dataesr/scientific-paragraphs-categorization huggingface dataset:
All peptide samples were analysed two separate times. All tandem mass (MS/MS) spectra were manually analysed utilizing Data Explorer software TM v4 (Applied Biosystems). Modification assignment was considered if a given spectrum contained peaks to confirm both the peptide's identity and modification. The modifications considered during spectra interpretation included n-butylamine transamidation of glutamine residues. In order to cross-validate our manual interpretation and minimize the occurrence of false positive results, the experimental data was also processed with the Protein Prospector software. This approach permitted the identification and assignment of a mass shift to a given amino acid residue. Cytotoxicity assay. Caco-2, a human colorectal adenocarcinoma cell line (Cell Line Services, AG, Eppelheim, Germany) was maintained in culture media consisting of Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (v/v) foetal bovine serum (FBS), 1 mmol/L L-glutamine and antibiotics (100 U/mL penicillin and 100 μ g/mL streptomycin) at 37 °C, 5% CO2/95% air environment and with controlled humidity (CO 2 incubator, Binder).
Acknowledgements We thank  Daniela P. Ferreira  for her valuable assistance in the isolation of gluten. We acknowledge  Ajinomoto Foods  ( Hamburg, Germany ) for kindly supplying the  ACTIVA ® WM. Miguel Ribeiro  has a PhD fellowship ( SFRH/BD/82334/2011 ) granted by the  Foundation for Science and Technology (FCT)  and  European Social Fund (ESF). We appreciate the financial support provided to the project  PTDC/QUI-QUI/100044/2008 , to the  Research Unit in Vila Real  ( PEst-OE/QUI/UI0616/2014 ), and to the  QOPNA Research Unit 62/94 (PEst-C/QUI/ UI0062/2013 ;  FCOMP-01-0124-FEDER-037296 ),  RNEM  ( REDE/1504/REM/2005  that concerns the  Portuguese Mass Spectrometry Network ) by  FCT  and  COMPETE.
Spot number Protein ID Accession number Gene name Mw (Da) Peptide sequence Start-End Peptide sequence P (pep) z mass (Da) Glutenin, high molecular weight subunit PW212 P08489 GLT4 89119. 8 K. GGSFYPGETTPPQQLQQR. I 82-99 1. 73E-09 2 1990. 9617 K. GGSFYPGETTPPQQLQ*QR. I 1. 54E-04 2 2048. 0322 1 Alpha/beta-gliadin P02863 GDA0 32942. 7 R. PSQQNPQAQGSVQPQQLPQFEEIR. N 233-256 2. 35E-08 3 2734. 3543 Alpha-amylase inhibitor 0. 19 P01085 IAA1 13328. 4 R. LQ*CNGSQVPEAVLR. D 26-39 2. 18E-06 2 1570. 8496 R. LQCNGSQ*VPEAVLR. D 3. 27E-05 2 1570. 8496 Alpha-amylase/trypsin inhibitor CM3 P17314 IAAC3 18209. 1 R. DYVLQQ*TCGTFTPGSK. L 45-60 4. 69E-06 2 1801. 8915 R. DYVLQ*QTCGTFTPGSK. L 7. 33E-04 Glutenin, high molecular weight subunit DY10 P10387 GLT0 69586. 7 K. GQQGYYPTSLQQPGQGQQGYYPTSLQHTGQR. Q 185-215 1.
e. human genome. Recently, AKR1B15 has been demonstrated to be a functional gene with low expression restricted to placenta, testes and adipose tissues. The AKR1B15 gene undergoes alternative splicing giving rise to two protein isoforms, designated as AKR1B15. 1 and AKR1B15. 2. The former is a 316-amino acid protein encoded by AKR1B15-201 mRNA (Ensembl database) and showing 92% amino acid sequence identity with AKR1B10, whereas AKR1B15. 2 (AKR1B15-001, Ensembl) has a longer N-terminus not homologous to other AKRs, and does not exhibit enzymatic activity or nucleotide binding  [16]. AKR1B15. 1 (henceforth referred to in this manuscript as AKR1B15 for brevity) is localized in the mitochondrial fraction and the recombinant protein was purified and characterized, showing limited in vitro activity with steroids and acetoacetyl-CoA  [16].
Fluorimetric and spectrophotometric assays NADPH binding was analyzed by quenching of Trp intrinsic fluorescence of 0. 5 μM protein, using a Cary Eclipse (Varian) fluorimeter, in 20 mM sodium phosphate, pH 7. 0, at 25°C in a final volume of 1 mL. The excitation wavelength was 290 nm and the emission wavelength was monitored at 340 nm. AKR1B10 was used as a control. The dissociation constant (K D ) values were calculated by nonlinear fitting of experimental data, using Grafit 5. 0 (Eritacus Software), to the Morrison equation: DF ¼ DF max Á ½E þ ½NADPH þ K D À ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi ð½E þ ½NADPH þ K D Þ 2 À 4 Á ½E Á ½NADPH q 2 Á ½E The activity towards aldehydes, with the exception of retinaldehydes, was analyzed spectrophotometrically following the decrease in the absorbance of the cofactor NADPH at 340 nm (ε 340 = 6,220 M -1 Ácm -1 ) or at 365 nm in the case of cinnamaldehyde (ε 365 = 3,510 M -1 Ácm -1 )  [24].
Determination of kinetic constants and inhibition screening All compounds tested as inhibitors were dissolved in DMSO and assayed in a final concentration of 0. 1% (v/v) DMSO using 6 mM D,L-glyceraldehyde as a substrate. Kinetic constant and IC 50 (compound concentration that inhibits enzymatic activity by 50%) values were calculated by fitting the initial rates to the appropriate equation using Grafit 5. 0 (Eritacus Software) and values were given as the mean ± standard error of three experiments. Standard error values were less than 20% of the mean values.
Homology model and conformational ensembles The structural model of apo-AKR1B15 was obtained from the AKR1B10 ternary complex crystallographic structure (PDB ID: 1ZUA), used as a template for homology modeling, by running the SCWRL program  [28]. Because of the high sequence identity (92%) between the two proteins, the approach that keeps invariant the conformation of the conserved residues was adopted. The flexibility features of both AKR1B10 and AKR1B15 were studied by means of computer simulations. The hydrogen atoms were added to the structural model of AKR1B15 as well as to the AKR1B10 crystal by the pdb2gmx tool of the GROMACS program package  [29]. The apo as well as holo forms of both structures were studied as follows: the all-atom models were energy minimized employing the Amber99sb-ildn force field  [30, 31]  for the protein, parameters of Holmberg et al.
AKR1B15 ternary complexes Geometries of the ternary complexes were derived from the homology model of holo-AKR1B15, which was built by superimposition of the apo form and holo-AKR1B10 (PDB ID: 1ZUA), including the cofactor coordinates into apo-AKR1B15. Considering that all-trans-retinaldehyde and 9-cis-retinaldehyde are substrates, the distance between the oxygen of retinaldehyde and the catalytic residues (i. e. His111 and Tyr49) should be less than 3 Å for productive catalysis to occur. Under this assumption, the substrates were manually docked into the active site of holo-AKR1B15. Inhibitors were automatically docked using AutoDock 4. 0  [38]. The inhibitor JF0064 coordinates were obtained from the PDB (PDB ID 4ICC). The target geometry was extracted from the energy minimized all-trans-retinaldehyde complex (see below).
(D) The inhibitor JF0064 (PDB ID 4ICC) bound to AKR1B15 is displayed as sticks with C atoms in magenta, while residues interacting with the inhibitor are shown as sticks with C atoms in grey. (E) Steric hindrance preventing tolrestat (in blue) and sorbinil (in orange) from binding to the active site of AKR1B15. For this analysis, the AKR1B15 structure model was superimposed with the AKR1B10 crystallographic structures with tolrestat (PDB ID 1ZUA) and sorbinil (PDB ID 4GA8). NADP + is colored in orange. Figures have been drawn using PyMOL. doi:10. 1371/journal. pone. 0134506. g006.
JGD, IC, XP, JF and SP received support from  Spanish Ministerio de Economía y Competitividad  [ BFU2011-24176 ] (http://www. mineco. gob. es) and  Generalitat de Catalunya  [2009 SGR 795] (http://www. gencat. cat/agaur). FXR, ACS and AP received support from  Centre National de la Récherche Scientifique  (http://www. cnrs. fr); Institut National de la Santé et de la Recherche Médicale  (http://www. inserm. fr); Université de Strasbourg (https://www. unistra. fr); Région Alsace  (http://www. region. alsace); Hôpital Civil de Strasbourg  (http:// www. chru-strasbourg. fr/Hopital-civi);lInstruct (part of the  European Strategy Forum of Research Infrastructures; ESFRI)  (https://www. structuralbiology. eu); and  French Infrastructure for Integrated Structural Biology (FRISBI)  [ ANR-10-INSB-05-01 ] (http://frisbi.
In vitro wound healing assay Infected MCF-7 breast cancer cells were seeded in 12-well cell culture plates at a density of 30 × 10 4 and 25 × 10 4 , respectively. Breast cancer confluent cell layers were serum starved for 16 h and then wounded by scratching with a sterile 100 μL pipette tip. Detached cells were removed by washing twice with PBS and fresh culture medium, in the absence of serum, was added, following 1 h incubation with the cytostatic agent cytarabine (10 μΜ) before the incubation periods with the agents. The wound closure was monitored at 0, 24 and 48 h using a digital camera connected to a microscope. Wound surface area was quantified by image analysis (ImageJ 1. 4. 3. 67 Launcher Symmetry Software).
Acknowledgments We wish to thank  Dr John Couchman  ( University of Copenhagen ),  Dr Stephane Brezillon  ( Université de Reims-Champagne-Ardenne ),  Drs Dimitris Kletsas  and  Harris Pratsinis  ( NCSR Demokritos ) and  Dr Dragana Nikitovic  ( University of Crete ) for technical assistance, suggestions and useful discussions during the course of this work. This research has been co-financed by the  European Union (European Social Fund -ESF ) and  Greek National Funds  through the  Operational Program "Education and Lifelong Learning " of the National Strategic Reference Framework (NSRF) Research Funding Program: Thales. Investing in knowledge society through the  European Social Fund. Estrogen receptor; EGFR; Epithelial to mesenchymal transition; Matrix metalloproteinases; uPA; tPA; Invasion; Migration.
Recognizing that reducing the resistance to flow could be a significant part of the overall energy needs of an obstructed patient during exercise,  17  to increase this ratio going from air to He/O 2 , with the exercise being the same, indicates that the change in gas mixture benefits the patient. 33 ata are reported as means with the 95% confidence interval. Statistical significance was set at P#0. 05. All data collected were tabulated descriptively by study disease and severity as well as by study disease only. On the per protocol data set, comparison of the measurements at rest and dur ing exercise while breathing each gas mixture, were made using the Dunnett's test following a parametric analysis of variance model.
Volumetric capnography Volumetric capnography was performed during exhalations from total lung capacity (TLC) using the FE141 differential pressure spirometer and the ML-206 gas analyser, both from AD Instruments (Oxford, UK). Signals were synchronized and digitized at a sampling frequency of 500 Hz using LabChart software v7. 3. 1 (AD Instruments). Patients were connected to the capnography apparatus through a non-resistive filter (PF30, Pall, Fribourg, Switzerland). Every five tidal breaths, patients were instructed to inhale to TLC, and to immediately exhale passively. Subjects were asked to maintain their expiratory flow at the level observed during tidal breathing by visual feedback of flow measurements. Expiratory volume and the expired fraction of CO 2 (FeCO 2 ) were exported to a spreadsheet and airway volume (VDaw) was calculated according to Fletcher's method for determination of anatomical dead space using equal area determination  [33].
Differences between subjects without and with BHR were determined by student's t-test for continuous variables and the Chi-square test for categorical variables. All statistical analyses were performed with Statview 5. 0 software (SAS institute, Cary, North Carolina, USA). A p-value <0. 05 was considered significant. Because multivariate analysis with 2 variables was scheduled, we aimed to recruit at least 20 patients with BHR. Because the expected prevalence of BHR is close to 25% among patients referred for provocation testing at our center, we thus planned to recruit at least 80 subjects. Original data are available as an Excel file in the online supplement (S1 Original Data).
Decreased airway volume and increased ventilation heterogeneity were independently associated with methacholine-induced changes in FEV 1 Post-methacholine capnography data were available for 78 subjects (n = 55 without BHR and n = 23 with BHR). To characterize relationships between variations in capnographic variables  Table  3  shows univariate relationships between the methacholine dose-response of FEV 1 and FVC, and the methacholine dose-response of capnographic variables. The DRS-FEV 1 was strongly associated with reductions in airway volume in subjects both without and with BHR (Fig  2A ). The relationship between variations in Slope3 adjusted for methacholine dose and DRS-FEV 1 , although significant, was weaker (Fig  2B ). Likewise, univariate associations were    Multivariate regression (Table  4 ) demonstrated the independent association of variations in both large airway volume and slope3 with FEV 1 reduction; the regression coefficient for the model was 0.
Acknowledgments The authors thank  Dominique De Piolens ,  Manteguebosh Wolde Selassie ,  Patrick Seince ,  Jocelyne Ganneau ,  Zakia Tajri , and  Ablewa Aduayo-Akue  for excellent technical assistance with lung function testing and methacholine testing, as well as  Flore Beintein  for precious help with data collection.
Statistical analysis Results are expressed as the mean±s. d. of three independent experiments for the in vitro studies, each consisting of three culture plates (n=9), and of five mice for the in vivo experiments. Significant differences were established by either the Student's t-test or one-way ANOVA, according to the number of groups compared, using GraphPad Prism software (GraphPad Software Inc. V4. 03, San Diego, CA, USA). When significant variations were found by one-way ANOVA, the Tukey-Kramer multiple comparison post-test was performed. The non-parametric Spearman rank correlation coefficient was used to calculate the correlation between Fos, miR-146a and TNF-α expression. Differences were considered significant at P<0. 05.
OBSERVATIONS During the period of March-May 2014, we observed four Galactic B[e]SGs in the L-band wavelength region using the CRyogenic high-resolution InfraRed Echelle Spectrograph (CRIRES,  Käufl et al. 2004 ) on the ESO VLT UT1-Antu 8-m telescope. Details on the objects and their observations are given in Table  1. Data were obtained at four different standard settings with reference wavelengths of 4048. 6, 4060. 1, 4135. 5, and 4147. 0 nm, so that the total spectra cover a continuous wavelength range from 3. 988-4. 176 µm. This range contains the first four band heads of the SiO first-overtone bands. We used the 0. 4 slit, which provides a spectral resolution of R ∼ 50 000, corresponding to a velocity resolution of ∼ 6 km s -1. Data reduction was performed with the ESO CRIRES pipeline (version 2.
CONCLUSIONS We report on the detection of SiO first-overtone band emission in the high-resolution L-band spectra of four Galactic B[e]SGs, which are known to display strong CO band emission. While SiO bands are commonly seen in absorption from the atmospheres of cool stars and giants, they were detected in emission, so far, only in spectra of SN 1987 A during the post-explosion period from day 160 to day 578. Hence, to our knowledge, this is the first discovery of SiO first-overtone band emission from hot, high-density environments of evolved massive stars. The high spectral resolution of our data allows us to precisely determine the rotation velocity of the SiO gas. For all of our target stars, this velocity is lower than that determined from the CO band forming region. Moreover, model fits to the observed three band heads in CPD-52 9243 demonstrate that, in contrast to the CO band emitting region, the emission of the SiO bands originates from a cooler and less dense disk region, indicating that SiO molecules form at larger distances within the Keplerian disks.
g. , SN 1987A), are the main sources of silicate dust, for which SiO molecules are regarded as a major building block. Studying the physical properties of SiO gas in the disks of B[e]SGs might, hence, provide indispensable insight into the early stage of silicate dust formation within the oxygen-rich environment of these enigmatic stars. We thank the referee, Dr. John Bally, for his valuable comments on the manuscript. This research made use of the NASA Astrophysics Data System (ADS) and of the SIMBAD database, operated at CDS, Strasbourg, France. MK acknowledges financial support from GA ČR (grant number 14-21373S). The Astronomical Institute Ondřejov is supported by the project RVO:67985815. LC, MLA, and AFT acknowledge financial support from the Agencia de Promoción Científica y Tecnológica (Préstamo BID PICT 2011/0885), CON-ICET (PIP 0300), and the Universidad Nacional de La Plata (Programa de Incentivos G11/109), Argentina.
Study Interventions Eligible participants were randomized 1:1 to receive 1 of 2 testing interventions for HIV, HBV, and HCV infection: a standard serology-based test (S arm) or a POC rapid test (RT arm). The central data management center (Inserm UMR_S1136, Paris, France) was responsible for randomization. A computerized random number generator was used to select permuted block of size 6. The randomization list was concealed from investigators, who assigned participants to testing groups through a Web site after validating eligibility criteria. In the S arm, participants received a prescription to perform venipuncture for HIV, HBV, and HCV serology at an outside laboratory. They were then asked to return to the clinic within 8 to 10 days and obtain their results. HIV, HBV, and HCV serostatus were determined using commercially available immunoassays (enzyme immunoassay or enzyme-linked immunosorbent assay) respectively detecting anti-HIV antibodies and HIV p24 antigen (Abbott Architect HIV Ag/Ab combo test), HBV HBsAg, anti-HB core (HBc) and anti-HB surface (HBs) antibodies (Abbott Architect HBsAg, anti-HBc, and anti-HBs Ab assay), and anti-HCV antibodies and HCV core antigen (Bio-Rad Monolisa HCV Ag-Ab ULTRA assay).
From estimates obtained in the overall tested population, the expected number of infected patients without testing was added to the denominator and the proportion was recalculated. A range of estimates was calculated based on the 95% confidence interval (CI) of disease prevalence. Because the number of infected individuals was assumed to be low and only few covariables were to be obtained during the study, no multivariable adjustments were planned. All statistical analysis were performed using STATA (version 13. 1; StataCorp, College Station, TX), and significance was determined using P <. 05. This trial is registered at ClinicalTrials. gov (number NCT01790633).
Acknowledgments We thank all study participants as well as all medical and paramedical staff from the  Parisian "Médecins du Monde " clinic and the data management center, especially  Frédéric Chau ,  Frédéric Fotre ,  Isabelle Goderel ,  Sylvain Bitschine , and  Grégory Pannetier. We also acknowledge  Lara Lhottelier ,  Amandine Quach , and  Emeline Dubief  for their extraordinary effort in data collection. Disclaimer. Gilead Sciences, Roche ,  Biomerieux , and Orasure were not involved in any part of the data collection, analysis, and writing. Financial support. This study was funded by the  Agence Nationale de Recherche sur le Sida (ANRS) et les Hépatites Virales, Gilead Sciences , and  Roche. Human immunodeficiency virus and hepatitis B surface antigen rapid tests were donated by  Biomerieux (Marcy-l′Etoile, France) , and hepatitis C virus rapid tests were purchased from  Orasure (Paris, France ).
Study population and patient treatment Patients presenting with stent thrombosis and undergoing catheter thrombectomy at participating centres were eligible for inclusion. Patients were prospectively enrolled using a centralized telephone registration system. A list of participating centres is provided in Supplementary material online, Appendix. Stent thrombosis was defined according to Academic Research Consortium (ARC) criteria for definite stent thrombosis. Data were collected according to a standardized protocol and was entered in a central electronic database (Open Clinica, Leuven Coordinating Centre, Leuven, Belgium). All patients provided written informed consent. Funding was provided by the European Commission under the Seventh Frame Work Programme (Grant agreement number 260309 PRESTIGE).
Histopathological sampling and analysis After crossing the lesion with a standard guide-wire, a thrombectomy catheter was advanced to the target lesion. Thrombus aspiration was performed using a manual suction device according to standard practice. The catheter type used was at the discretion of the cardiologist and was not recorded in the database. Thrombus was collected according to a standardized protocol, fixed in formalin 4%, and transported to the core laboratory for thrombus analysis (Deutsches Herzzentrum Mu ¨nchen, Munich, Germany). Here thrombus specimens were embedded in paraffin after 48 h of formalin fixation. Thrombus aspirates were processed and analysed wherever practicably possible. Some thrombi were received as small fragments and could not be processed for histological analysis.
Data were normalized to square meter thrombus area. For the assessment of cell counts, coefficient of variation for inter-and intra-observer variability was 0. 78 and 0. 77%, respectively. The following preconditions had to be fulfilled for quantification of NET formation: (i) attendance of filamentary structured extracellular DNA, (ii) respective DNA had to originate from cells that stained positive for a neutrophil marker, and (iii) filamentary structures had to be decorated with a marker for neutrophil granule proteins such as NE. Eosinophils were counted on whole sections stained with Luna and the results were presented as cells/mm 2 thrombus area. The percentage of fibrinogen, erythrocyte, and platelet area in relation to the whole thrombus area was investigated in overview images of the thrombi taken with the above-mentioned camera and analysed using Cap-Image 7.
1 software (Dr Zeintl, Heidelberg, Germany) and Adobe Photoshop. Images were acquired using either a Zeiss Imager M2 Axio epifluorescence microscope and processed using AxioVision Ax-ioVision SE64 Rel. 4. 9 software, or a Leica DMRB epifluorescence microscope equipped with a Zeiss AxioCam and processed using AxioVision 4. 6 software (Zeiss).
Statistical analysis Statistical analyses were performed using the Statistical Package for the Social Sciences (IBM SPSS Statistics) version 23. 0 (IBM, Ehningen, Germany) and Prism 5 (GraphPad Software, La Jolla, USA). Data were tested for normal distribution using the Kolmogorov-Smirnov test. For comparison of continuous data between two groups, we used Student's t-test or Mann -Whitney U-test, for three and more groups, we used analysis of variance ANOVA or Kruskal -Wallis test, according to the distribution of the data. For comparison of categorical data between two groups we used x 2 or Fisher's exact test as appropriate. For comparisons of multiple groups, post hoc testing was performed applying the methods of Bonferroni (Dunn's test). Significance level was set at a two-sided a of 0.
Secondly, in terms of planning tools, the City of Nairobi bylaws that were passed in 2007 reactivated "dormant bylaws"  45  on street trading: they made cosmetic updates to the colonial document of 1963 that had fallen into disuse. Under these bylaws, street traders are compelled to design a clear outline for their stalls and to display individual registration numbers, a measure that was contested by the Kenya Auctioneers, Hawkers, Marketers and Traders Union in the 1960s. Moreover, after decades of disruption due to its inability to enforce it, in the 2000s, the NCC reintroduced the compulsory licensing. This led to the creation of a centralised database. Anthropometric photographing was abandoned, but censuses were undertaken, a measure that was seen as a way to discern the "authorised" traders from the "outlaws".