dataesr/scientific-paragraphs-categorization huggingface dataset:
NL acknowledges financial support from  European Research Council Advanced  Grant  FP7/669253. JG and NC acknowledge financial support from  Spanish MINECO  ( AYA2016-75808-R ). MB acknowledges support from  AYA  grant  2009-11139. This paper is based on observations obtained with WIRCam, a joint project of  CFHT, Taiwan, Korea, Canada, France , and the  Canada-France-Hawaii Telescope (CFHT)  which is operated by the  National Research Council (NRC) of Canada , the  Institute National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France , and the  University of Hawaii. Funding for the DEEP2 survey has been provided by  NSF  grants  AST95-09298 , AST-.
DEV Genome Extraction and High-Resolution Melting (HRM) CEF cells were transfected with 1 µg of sgRNA per well of a 12-well plate before infection with DEV at MOI 1. 0. The DEV infected cells were harvested at 48 h post infection and lysed in 1× squishing buffer (10 mM Tris-HCl, pH 8, 1 mM EDTA, 25 mM NaCl, and 200 µg/mL Proteinase K) at 65 • C for 30 min. Primers for HRM analysis were designed using Primer Express 3 (Thermo Fisher Scientific). The PCR was performed in a 7500 fast real-time PCR machine (Applied Biosystems, Foster City, CA, USA) and analysed using Applied Biosystems™ HRM Software v3. 0 according to the manufacturer's instructions.
Acknowledgments: This study was supported by the  BBSRC ZELS  grant number  BB/L018853/1 ,  BBSRC ISPG  grant number  BBS/E/I/00007032 ,  BBSRC  grant  BB/P016472/1  and  British council Newton Fund Institutional Links  grant  IL3261727271. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. The authors would like to thank  Yaoyao Zhang  and microbiological service unit for the help of CEF preparation. Author Contributions:  Munir Iqbal ,  Pengxiang Chang ,  Juliet E Bryant  and  Muhammad Munir  conceived and designed experiments;  Pengxiang Chang ,  Yongxiu Yao ,  Na Tang ,  Jean-Remy Sadeyen ,  Joshua Sealy ,  Anabel Clements , Sushant Bhat performed experiments;  Pengxiang Chang  and  Yongxiu Yao  analyzed the data;  Pengxiang Chang ,  Joshua Sealy ,  Anabel Clements ,  Juliet E Bryant ,  Muhammad Munir  and  Munir Iqbal  wrote the paper.
X-ray micro-tomography The porosity quantification by crossed use of X-ray tomography and MIP is strongly dependent on the scanning resolution  (Peng et al. , 2012). X-ray tomography imaging was thus performed on a Phoenix Nanotom S ®, at the highest resolution, i. e. with a magnification of 250. This allowed a resolution of 1 voxel = 1 µm 3. Five representative samples of the different facies, with small chips of 3*5*3 mm, were analyzed to calibrate the meso-pore network characteristics (connectivity, percentage of porosity, tortuosity, and equivalent pore radius). The 3D image of each sample was treated with VG Studio software (Volume Graphics), to extract the porosity and estimate volume, surface, and sphericity. Equivalent radii could be determined from the volume and sphericity for each connected volume, assuming a pore to be a deformed sphere.
Microstructural and petro-physical property relationships To better decipher the interdependency between fracture distribution visible at a macroscopic scale, pore network features, microstructural characteristics, and permeability, a Principal Component Analysis (PCA) is performed. This concerns two datasets: Fa1 and Fa2 samples (Fig. 11 ). The main conclusion drawn is that the control of pore network properties ensured by the structure of the damage zone is not directly linked to the fault core distance. However, at the macroscopic scale, strain in the damage zone induces the development of corridors with decreasing fracture intensity, lowering the thickness of a corridor with its distance from the fault core. The control scale of petrophysical properties depends on the organization within the corridors, including a dependency toward the distance from the closest fracture.
, 2016) , and regionally known hydrothermal events (he) associated with major fault zones  (Cathelineau et al. , 2004 (Cathelineau et al. , , 2012;; Clauer et al. , 2008; Blaise et al. , 2016). The paleo-stress orientations are represented in black-σ1, shaded -σ2, or white -σ3. For each facies, the increase of the fissuration ratio is correlated with the increase of permeability. On the global dataset, this log-relationship is not clear, because it is influenced by intrinsic properties of each facies. B) Permeability versus Young's Modulus. The two facies seem to have similar Young's Moduli for high to very high permeability samples. The lower Young's Modulus is, the more permeable the sample. Figure  13 : Evolution of porous network dimensions with increasing distance from the macro-fracture, with best line data fits (BF) for each property and each facies.
Acknowledgements This work was supported by a PhD grant from  ENGIE  and the  University of Lorraine. We would like to thank  Rauscher Company  for access to the quarry and sampling authorizations. All the GeoRessources and LEMTA laboratories and ENGIE collaborators are also thanked for numerous advice, settings supplies and help with measurements. Special thanks are due to  Dr. Sebastien Leclerc  from LEMTA,  Dr. Marc Diraison  from  GeoRessources , and  Dr. Andrei Lecomte  and  Christophe Morlot , from  SCMEM  ( Université de Lorraine ), for SEM and X-ray tomography data treatment respectively. We are also grateful to the editor  Dr. Toru Takeshita , the reviewers Dr. Fabrizio Agosta ,  Dr. Nathalie Farrell , and the third anonymous reviewer for their time and suggestions for improvement of the manuscript.
We observed lower induction of mRNA RARß2 synthesis, 6 h post ATRA treatment in shXPC and shXPA cells, compared with shCTL cells (Supplementary Figure  2A , middle panel). We also determined the transcriptome profiles of shCtrl, shXPC, and XP-C DEL cells by comparing mRNA induction in untreated and 6 h ATRA-treated cells. In shCtrl cells, 77 genes show a fold induction >2, including several well-characterized genes, such as RARß2 (Supplementary Figure  2B , Supplementary Data 4, and Supplementary Methods). Surprisingly, ~90% of genes activated in shCtrl showed a lower induction in both shXPC and XP-C DEL cells (Supplementary Figure  2B  and Supplementary Data 4). The RARß2 mRNA induction at 6 h post ATRA treatment in shCtrl cells followed the recruitment of the transcriptional machinery together with the NER factors at the promoter (Supplementary Figure  2A , right panels)  6.
The primer sequences for the different genes used in qPCR are indicated in Supplementary Data 3. The mRNA expression of the different analyzed genes represents the ratio between values obtained from treated and untreated cells normalized with the housekeeping GAPDH mRNA. Chromatin immunoprecipitation. Cells were crosslinked at room temperature for 10 min with 1% formaldehyde. Chromatin was prepared and sonicated at 4 °C for 30 min using sonicator Q800R (Qsonica) as previously described  6. Samples were immunoprecipitated with antibodies at 4 °C overnight, and protein G-coated Dynabeads (Invitrogen) were added, incubated for 4 h at 4 °C, and sequentially washed. Protein-DNA complexes were eluted and decrosslinked. DNA fragments were purified using QIAquick PCR purification kit (QIAGEN) and analyzed by qPCR using a set of primers indicated in Supplementary Data 3.
RNA-seq analysis. Total RNA from XP-C WT and XP-C DEL cells were extracted before or 6 h after ATRA treatment (10 μM) using TRI REAGENT (MRC) and purified by phenol-chloroform extraction. Libraries were prepared with TruSeq Stranded mRNA Sample Preparation kit following guide instruction and subsequently proceed on an Illumina Hiseq 4000 as single-end 50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 2. 7. 3 and bcl2fastq 2. 17. 1. 14. Reads were mapped onto the hg19 assembly of the human genome. Reads count was performed with HOMER v4. 8. 3(65) and expression was estimated with EdgeR. Genome ontology was performed with The Database for Annotation and Integrated Discovery v6. 7 (https://david. ncifcrf. gov). ChIP-seq analysis. Purified DNA fragments analyzed by ChIP-seq were prepared by using the ChIP-IT High Sensitivity Kit (Active Motif) and the related antibodies.
ChIP-seq was performed on an Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions. Image analysis and base calling were performed using RTA 1. 17. 20 and CASAVA 1. 8. 2. Reads were mapped onto the hg19 assembly of the human genome. Peak detection was performed using MACS (http://liulab. dfci. harvard. edu/MACS/) under settings where the input fraction was used as negative control. Peaks detected were annotated using HOMER (http:// biowhat. ucsd. edu/homer/ngs/annotation. html) as well as TSS protein enrichment comparison. Quantitative comparison of Pol II gene body enrichment was performed using seqMINER (http://bips. u-strasbg. fr/seqminer/). As reference coordinates, we used the MACS-determined peaks or the annotated TSS/TTS of human genes as defined by RefSeq database.
Acknowledgements We are grateful to  A. Poterszman  and  L. Tora  ( IGBMC ) for the VEAP5317 and KAT2A constructs, respectively, to members of our team, and to  Didier Devys  ( IGBMC ) for fruitful discussion. Sequencing was performed by the  IGBMC Microarray and Sequencing platform , a member of the " France Génomique "  consortium  ( ANR-10-INBS-0009 ). This study was supported by l' Association de la Recherche contre le Cancer  (ARC no. SL220130607082 ) and the  National Research Foundation of Korea for International Collaboration. This study was supported by the  Ligue contre Le cancer  ( CCIR-GE 2015 ). This study was supported by the grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de la Recherche  under the  frame program Investissements d'Avenir   ANR-10-IDEX-0002-02.
Individual trajectories are propagated with the following stochastic Schrödinger equation (SSE)  [15] : d |ψ(t) = j dξ j (t)   a j n j (t) -1   |ψ(t) + dt γ 2 j n j (t) -a † j a j -iH(t) |ψ(t) , (4) where the time dependent populations of the two sites j = 1, 2 are given by n j (t) = ψ(t)| a † j a j |ψ(t). (5) and the stochastic increments dξ j have the following properties: dξ k (t)dξ j (t) = dξ k (t) δ kj (6) E[dξ j (t)] = γn j (t)dt. (7) Here E[• • •] denotes the average over trajectories. The solution of equation (  3 ) is approached by taking the average of many trajectories. The stochastic equation, ‡ For the calculation used in the present work we typically have a basis with dimension ∼ 400. equation (  4 ), was solved using the XMDS package  [18, 19]. Note that equation  (6)  implies that the stochastic increment is either 0 or 1.
acknowledges support from Henes Center for Quantum Phenomena at Michigan Technological University; and the Max Planck Institute for the Physics of Complex Systems (MPIPKS). R. E. thanks the visitors program of the MPIPKS for making an extended stay at the MPIPKS possible during which most parts of the present work have been produced. A. M. Y. acknowledges support from the "Investissements d'Avenir" program (Labex NanoSaclay, Grant No. ANR-10-LABX-0035), and the ANR UNIQ DS078. A. E. and C. D. B. B. gratefully acknowledge discussions with Francesco Piazza and Jad C Halimeh.
Congo red dye (CR) Congo red dye (Sigma Aldrich, USA) at a concentration of 50 μM in PBS was mixed with the 10 μM peptide. As a control, a similar sample was used in which a buffer was added instead of the peptide. Absorption spectra were recorded on an Avantes Ava Spec 2048 instrument (Avantes, The Netherlands). The Congo red dye absorption spectrum characteristic maximum is in the region of 500 nm (the exact value depends on the buffer used). In the presence of beta structures in the sample, the dye binds to them, which leads to a shift of its characteristic maximum to the right by 10-20 nm. The spectra were visualized using Origin2015 software.
Atomic force microscopy (AFM) Five microliters of PB1(6-13) peptide, at a concentration of 1 mM in PBS, was applied to a freshly cleaved mica surface (SPI supplies, USA) and incubated for about 30 seconds, after which the sample was washed three times with 50 μl of water and dried in a thermostat for 30 minutes at 55°C. The scanning was performed in a semi-contact mode on the SolverNext atomic force microscope (NT-MDT, Russia, Zelenograd) under the NovaPx program (production of NT-MDT) using an NSG-03 probe. The resulting images were processed in the Gwyddion software  [16].
Small-angle neutron scattering (SANS) In order to measure the peptides' scattering spectra by the SANS method, solutions were prepared in PBS/D 2 O at a concentration of 1 mM. The spectra were obtained with the YuMO spectrometer located on the fourth channel of the IBR-2 high-flux reactor (Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia). The measurements were carried out in the standard geometry described previously  [17] ,  [18]. The scattering detection was performed by two detectors simultaneously in the Q region from 0. 006 to 0. 3 Å. Preliminary processing of the data was also carried out according to the scheme described in the reference  [19]. In the method, obtaining and normalizing the curves, in absolute units, is realized with the help of metallic vanadium located directly before the detector.
Time-resolved small-angle X-ray scattering (TR-SAXS) TR-SAXS experiments were carried out at the synchrotron radiation source ESRF (Grenoble, France) using the ID02 spectrometer in accordance with the corresponding protocols. Peptide monomers were dissolved in PBS with 10% DMSO and then mixed in an equimolar ratio, at final concentrations of 0. 2 mM, using a "stopped flow" system. Five milliseconds after mixing, the 100 SAXS spectra registration was measured at 3 s intervals. Data processing was performed using original software developed by N. V. Klopov et al. , NRC KI PNPI, Gatchina, Russia. The program is built around the singular value decomposition (SVD) method and is capable of identifying the main spectral components (U(q)) and the variation of such components over time (V(t)). Based on the exponential kinetics of the main components, the SAXS spectra for the initial (t=0) and the final (t=∞) states of the system were calculated in order to determine the state of the peptide system before and after mixing.
MicroScale Thermophoresis (MST) Experiments using MST were performed on the Monolith NT. 115 (NanoTemper Technologies GmbH, Germany), in accordance with manufacturer protocols using 80% laser intensity, 25 o C. A 0. 5 μM concentration of the FITC-PB1(6-13)-Ala peptide and a range of 16 PB1(1-25) peptide concentrations (from 0. 012 to 400 μM) were used. The measurements were carried out in PBS containing 10% DMSO. In the concentrations used, the peptides were in the form of monomers. The data were processed in instrument software and were visualized using Origin2015 software.
Analysis and statistics Relevant variables from electronic database of the hospital were extracted into Excel and imported to Stata/IC version 12. 1 (StataCorp LP, TX, USA) for analysis. The demographic and clinical characteristics of the study population have been described using numbers and proportions. We used unadjusted Kaplan-Meier survival methods and curves to assess the differences in the survival of children with various demographic and clinical characteristics. We used Cox proportional hazards models to estimate the hazard ratios and adjusted hazard ratios (HRs & aHRs) of the association between demographic and clinical factors and adverse treatment outcomes. We assessed for violations of the proportionality assumption using schoenfeld and scaled schoenfeld residuals (using stphtest command in Stata).
The specific reasons for these delays need further evaluation. Finally, it is commendable to note that pediatric ART center at this hospital has maintained electronic database of all children ever enrolled into pediatric ART care since its inception in 2005. This allowed us to use this database to conduct our study and assess long term survival in children. The maintenance of electronic database can act as a model for other similar centers in the world. In conclusion, only 10% of the children ever enrolled into pediatric ART care had an adverse outcome (death or loss to follow-up) in the pediatric cohort with nearly 1. 5 million person days of follow-up. This indicates good survival and/or good pediatric care programme implementation and this should continue. Of all the major demographic and clinical factors at enrollment, those associated with adverse outcomes included entry into ART care from inpatient department, CD4 Cell count <50, enrollment during 2005, 2011 and 2014 ART guideline periods.
org/10. 1371/journal. pone. 0195435. t001Data variables, sources of data and data collectionData variables included (i) socio-demographic and clinical characteristics at enrollment into ART care and (ii) treatment outcomes of the HIV infected children. We obtained individual patient data from electronic patient database of Mingalardon Specialist Hospital. The demographic and clinical factors that we assessed for its association with adverse outcomes were those that are routinely maintained in this electronic database. These included age, sex, residence in urban or rural areas, point of entry into ART care (from outpatient department/ or from in-patient care), WHO Stage, CD4 Cell count, and ART guidelines at the time of enrollment, presence or absence of TB at the time of enrollment into ART care, type of TB, ART regimen (NNRTI-based regimen or PI-based regimen) and whether the child received cotrimoxazole prophylaxis for opportunistic infection at enrollment.
Acknowledgments This research was conducted through the  Structured Operational Research and Training Initiative (SORT IT ), a global partnership led by the  Special Programme for Research and Training in Tropical Diseases at the World Health Organization (WHO/TDR ). The model is based on a course developed jointly by the  International Union Against Tuberculosis and Lung Disease  ( The Union ) and Medecins sans Frontières (MSF/Doctors Without Borders). The specific SORT IT programme which resulted in this publication was jointly organized and implemented by: The  Centre for Operational Research, The Union, Paris, France ;  The Department of Medical Research, Ministry of Health and Sports, Myanmar ; The  Department of Public Health, Ministry of Health and Sports, Myanmar; The Union Country Office, Mandalay, Myanmar ;  The Union South-East Asia Office, New Delhi, India ; the  Operational Research Unit (LUXOR) ,  MSF Brussels Operational Center, Luxembourg ;  Burnet Institute, Australia.
In Vivo Imaging In vivo fluorescence imaging was performed according to  [3]. Each live cyp19a1b-GFP transgenic embryo was photographed once in dorsal view using a Zeiss AxioImager Z1 fluorescence microscope equipped with an AxioCam Mrm camera (Zeiss GmbH, Göttingen, Germany). The same exposure conditions were used to acquire each photograph (X10 objective, 134 ms of fluorescent light exposure, maximal light intensity). Fluorescence quantification was performed using Image J software (available online: http://rsb. info. nih. gov/ij/). For each picture, the integrated density (IntDen) was measured, i. e. , the sum of the gray-values of all the pixels within the region of interest. All gray-values of 300 or less were considered as background values.
Data Normalization In the in vivo assay with cyp19a1b-GFP transgenic zebrafish, induction of GFP fluorescence was measured as IntDen and, since the data were obtained from several independent experiments, they were normalized by dividing by the geometric mean of the IntDen in the DMSO control group, thus expressing results as Log Fold inductions. In the in vitro assays with U251-MG cell cultures, data normalization was performed by dividing by the geometric mean of the corresponding solvent control group. The mixture dose-response experiments were reproduced twice in vivo and in the ERα assay, and three times in the ERβ2 assay. However, due to high variability in replicate measures within each experiment, the three replicate datapoints at each concentration within each experiment were averaged, and the mixture dose-response model was based on two (ERα) or three (ERβ2) average values at each concentration.
As a second step, common values of Min, Max and Slope were estimated for E2 and GEN. Lack-of-fit F-tests were performed to check that the model did not fit less well than when the slope varied freely. The parameters were estimated by least squares, using R 3. 1. 1 [38]  and package drc  [39]. All the data and R codes used in this study are available in Supplementary materials (Supplementary Figure  S3 ).
Mixture Experimental Designs The mixture experimental design was developed based on relative potency of single compounds according to  [12]. In the in vivo assay, relative potency of E2 and GEN were estimated with the EC50 obtained by modelling dose-response data from respectively four and two experiments with the 4-parameter Hill model. Mixture experiments were performed according to a ray design with one ray for each single chemical and three mixture ratios (3:1, 1:1, and 1:3 expressed as relative potencies). Each ray was tested with five concentrations with 4-fold serial dilutions, centered around the EC50, except for GEN for which the highest concentrations were reduced because of their toxicity to fish (range of E2 concentrations from 4. 8 × 10 -12 to 5 × 10 -9 M and range of GEN concentrations from 2.
ECx i For example, for simple synergism or antagonism, these toxic units are used in the following deviation function used by  Jonker et al. (2005)   [18]. G(z 1 ,. , z n ) = a n ∏ i=1 z i We therefore tested both implementations of the interaction definitions. Significance of the interactions was assessed using approximate F-tests on the residual sums of squares by considering that the models were nested. Acceptability of the concentration-response surface models was assessed with a lack-of-fit F-test compared to the analysis of variance model. Optimisation of parameter values for the dose-response surfaces was performed with R 3. 1. 1 [38] , package dfoptim [55].
A. Molecular dynamics simulations The simulated system consists of two nanoporous carbon electrodes and an aqueous NaCl solution as an electrolyte (see Fig. 1 ). The carbon structure for the porous electrodes was obtained by quenched molecular dynamics  [60] , and it corresponds to the structure of a CDC synthesized at 800 °C. The geometrical analysis of the porous structure, which has a mass density ρ solid ¼ 0. 939 g cm -3 , is performed with the ZEO++ software  [61]  using a probe radius r probe ¼ 1. 3 Å, which corresponds approximately to the radius of a water molecule, resulting in a porosity of Φ ¼ 23. 3% and a specific surface area of S ¼ 1934 AE 2 m 2 g -1 (for a probe size of 1. 7 Å corresponding to an argon probe, the values are 18% and 1553 AE 2 m 2 g -1 , respectively). Two systems are simulated, corresponding approximately to average salt concentrations of 0.
In such cases, only data obtained during the untreated period were used for the analysis. Baseline IOP was defined as the mean of at least two measurements at the baseline examination. Mean follow-up IOP was defined by averaging the IOPs measured at every visit and IOP fluctuation was determined using the standard deviation of these values. A DH, defined as an isolated hemorrhage seen on the optic disc tissue or in the peripapillary retinal tissue connected to the optic disc rim, was detected by slit-lamp examination using a 78-diopter lens or stereo disc photography. One of these examinations was performed at every follow-up visit. EDI-OCT of the optic disc and adaptive compensation to evaluate LC. The LCD and degree of LC curve (from flat to steeply curved shape) were measured using optic disc B-scan images  25.