 × 1. 4 HCX PL APO CS oil immersion objective lens (Leica Microsystems GmbH, Wetzlar, Germany). Images were analyzed using LAS AF software (Leica) and Adobe Photoshop CS5 (Adobe Systems, San Jose, CA, United States).
" Mounting of cells was performed with ProLong TM Gold Antifade Mountant without DAPI (Life Technologies GmbH). After acquisition (see Detection of COL4 Protein Expression), images were analyzed and signal intensities were quantified using LAS AF software (Leica) and Adobe Photoshop CS5 (Adobe Systems). For quantitative evaluation, manual counting of cells was performed, analyzing in total 1524 cells of 83 optical fields. Transfer of Gag and/or COL4 protein from MS-9 donor cells to Jurkat acceptor cells was determined and normalized on the number of Gag or COL4 positive MS-9 cells and on the ratio of Jurkat acceptor to MS-9 donor cells.
ACKNOWLEDGMENTS We are grateful to  Raymond Césaire  ( CHU of Martinique ) and  Gildas Belrose (CeRBiM)  for kindly providing us with HAM/TSP patient samples. We are grateful to  Jens Albrecht  and  Brigitte Biesinger [Institute of Clinical and Molecular Virology, Universitätsklinikum Erlangen (UKER) ,  FAU ,  Erlangen, Germany ] for providing Herpesvirus saimiri-transformed T-cell lines and reagents. We thank  Frank Neipel  ( Institute of Clinical and Molecular Virology, UKER, FAU ) for providing transformed B-cell lines,  Ruth McPherson  ( University of Ottawa, Canada ) for providing COL4A1-/COL4A2-reporter vectors, and  Donna M. D'Agostino  ( University of Padua, Italy ) for providing a Rex-GFP expression vector. We are grateful to  Erwin Strasser  for providing lymphocyte cones ( Transfusion Medicine  and  Haemostaseology Department , UKER).
FUNDING This work was funded by  Deutsche Forschungsgemeinschaft (DFG)  (project  TH2166/1-1 ) and by the  ELAN-Fonds at the University Hospital of the Friedrich-Alexander-Universität Erlangen-Nuremberg. AT-K was further supported by the Exploration Grant of the  Boehringer Ingelheim Foundation (BIS). AT-K and J-MP were supported by the  BFHZ (Bayerisch-Französisches Hochschulzentrum ).
DATA AVAILABILITY STATEMENT The microarray data have been deposited in NCBI's Gene Expression Omnibus  (Edgar et al. , 2002)  and are accessible at http://www. ncbi. nlm. nih. gov/geo and GEO Series accession numbers are GSE10508 and GSE17718 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE10508; https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE17718).
In vitro integration assay with recombinant integrases Recombinant purified IN (200 nM final concentration) was incubated with radiolabelled vDNA containing U5 viral ends (10 nM) and 50 ng of pBSK-derived p481 acceptor plasmid DNA. The reaction was initiated by the addition of a reaction buffer (final concentration: 17% DMSO; 6 mM DTT; 11 mM MgCl 2 ; 22 M ZnCl 2 ; 8% PEG; 100 mM NaCl) for 2 hours at 37 • C. After the reaction, the resultant integration products were deproteinized by proteinase K treatment (Promega) and phenol/chloroform/isoamyl alcohol (25/24/1 v/v/v) extraction before loading onto a 1% agarose gel. Nucleic acids were fixed with 5% TCA solution, and the gel was then dried and imaged by autoradiography with a PharosFX. The bands corresponding to free substrate (S), donor/donor, linear two-end full site integration products (FSI) and circular one-end half site integration products (HSI) + FSI products were quantified using Quantity One software.
Processing assay Processing assays were performed using the same conditions used for the integration assay, except that the concentration of IN was 400 nM and a short 21 bp DNA was used as the substrate (20 nM). The reaction was stopped by the addition of 90 l of a buffer containing 750 mM urea, 4. 5 mM EDTA, 0. 75× TE, 300 mM AcNa and 0. 45 mg/l glycogen. The products were then extracted by phenol/chloroform and precipitated with ethanol overnight before loading on a 12% polyacrylamide denaturing gel. An image of the gel was obtained by autoradiography with a PharosFX, and the bands corresponding to the processed 19 bp DNA were quantified using Quantity One software.
Solubility assay The assay was performed as previously described  (20). Recombinant IN (3 M) was incubated with either LEDGF/P75 or the H4 histone tail for 30 min at room temperature in a buffer containing 20 mM HEPES pH 7. 5, 10% glycerol, 5 mM DTT, 1 mM EDTA and 100 mM NaCl. After centrifugation at 15 000 g for 15 min, the soluble protein in the supernatant and the insoluble protein in the pellet were separated and analysed by SDS-PAGE. The amount of soluble IN was then quantified using ImageJ software.
NMR analysis A sample containing the uniformly 15 N/ 13 C-labelled carboxy-terminal domain (CTD) of the integrase in 25 mM HEPES buffer, 150 mM NaCl, 5 mM DTT and 10% D2O was introduced into a 3 mm NMR tube at the concentration of 280 M in a final volume of 200 l. In order to achieve sequential assignment the following experiments were performed: 1 H- 15 N HSQC (  21 ), 1 H- 13 C HSQC  (21) , HNCA  (22, 23) , HNCO  (22, 23) , HNCACB  (22, 23)  and CB-CACONH  (24, 25). All NMR experiments were carried out at 303 K on an Avance III Bruker spectrometer operating at 600. 13 MHz in proton mode, equipped with a cryogenic probe. The acquisition and processing of the experiments were performed using the Bruker software Topspin (version 3. 5 Bruker, Karlsruhe, Germany). The spectral analysis and assignment were performed with CCPNMR 2.
To specifically analyze the effect of the H4 tail on the FSI events, circular products were cloned and sequenced. The results showed an increased proportion of FSI integration prod-ucts containing the correct 5 bp duplications (Figure  4D  and E ). These data suggest that the H4 peptide exerts its stimulatory effect preferentially on the tDNA capture or strand transfer steps. To confirm this finding, we next tested the peptide on fully assembled retroviral intasomes. Lentiviral MVV intasomes were tested in concerted integration assay since their assembly was previously fully described  (18, 19). As shown in Figure  5 , integration catalysed by the purified MVV intasome was also stimulated by the H4 peptide. To confirm the specificity of this stimulation, PFV intasomes were also tested, and no effect of the H4 tail was detected.
ACKNOWLEDGEMENTS The manuscript was edited by  NPG Language Gold Editing FUNDING French National Research Agency against AIDS (ANRS)  [ AO 2016-2 ,  ECTZ18624]; SIDACTION [AO-27-1 10465 ,  16-1-AEQ-10465 ];  French Infrastructure for Integrated Structural Biology (FRISBI)  [ ANR-10-INSB-05-01 ]; Instruct, a part of the  European Strategy Forum on Research Infrastructures (ESFRI) ;  Centre National de la Recherche Scientifique (CNRS) ; the University Victor Segalen Bordeaux 2;  ECOS-CONICYT C12B03 program. Funding for open access charge:  ANRS [AO 2016-2 ].
ClusterQuant 3D analysis indicates single-color cDC clustering in Clec9a Confetti mice To quantify flurophore-based clustering of cDCs in SI and lung, we developed a 3D version of the ClusterQuant software previously used for analysis of cell clusters in single tissue planes  (33). Briefly (Fig. 3A ), the workflow involves different steps: (1) separation of 3D confocal images into individual z planes, corresponding to the optical slices used for image acquisition, (2) manual segmentation and annotation of cDCs in each plane, and (3) computation of 3D Voronoi polyhedrons using the x, y and z-cell coordinates. Each polyhedron contains all voxels closer to the centroid of that Confetti + cell than to the centroids of all other cells and is used to compute neighbor and proximity relationships in subsequent analysis steps (Fig.
These results suggested that high demand for cDCs induced by infection is met by rapid mobilization of cDC progenitors from the BM. Consistent with that notion, there was a clear increase in total number of pre-cDCs circulating in peripheral blood of mice at 7 days postinfection, when the increase in lung pre-cDCs and cDCs became apparent (Fig. 7F ), with no differences in pre-cDC1/pre-cDC2 commitment (Fig. S9E ). To extend these data to humans, we carried out an analysis of transcriptome datasets from peripheral blood of patients prior to or post infection with influenza A virus (35) using the CIBERSORT algorithm  (36). This revealed a marked increase in the blood frequency of DCs, annotated in CIBERSORT as "activated DCs" (Fig. 7G, H ), consistent with a demand-driven increase in DCpoiesis.
To assess whether pre-cDC numbers were also increased in human blood, as in mice, we assessed levels of transcripts for SEMA4D, a recently identified marker for cDC progenitors  (37). SEMA4D transcripts were increased post infection (Fig. 7I ). Although SEMA4D can also be expressed by T and B cells, T and B cell markers (CD3E or CD79A/B) were either unchanged or decreased in the same datasets following influenza virus infection (Fig. 7I ). Taken together, these data suggest that, in mice and, possibly, humans, influenza virus infection leads to local demand for cDCs that is met not by increased local clonal expansion of pre-cDC and their progeny but by communicating need to the BM, resulting in an efflux of pre-cDCs into blood and influx into lungs.
Flow cytometry Up to 4 million cells (see isolation protocol in Supplementary Methods) were pre-incubated with blocking anti-CD16/32 in FACS buffer for 10 min at 4°C and then stained for 20 min at 4°C with staining cocktail in FACS buffer in the presence of anti-CD16/32. DAPI was used to exclude dead cells, except for when cells were fixed. In the latter case, dead cells were excluded by live/dead fixable blue or aqua dye (Invitrogen). For Ki67, DNA content (FxCycle, Invitrogen) and phospho-H3 staining cells were fixed and permeabilised using Foxp3 Fix/Perm buffer set (eBioscience, 00-5523-00). For DNA content examination, samples were collected on a LSR Fortessa flow cytometer (BD Biosciences) or a SP6800 Spectral Analyzer (Sony) and analyzed using FlowJo 9 or 10 software (TreeStar Inc. ).
Tissue sections were stained as explained in Supplementary Methods. Antibodies used in microscopy are listed in table  S3. Sections were mounted on slides in the clearing solution Rapiclear 1. 47 (SunJin Lab) for image acquisition while lymph nodes were clarified instead using uDISCO  (46)  and mounted on a metallic glass-bottom dish. Images were acquired on a LSM880 inverted confocal microscope as explained in supplementary information. Images and Videos were generated after adjusting channels using Imaris software.
Acknowledgements This work was supported by  The Francis Crick Institute , which receives core funding from  Cancer Research UK  ( FC001136 ), the  UK Medical Research Council  ( FC001136 ), and the  Wellcome Trust  ( FC001136 ) and by  ERC Advanced Investigator Grants  ( AdG 268670  and  786674 ), as well as, in part, by the  Intramural Research Program  of  NIAID ,  NIH. M. C-C. and J. v. B. were supported by  Boehringer Ingelheim Fonds. BS is member of the  DFG funded Collaborative Research Center 914  (project  A11 ). We thank members of the  Immunobiology Laboratory  for.