dataesr/scientific-paragraphs-categorization huggingface dataset:
Real-time quantitative PCR Total RNA (1 lg) was used as a template for cDNA synthesis, using the GoScript TM reverse transcription kit (Promega, Madison, WI, USA). The GoTaq â qPCR 2X Master Mix (Promega, Madison, WI, USA) that include all components for quantitative PCR, except sample DNA, primers and water, was used to quantify the sixteen MYC-high signature markers. Primer lists for each transcript are available in Appendix Table  S2. Reaction conditions were denaturation at 95°C for 2 min; 40 cycles of 15 s at 95°C, 45 s at 60°C. Reactions were carried out using the AriaMx real-time PCR system and analyzed using the AriaMx software v1. 1 (Agilent Technologies, Santa Clara, CA, USA).
23, 24 X-ray diffraction data collected on beamlines I04 and I03 of the Diamond Light Source (Oxfordshire, UK) were processed using XDS  46  and Aimless. 47 tructures were determined via rigid-body refinement of model generated from PDB ID 4BDZ by removing small molecule atoms, and the compounds were fitted into resulting F o -F c difference maps. The models were built in Coot,  48  refined in Phenix,  49  and validated using MolProbity. 50 Relevant data collection and refinement statistics are given in Table  5.
10. 1021/acs. jmedchem. 7b00596. Overlays of the PFV crystal structures of several bound INSTIs highlighting the correspondence of features corresponding to the 4-position of the current compounds; predicted molPAINS values for final products (PDF) Molecular formula strings (CSV) Atomic coordinates and structure factors for PFV intasomebound 5′g, 5g, and 6p have been deposited in the RCSB Protein Data Bank (PDB codes 5MMA, 5NO1, and 5MMB, respectively). Phone: 301-846-5906. Fax: 301-846-6033. E-mail: burkete@ helix. nih. gov. We thank the staff of the Diamond Light Source beamlines I04 and I03 for assistance with X-ray data collection. Our studies are supported by the NIH Intramural Program, Center for Cancer Research (ZIA BC 007363, Z01 BC 007333), National Cancer Institute, and by grants from the NIH AIDS Intramural Targeted Program (IATAP).
■ ABBREVIATIONS USED HIV-1, human immunodeficiency virus type 1; PFV, prototype foamy virus; AIDS, acquired immune deficiency syndrome; FDA, Food and Drug Administration; IN, integrase; RAL, raltegravir; EVG, elvitegravir; DTG, dolutegravir; 3-P, 3processing; ST, strand transfer; INSTIs, integrase strand transfer inhibitors; DNA, DNA; IC 50 , half-maximum inhibitory concentration; EC 50 , half-maximal effective concentration; WT, wild-type; DMF, dimethylformamide; HPLC, high-pressure liquid chromatography; HRMS, high-resolution mass spectrometry; PBS, phosphate-buffered saline; RLUs, relative luciferase units Accession Codes ■ AUTHOR INFORMATION Corresponding Author ORCID Terrence R. Burke Jr. : 0000-0001-9925-8586 Notes The authors declare the following competing financial interest(s): Certain of the reported compounds are included in patent applications.
Phylogenetic analysis was conducted in MEGA6 software with the Neighbor-Joining method from a Kimura 2-parameter distance matrix. Genotype was determined by using reference sequence belonging to different HAV genotypes (GenBank accession numbers X75215, AB020567, AB020564 and AF357222 for IA; M14707 and M20273 for IB; AY644676 for IIA; AY644670 for IIB; AY644337 and AJ299464 for IIIA and D00924 for V).
HAV sequences analysis Nucleotide sequences were obtained for the 20 HAV RNA-positive cases of the acute hepatitis group (GenBank accession numbers KY172049 to KY172068). Estimates of genetic diversity were conducted on MEGA6 and included 395 positions. The genetic diversity of the 20 HAV sequences was low with a mean Kimura 2-parameter distance of 0. 005. Phylogenetic analysis identified 2 clusters and 5 unique sequences, all belonging to genotype IA (Fig  1 ). A first cluster of 10 sequences included most sequences from Gabès (10/13), isolated both in autumn 2014 and autumn 2015. A second cluster of five sequences included all the sequences from Medenine. Unique strains were responsible for the remaining 3 cases from Gabès, diagnosed between January and May 2015, and for the 2 cases from Tataouine.
Additional, phylogenetic analyses conducted with previously published sequences from North and Central Tunisia  [12]  identified a specific clustering of Southern Tunisian sequences. However, within a common analyzable fragment of 274nt a strict homology was observed between published sequences and 2 unique strains from Gabès isolated from adults: HA62 (GenBank KY172065) with KP091382 isolated in 2013 in Monastir, and HA68 (GenBank KY172066) with KP091362 isolated in Tunis in 2012. The remaining 18 sequences also showed a high homology with sequences recovered in Tunis and Monastir in 2012-2013 (KP091378 and KP091359).
the name of the isolate (GenBank accession numbers KY172049 to KY172068). • cluster from Gabès, ◆ cluster from Medenine, Å unique strains https://doi. org/10. 1371/journal. pone. 0175887. g001 Indeed, water, sanitation and hygiene (WASH) are critical in the prevention and care for all of the 17 neglected tropical diseases, which include HAV, scheduled by the World Health Organization (WHO) for intensified control or elimination by 2020 (http://www. who. int/water_ sanitation_health/publications/wash-and-ntd-strategy/en/). Universal immunization programs in early childhood (1-2 years-old)) may also reduce dramatically the incidence of hepatitis A, particularly in areas that are transitioning to lower levels of transmission resulting in an increasing proportion of susceptible adolescents and adults, often in urban areas or higher socioeconomic classes.
Methods Patients This 5-year retrospective study included consecutive COPD patients who were following a home-based PR program. COPD diagnosis was confirmed in each patient before PR by persistent airflow limitation (post-bronchodilator forced expiratory volume in 1 second [FEV 1 ]/forced vital capacity [FVC] ,0. 70). 4 COPD patients were excluded if they had mild airflow limitation (post-bronchodilator FEV 1 $80% predicted), dementia or poorly controlled psychiatric illness, neurological sequelae, or bone and joint diseases preventing physical activity. Patients were classified into LTOT, NIV, CPAP, or no equipment (NE) groups according to their medical equipment. The observational research protocol evaluation committee of the French Language Society of Pulmonology (CEPRO 2011-036) approved the analysis of the data collected from these patients, and written informed consent was obtained from each participant.
75) or the Huynh-Feldt procedure (epsilon correction factor $0. 75). When significant differences were obtained, a Bonferroni post hoc test was conducted. For categorical data about the number of responders, the frequencies were compared using Pearson's chi-square test. Statistical significance was set at p,0. 05, and all analyses were performed with the IBM Statistical Package for the Social Sciences (version 18. 0; IBM Corporation, Armonk, NY, USA).
Acknowledgments The authors would like to thank the rehabilitation team who managed the patients:  G Tywoniuk ,  S Duriez ,  F Urbain ,  V Wauquier , and  M Lambinet. The authors would also like to thank  Adair, France Oxygène, Homeperf, LVL Medical, Orkyn, Santélys, SOS Oxygène, Sysmed, VitalAire , and the  ARS Hauts-de-France  for their support of the home-based  PR program.
Colonies were circular, greyish and translucent with a diameter of 1-1. 5 mm. Strain Marseille-P3195 cells were Gram-positive cocci, ranging in diameter from 500 to 900 nm. The strain Marseille-P3195 does not exhibit oxidase activity but it is catalase positive. The complete 16S rRNA gene was sequenced using fD1-rP2 primers as previously described  [4]  and a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). The strain Marseille-P3195 exhibited a sequence similarity of 97. 9% with Peptoniphilus pacaensis strain KHD5 T (GenBank Accession number LN998072) and 96. 2% with Peptoniphilus coxii strain RMA 16757 (GenBank Accession number NR_117556), the closest species with a valid name (Fig. 1 ), which was first described by Citron et al. in 2012  [5]. Consequently, as the 16S rRNA gene sequence similarity is <98.
MALDI-TOF MS spectrum accession number. The MALDI-TOF MS spectrum of 'Peptoniphilus urinimassiliensis' strain Marseille-P3195 T is available online (http://www. mediterranee-infection. com/article. php?laref=256&titre=urmsdatabase). Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LT598577. Deposit in a culture collection. Strain Marseille-P3195 T was deposited in the Collection de Souches de l'Unité des Rickettsies (CSUR, WDCM 875) under number P3195.
EXPERIMENTAL SECTION 4. 1. Materials and Equipment. 1 H and  13  C NMR spectra were recorded with Bruker Avance DPX 300, Bruker Avance 400, or Bruker Avance 500 spectrometers. The NMR chemical shifts were reported as δ in parts per million (ppm) relative to the traces of nondeuterated solvent (e. g. , δ = 2. 50 ppm for d 6 -DMSO or δ = 7. 26 for CDCl 3 ). Data were reported as chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, m = multiplet, br = broad), coupling constants (J) given in Hertz (Hz), and integration. Fourier transform infrared-attenuated total reflection (FTIR-ATR) spectroscopy was performed with a ThermoFisher Nicolet 6700. Gel permeation chromatography (GPC-SEC) was performed using an Agilent Technologies PL-GPC 50 Integrated GPC system, with a Shodex KD-806 M column.
Red cells were washed four times in PBS by centrifugation at 2000 g for 10 min. The RBC solution was diluted in PBS to give a standardized absorbance value of 0. 6 at 412 nm when diluted 1:100. Dry hydrogels were cut into 5 mm 2 squares, weighted to ensure the same amount of material for all the samples, and placed in 1. 5 mL centrifuge tubes. 1. 5 mL of rRBC solution was added to each tube, and at each incubation time 200 μL of sample was collected. All samples were centrifuged 10 min at 2000 g and the supernatants were diluted 1:10 in PBS to measure the absorbance at 412 nm. As a positive control, using the same standard concentration, a 100% hemolysis rRBC solution was lysed in water. As a negative control, a rRBC solution was treated without the hydrogels. The data were normalized using the positive control as 100% hemolysis.
■ ACKNOWLEDGMENTS The authors thank the  European Commission  for its financial support through the projects of OrgBIO-ITN 607896 and SUSPOL-EJD 642671. The authors are also thankful for the technical and human support provided by  IZO-SGISGIker of UPV-EHU and European funding (ERDF and ESF) , and  Daniel Sańchez-de Alcaźar  for support with SEM images acquisition. This work was partially supported by  Ministerio de Economi ́a y Competitividad (MINECO)   BIO2016-77367  project (ALC) and the  Institute of Bioengineering and Nanotechnology (Biomedical Research Council, Agency for Science, Technology and Research, Singapore).
, 1999; Yu et al. , 1999) ]. Although relevant and useful tools, these methods only provide a partial picture of the structure, and are by nature unable to provide a full structural model. Previous studies have demonstrated that the use of the pair distribution function (PDF) analysis of highenergy X-ray scattering data is a very efficient way to determine the short-range order of highly disordered phases  (Billinge & Kanatzidis, 2004 ). In the case of C-S-H, this method has, up to now, only been qualitatively used for the study of C-S-H structure  (Skinner et al. , 2010; Soyer-Uzun et al. , 2012)  or carbonation mechanisms  (Morandeau & White, 2015). We performed a quantitative PDF analysis of high-energy X-ray scattering data to study the evolution of C-S-H structure as a function of its Ca/Si ratio.
Electron probe micro-analyser Electron probe micro-analyser (EPMA) analyses were performed using a Cameca SX50 electron microprobe (acceleration voltage of 15 kV, beam current of 12 nA) and a 1-2 mm beam width. Prior to analysis, a 10-20 nm-thick carbon layer was sputter-coated on the samples (Edwards Auto 306). Ca and Si were analysed simultaneously. Ca K and Si K were analysed using a pentaerythritol crystal and a thallium acid phthalate crystal, respectively. The standards used were albite (NaAlSi 3 O 8 ) for Si and wollastonite (CaSiO 3 ) for Ca. A ZAF data correction  (Merlet, 1994)  was applied to the raw data.
High-energy X-ray scattering Tobermorite and the first series of C-S-H samples (1 d ageing time) were measured in 1 mm polyimide capillaries at beamline ID15B at the ESRF (European Synchrotron Radiation Facility, Grenoble, France) using an energy of 87 keV ( = 0. 142 A ˚). Instrument calibration was done using a NIST-certified CeO 2 standard. A PerkinElmer flat panel detector was used to detect X-ray scattering. Data were automatically corrected for internal dark current and the signal from the empty capillary was subtracted as a background. Forty frames were collected for each sample, with acquisition time ranging between 5 and 12 s, adjusted to optimize the signal-to-noise ratio, and the obtained data were integrated and averaged in Fit2D  (Hammersley, 2016). The second series of samples (1 year ageing time) was measured at beamline CRISTAL at the SOLEIL synchrotron (French National Synchrotron Facility, Paris, France) using an energy of 28 keV ( = 0.
436 A ˚) and an XPad hybrid pixel detector. Data were collected in the 1. 2-124. 5 2 angular range with a total collection time of 30 min, owing to the fact that the detector had to record the data set step by step, and were processed with specific software  (Ounsy et al. , 2013). All diffraction data were Fourier transformed to PDF data using PDFgetX3 (Juhas et al. , 2013) and data simulation was performed either using PDFGui  (Farrow et al. , 2007) , for all C-S-H and tobermorite PDF data, with tobermorite  (Merlino et al. , 2001)  as a structure model, or using the Diffpy-CMI framework  (Gagne& Hawthorne, 2015) , for analysis of differential PDF data. The full structure model used for PDF data modelling is available in the supporting information. Reciprocal-space broadening and damping factors were, respectively, refined to Q broad = 0.
Acknowledgements SG acknowledges funding by the  French National Research Agency  ( ANR , grant  ANR-14-CE01-0006 ) and thanks  Dr Jacques Deparis  and  Julie Philibert  for fruitful discussions. SOLEIL data were acquired in the frame of proposal 20141260. ESRF data were acquired through an in-house research program on ID15. This article benefited from constructive comments and suggestions made by two anonymous reviewers.
Kinetics of photopolymerization were measured by following the disappearance of the C=C bond stretching vibration band at 1637 cm -1 and degree of conversion was calculated as: Conv(%) = (𝐴 1637 ) 0 -(𝐴 1637 ) t (𝐴 1637 ) 0 × 100 (1) where (A1637)0 and (A1637)t are, respectively, the areas of the 1637 cm -1 vibration band of the sample before exposure and at a given irradiation time t. Rate of polymerization Rp (in M s -1 ) was obtained from the Conv(%) vs time curve and the initial acrylate double bonds concentration in the formulation [DB]0: Rp = dConv(%) d𝑡 × [DB] 0 100 (2) Conversion data were smoothed (adjacent-averaging method -5 points) in order to avoid spikes in the Rp curve due to local fluctuations of the conversion values, especially at early times. Each experiment was repeated at least three times in order to ensure a good reproducibility and presented results are the average of these data.
Computational Methods Photopolymerization kinetics were modeled with Wolfram Mathematica 9 software. Rate constants were defined as functions of the fractional free volume f and differential equations were numerically solved with the NDSolve function. Time evolution of all the species were generated in form of interpolating functions evaluated each 0. 05 s. Conv(%) was directly calculated into the Mathematica notebook with Eq. 4 (where [DB] refers to the acrylate double bond concentration) and Rp values were calculated after export with Eq. 2.
Acknowledgements:  ANR  and  Mäder  are fully acknowledged for financial support of the  DeepCure  project # ANR-13-CHIN-0004-01. Received: Month XX, XXXX; Revised: Month XX, XXXX; Published online: ((For PPP, use " Accepted: Month XX, XXXX" instead of "Published online ")); DOI: 10. 1002/marc. ((insertnumber)) ((or ppap. , mabi. , macp. , mame. , mren. , mats. ))Keywords: photopolymerization, radical polymerization, kinetic modeling, initiation mechanism, photochemistry.
and are positive for pax2, cd44, cd133, ssea ¾, c-met, oct3/4, aldh and telomerase. HKCSCs form tumors in SCID mice and is vhl-proficient (data not shown). The cell lines described below were obtained from ATCC. Caki-1, human metastasis of clear-cell renal cell carcinoma to the skin, expresses wild-type vhl.
Soft agar colony formation assay Colony formation assay was performed on HKCSCs, 769-P and Caki-1per the STEMTag 96-well Stem Cell Colony Formation Assay (Cell Biolabs, Inc. , Cat. No. CBA-325). Each sample as well as control was prepared in triplicate. Pictures of colonies were taken on day 17 (data not shown) and day 30 under an inverted microscope. The medium was changed every 4-5 days. Cells were cultured in normoxia (pO 2 18. 75%) and hypoxia conditions (pO 2 1%, SANYO MCO-5 M incubator).
Protein isolation and mass spectrometry Mass spectrometry and western blot analysis were both performed on untreated and resistant groups of papillary RCC cells (rAN, N, rSH, H). Briefly, total protein was isolated using an RIPA buffer (Sigma-Aldrich, Cat. No. R0278) and a Protease Inhibitor Cocktail (Sigma-Aldrich, Cat. No. P8340). Protein pellet was obtained and densed after overnight incubation under acetone for mass spectrometry analysis. Three biological replicates were prepared for each analytical group. Protein extracts were trypsin digested overnight with 10 ng/µl trypsin, then reduced with 5 mM TCEP for 60 min at 60 °C; cystein thiol residues were blocked with 10 mM MMTS for 10 min at room temperature. Resulting peptide mixtures were analyzed with a LC-MS system composed of a nanoHPLC chromatograph (nanoAcquity, Waters), directly coupled to the ion source of the LTQ Orbitrap Velos working in MS mode (profile datasets, no data sequencing).
Tandem mass spectrometry for peptide sequencing was carried out separately for each group by the following procedure: peptide mixtures from all biological replicates were mixed into a single sample and measured in triplicate. To increase the proteome coverage, each of the three MS/MS measurements covered different m/z ranges: 300-600, 600-900 or 900-2000 Th. During further qualitative analysis, data from these three measurements were merged into one data file so that each analytical group was characterized by a single set of proteins. Statistical analysis concerning mass spectrometry was performed as described in the protein quantification section and described in more detail previously  [40].
Protein identification The acquired MS/MS data were pre-processed with Mascot Distiller software (v. 2. 5, Matrix Science), and a database search was performed using the Mascot Search Engine (Matrix Science, Mascot Server 2. 4. 1) against the SwissProt database (release 2015_01, 547,357 sequences; 194,874,700 residues) restricted to human proteins (20,274 sequences). To reduce mass errors, the peptide and fragment mass tolerance settings were established separately for individual LC-MS/MS runs after a measured mass recalibration. Other Mascot search settings were as follows: enzyme-semiTrypsin, missed cleavages-1; fixed modifications: Methylthio (C); and variable modifications: oxidation (M). A statistical assessment of peptide assignments was based on the concatenated target/decoy database search strategy (merged target/decoy databases generated with software developed in-house  [40] ).
This procedure (Supplementary Method 2) provided q-value estimates for each peptide spectrum match (PSM) in the dataset. All PSMs with q-values > 0. 01 were removed from further analysis. A protein was regarded as confidently identified when at least two peptides of this protein were found. Proteins identified by a subset of peptides from another protein were excluded from analysis. Proteins that exactly matched the same set of peptides were combined into a single group (cluster). The mass calibration and data filtering described above were carried out with Mscan  [41]  software, developed in-house. Peptide/protein identifications derived from all analytical groups were exported and used in further quantitative analysis.
Protein quantification Label-free quantification was performed essentially as described in  [40]  using 2D heat-maps generated from LC-MS profile datasets and the list of protein/peptide identification. The abundance of each peptide was determined as the height of a 2D fit to the monoisotopic peak of the isotopic envelope. Quantitative values were next exported into text files, along with peptide/protein identifications into pairwise statistical analysis using Diffprot software  [40]. A non-parametric resampling-based test statistics with local variance estimate makes Diffprot an appropriate tool for analysis of small scale biological experiments. Diffprot was run with the following parameters: number of random peptide sets = 106; clustering of peptide sets with 80% similarity or higher; and normalization by LOWESS.
No. 162-0094); protein transfer and loading was confirmed by Ponceau S staining (Sigma, Cat. No. 09189). After washing, membrane was blocked with Nonfat Powdered Milk (Amresco, Cat. No. M203) and then probed with primary antibodies: anti-eif4b (D-4) (Santa-Cruz Biotechnology, Inc. , Cat. No. sc-376062), anti-map2k1 (Sigma-Aldrich, Cat. No. HPA026430). Detection was performed after incubation with secondary antibodies: goat anti-rabbit IgG-HRP (Cell Signalling Technology, Cat. No. 7074) or goat anti-mouse IgG-HRP (Santa Cruz, Cat. No. sc-7023), according to recommendations from the manufacturer using chemiluminescent horseradish peroxydase substrate Luminol (SantaCruz Cat. No. sc-2018) using X-ray films. Prism Ultra Protein Ladder (10-245 kDa) (Abcam, Cat. No. ab116027) was used for protein size estimation.
Single strand complementary DNA (cDNA) generated in rtPCR was used as a template for amplification by sqPCR. Real-time PCR was performed either with PowerUp SYBR Green Master Mix or TaqMan Gene Expression Master Mix (both Applied Biosystems) in 7500 Real-Time PCR System (Applied Biosystems) in 96 well plates. Tested genes included: flt1 (vegf-1, forward CCTGCAGAGCCAG-GAATGTAT, reverse GTTGCAGTGCTCACCTCTGA), b-raf (forward AAAACACCCATCCAGGCAGG, reverse ACTCTCCTGAACTCTCTCACTCA) and c-kit (Hs00174029_m1 TaqMan probes). For the confirmation of no contamination with gDNA, minus-RT controls were performed for each sample. Data were calculated with the 2(-Delta C(T)) method, with normalization to mean expression of peptidylprolyl isomerase A (PPIA) as a housekeeping gene (sequences for SYBRGreen assay: forward CGTGGTATAAAAGGGGCGG, reverse, TGTCTGCAAACAGCTCAAAGG, assay Hs01565699_ g1 for TaqMan probes).
Statistical analysis For Alamar blue statistical measurements, ANOVA test was used (all results from all 4 doses from day 1 were compared with all results from all 4 doses from day 6 of the experiment). Statistically significant results are marked with * when P < 0. 001. For mass spectrometry protein quantification, Diffprot software  [40]  was used as described in "Protein quantification" section. For Muse ™ flow cytometry analysis, ANOVA test was used (statistically significant results are marked with * when P < 0. 001 and ** when P < 0. 05). Error bars on all figures are presented as mean ± SD.