dataesr/scientific-paragraphs-categorization huggingface dataset:
PMF calculations has been carried out with the umbrella sampling (US) method  [43] [44] [45]  with both isomers. Initially, these calculations were carried out with the most stable trans isomer, then with the cis form by blocking the C-N-N-C dihedral. The simulation box length has been increased up to 57 Å with more than 6000 water molecules. The cut off has been also increased to 10 Å. PMF simulations has been performed using the LAMMPS package with the COLVARS module. The PMF has been defined as the distance between the centers-of-mass of CB7 and 4AA. The transversal freedom of move has been limited in order to get a valid PMF result. A global equilibration in the NPT ensemble was performed for 100 ps and then a NVT one for 100 ps. The PMF was run in the NVT ensemble and was separated into six different stages.
CONCLUSIONS Detailed NMR and UV studies provided a set of thermodynamic data for the formation of inclusion complexes between 4AA and cucurbit [7]uril in acidic solution. Indeed, the thermodynamic parameters of this complex were determined both by UV spectroscopy and NMR experiments while the structure was specified using NMR and molecular simulations. As expected, a significantly larger binding constant with CB7 (log K around 5) than that previously obtained with the other hosts was measured. This larger constant is the result of a large negative change in Δ r H°(-19 kJ/mol) and a small positive change in TΔ r S°(9 kJ/mol). The major contribution to the enthalpy of complexation comes from the ion-dipole interaction associated with the inclusion of the 4AA into the CB7 cavity. Indeed, 1 H NMR results pointed out the inclusion of the azobenzene within the cavity of CB7.
3b ). Lastly, incubation of the colon cell lines with Ac 4 ManNAz led to a strong and diffuse nuclear and cytosolic labeling (Fig. 3a-c ), as previously reported in another cancerous cell lines  19. There was no colocalization of Strept signal with TGN46 in these cells, as confirmed by the quantification that showed that most of the signal was quantified as "out of Golgi" (Fig. S5a-c ). This indicates that the signal obtained with Ac 4 ManNAz appears to be non-specific to the Golgi complex compared to the other analogs. Taken together, these data highlighted that  with either the indicated analog or ManNAc (negative control). Then they were fixed and permeabilized before CuAAC with the appropriate biotin probe, followed by overnight incubation with anti-TGN46 (Golgi marker). Biotinylated proteins and TGN46 were revealed with Streptavidin-DyLight488 and AF568-conjugated secondary antibody, respectively.
05% Tween-20) before blocking in TBST with 5% (w/v) nonfat dry milk. Membranes were incubated overnight at 4 °C with peroxidase-conjugated monoclonal mouse antibiotin (200-032-211, Jackson ImmunoResearch) (1:10,000) in blocking buffer. After four washes with TBST, chemiluminescence signal (SuperSignal West Pico Plus, Life Technologies, Courtaboeuf, France) was detected on a CCD camera (FUSION Solo, Vilber Lourmat, France) using the FUSION-Capt Solo software for acquisition and processing merge images. Western blot with the following antibodies were done as previously described  46  : GNE (ab189927, Abcam; 1:1,000), E-cadherin (sc-7870, Santa Cruz;1:1000), GAPDH (sc-32233, Santa Cruz; 1:2000), alpha-tubulin (sc-23948, Santa Cruz; 1:2000). For detection of O-linked glycoproteins, membranes were incubated overnight at 4 °C in blocking buffer (1% (w/v) BSA in PBS-Tween 0.
05% (v/v)) before incubation with Jacalin-FITC (1:100) in blocking buffer for one hour at r. t. After washes, fluorescence was read with ImageQuant™ LAS 4000 (GE Healthcare). N-linked glycoproteins were revealed using L-PHA-biotin (1:500 in PBST with 1% BSA), followed by incubation with the anti-biotin-HRP. Densitometry analysis was done using the ImageJ® software.
Flow cytometry analysis. Cell surface fluorescence was measured on a BD ACCURI C6 Plus flow cytometer (BD Biosciences, Rungis, France), either in the FL1 channel for labeling with the Alkyne-AF488 probe and lectin-FITC, or in the FL2 channel for labeling with the picolyl-azide-AF594 probe. Data were analyzed with FlowJo software (vX 0. 7). Cell population was gated based on SSC/FSC dot plot to remove cell debris and doublets. The means of fluorescence intensity (MFI) were obtained for each condition (FL1A or FL2A), unspecific MFI was quantified from cells incubated with ManNAc (negative control). Raw values of MFI are indicated on the respective histograms in order to be able to compare the MFI obtained with a given fluorescent probe for the different analogs performed in the same experiment.
t. in the dark and under gentle agitation with 100 µl of the freshly prepared click reaction mix containing the appropriate biotinylated probe (50 µM). After three washes with PBS, immunofluorescence was performed as previously described with the rabbit polyclonal anti-TGN46 (1:100, AHP1586, BioRad, Marnes-la Coquette, France) and the goat anti-Rabbit IgG Alexa Fluor 568® (1:600)  46. Streptavidin-DyLight®488 (1:600) was added at the same time to reveal click chemistry reaction. Nuclei were stained with DAPI (50 µg/mL) and coverslips were mounted on microscope slides using a drop of mounting medium (Dako mounting medium, Agilent). Images were acquired on a Nikon A1R confocal microscope (Apo 60X, NA1. 4, oil immersion) using NIS-Elements software, and further analyzed with ImageJ® software.
We developed a home-made macro on Image J® to quantify the relative fluorescence signal of streptavidin in whole cell vs. Golgi apparatus (https:// doi. org/ 10. 5281/ zenodo. 67780 42). Briefly, a threshold value was first applied to confocal images based on the streptavidin channel intensity of each condition's control to get rid of the background signal emanating from the binding of the streptavidin into cells (negative controls, i. e. CuAAC performed on cells cultured with ManNAc for 24 h). Regions of interest (ROI) of the whole cells were generated on the thresholded images. Golgi ROIs were created using the TGN46 detection channel. These ROIs allowed us to discriminate regions in and out of the Golgi apparatus, and to measure and export the streptavidin signal values (min, max and mean grey values, integrated densities) of these regions.
Acknowledgements This work was supported by the  CNRS  and the  University of Lille. J. S. is a recipient of a research grant from the  Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation. V. R. is a recipient of a research grant from  ANR NEURAPROBE  ( ANR-18-CE07-0042 ) (C. B. ). We thank  Dr Corentin Spriet  ( Plateformes Lilloises en Biologie et Santé (PLBS) -UAR 2014-US 41 ) for helpful discussions on Image J analysis and  Dr Clément Delannoy  for his technical help for glycolipid extraction.
Acknowledgement The results of this paper have been announced by the author in his "Cours Peccot" in April-May 2017. I would like to thank the Collège de France for giving me the opportunity to give this course and I apologize for the delay in writing the details of this work. I am very grateful to Jean-Loup Waldspurger for a thorough reading of a first version of this manuscript allowing for many improvements and in particular for catching a fatal error in the proof of Proposition 5. 1. 1. The project leading to this publication has received funding from Excellence Initiative of Aix-Marseille University-A*MIDEX, a French "Investissements d'Avenir" programme.
Acknowledgements We are grateful to the  ANR (MMdash) ,  MAP silicon, JSPS  (grant for S. Takahashi), the  DGA (RAPID-LIMS ,  Spherea/CNRS ) and  Marelli corporation (Marelli next-generation scholarship ) and the  Spanish AEI  (grant  PID2020-116861GB-I00 ) for financial support of this work.
Potentialities for complex sample analysis We assessed the capability of our sensor to work under real-life conditions. We chose the Ade-5 ′ -TR-apt-A pair and a biological fluid as study model. A 5% human urine sample was spiked with the Ade analyte at different concentrations, in the presence of 40 μM Ni 2+. The Ade dose-response curve was then constructed as depicted in Fig. S11. The normalized response was shown to be comparable to that recorded in buffered solution, suggesting that the sensor could retain its activity in diluted complex matrices. The time-dependent FI output of 5 ′ -TR-apt-A upon addition of 200 μM Ade to the urine sample was also recorded. We found that the reaction equilibrium can be reached in a short period of time, i. e. within 1 min or less (Fig. S11 ). This data demonstrates that the aptasensor is able to promptly respond to the presence of the target, even in a realistic medium.
Production of the disaccharide GlcNAc-1,6-anhMurNAc (1) To produce the GlcNAc-anhMurNAc disaccharide 1, the nagZ gene of the E. coli K12 strain DH1 (DSM 4235) was inactivated. First, bacteria were grown in minimal medium to confirm the viability of the E. coli ΔnagZ strain under high cell density culture conditions and to validate the accumulation of 1. The impairment of the PG recycling pathway was not lethal to the bacterium and the presence of the disaccharide in the cytoplasm was confirmed by mass spectrometry analysis (data not shown). As a control, the wild type strain was grown under the same conditions and the disaccharide 1 was not detected. [26] [27]  This process takes place in two phases: an initial exponential growth phase, which starts at the inoculation of the bioreactor and lasts until exhaustion of the carbon sources initially added to the medium, then a fedbatch phase with a high glycerol feeding rate.
79 ppm. Data for 1 H NMR are reported in the conventional form: chemical shift (δ ppm) (multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet), coupling constant (Hz), integra- Reactions were monitored using thin layer chromatography (TLC) on silica gel (Merck Silica gel 60 F254, Darmstadt, Germany). Carbohydrates or peptides were visualized with either a 30 % ammonium bisulfate solution in H 2 O or diphenylamine-anilinephosphoric acid (4 g diphenylamine, 4 mL aniline, 2 mL 37 % HCl, 20 mL 85 % H 3 PO 4 in 200 mL ethyl acetate) staining solution followed by heating with a heat gun. The intra-and extracellular concentrations of GlcNAc-anhMurNAc 1 were determined against a calibration curve obtained with pure disaccharide using high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD, ICS-6000 Dionex) equipped with a CarboPac PA1 guard column and CarboPac PA1 analytical column (Thermo Fisher Scientific) thermostated at 30 °C.
Acknowledgements This work was supported by the  French National Research Agency (ANR)  through  Glyco_SWIM  ( ANR-20-CE07-0012-01 ),  Labex ARCANE  and  CBH-EUR-GS  ( ANR-17-EURE-0003 ),  Glyco@-Alps  ( ANR-15-IDEX-02 ),  Carnot PolyNat  ( CARN-025-01 ). We acknowledge the  NanoBio ICMG (UAR 2607 ) for providing facilities for mass spectrometry ( A. Durand ,  L. Fort ,  R. Gueret ) and NMR analyses (I. Jeacomine). We thank  E. Samain  for fruitful discussions and support.
6H 2 O (99. 9 % purity) and phenylarsonic acid, C 6 H 5 AsO(OH) 2 (97 % purity) were purchased from Sigma-Aldrich, Steinheim am Albuch, Germany and used without any further purification. The X-ray crystallographic data for compounds 1 and 2 were collected using a Bruker Kappa APEX-II diffractometer operating at 150 K and a Nonius Kappa CCD working at 293 K, respectively.
The X-ray crystallographic data were collected using a Bruker Kappa Apex II diffractometer operating at T = 150 (2) K. Data were measured using φ and ω scans using MoKα radiation (λ = 0. 71073 Å) using a collection strategy to obtain a hemisphere of unique data determined by Apex2 (Bruker AXS Inc. , Madison, WI 53719-1173. , 2012). Cell parameters were determined and refined using the SAINT program (SAINT (2012)). Data were corrected for absorption by multi-scan absorption using SADABS (SADABS2012/1). The structure of 1 was solved by dual-space analysis using SHELXT  (Sheldrick, 2015)  and refined using least-squares minimization with SHELXL97  (Sheldrick, 2008). Programs used for the representation of the molecular and crystal structures: Olex2  (Dolomanov et al. , 2009)  and Mercury  (Macrae et al.
, 2008). The Crystallographic data and experimental details for structural analyses are summarized in Table  1. Selected bond lengths and angles are listed in the caption of Figure  1. CCDC 2172774 (1) contains the supplementary crystallographic data for this paper. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via www. ccdc. cam. ac. uk/data_request/cif,or by emailing data_request@ccdc. cam. ac. uk, or by contacting the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44(0)1223-336033.
Programs used for the representation of the molecular and crystal structures: Olex2  (Dolomanov et al. , 2009)  and Mercury  (Macrae et al. , 2008). The Crystallographic data and experimental details for structural analyses are summarized in Table  1. Selected bond lengths and angles are listed in the caption of Figure  5. CCDC 2172775 (2) contains the supplementary crystallographic data for this paper. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via www. ccdc. cam. ac. uk/data_request/cif, or by emailing data_request@ccdc. cam. ac. uk, or by contacting the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44(0)1223-336033. 2 ). 695 = Σ(||F o |-|F c ||)/ Σ |F o |; b wR 2 = [Σw(F o 2 -F c 2 ) 2 / Σ[w(F o 2 ) 2 ] 1/2 where w = 1/[σ 2 (F o 2 )+(0.
(Padalwar et al. , 2013)2016; Shi et al. , 2014; Zhang et al. , 2020; Firmino et al. , 2020; Ayhan et al. , 2020; Jiao et al. , 2016; Chu et al. , 2013; Dai et al. , 2014; Yang et al. , 2016; Zhao et al. , 2016) have also been reported. New materials either usable as electrodes or electrolyte components has been reported too (Peng and Chen, 2009). Related phenylarsonates with diverse substituents at the ortho, meta or para position, have widely been investigated, though hydrogen phenylarsonate compounds are most scarcely encountered in the literature (Smith and Wermuth, 2010; Reck and Schmitt, 2012; Yi et al. , 2009; Padalwar and Vidyasagar, 2016; Padalwar et al. , 2013; Reddy et al. , 2006). Indeed, several singly protonated phenylarsonate crystal compounds are reported to date, according to the Cambridge Structural Database CSD (Smith and Wermuth, 2010; Reck and Schmitt, 2012; Yi et al.
) occurs on the catalyst's body during the fluidized bed catalytic cracking process and evolves gradually over time. Since the content of metal pollutants depend on the duration of a catalytic run, two representative examples, ACM-101-M200 and ACM-101-M400, were examined to unveil any morphological transformation caused by cumulative deposition of poisoning contaminants. As shown in Fig. 2c  and d , the catalyst body preserves its pristine shape regardless of the level of metal content. The ). c Aluminum content (molar fraction) in the framework based on the calculation involved unit cell size parameters and NH 3 -TPD data for pristine zeolite taken as acidity reference (see ESI †). d Compared to aluminum fraction in pristine zeolite calcined at 550 °C for 5 h (1 °C min -1 ). Table  7  Textural properties of samples obtained from N 2 uptake measurements at 77 K Samples S BET (m 2 g -1 ) S ext (m 2 g -1 ) V total (cm 3 g -1 ) V micro (cm 3 g -1 ) V meso (cm  Catalysis Science & Technology Paper absence of nodes or lumps, typically associated with a localized agglomeration of metal oxides on the surface of the catalyst particle, indicates a homogeneous distribution of the poisons over the catalyst body.
Next, we focus on the spent catalyst that contains the largest metal content (ACM-101-M400) to evaluate the distribution of various chemical elements. SEM-EDS data were acquired on a particle cross-section embedded in a conductive resin. Elemental maps were computed from the integration of the K or L fluorescence lines of the most concentrated elements (Si/Al/Fe/P/Ti). Those chemical maps are displayed on Fig. 3a  together with the original micrograph acquired with a back-scattered electron detection. The first observation is related to the morphology of the particle which highlights that the main body corresponds to a fusion of three spherical particles embedded in each other. This suggests that the smallest drops of suspension sprayed by the nozzle are dried before leaving the spraying area, so there is a chance that a subsequent drop of liquid may spread over the surface of these dried particles, increasing the overall particle size.
Acknowledgments: The authors would like to acknowledge financial support from the  Royal Society-Foreign, Commonwealth & Development Office (FCDO) Africa Capacity Building Initiative (ACBI) Programme  (Grant  AQ150029 ), the  Council for Scientific and Industrial Research (CSIR) , and the  South African Department of Science and Innovation (DSI)  for research activities under HySA Infrastructure (Grant No. CNMH20X ) and the  South Africa-France PROTEA  Programme which is a bilateral incentive programme dedicated to the strengthening of research collaborations between the two countries (Project No. CNMH02X ).
Acknowledgements Q. Y. thanks  NSFC  (Grant No. 22071095 ),  Technology Innovation Commission of Shenzhen Municipality  ( 20200925152822004 ),  SUSTech and Julius-Maximilians-Universität Würzburg  for financial support. L. M. is a senior member of the  Institut Universaire de France. The Humboldt foundation is acknowledged for support as well as CalMip for a generous grant of computing time. We are grateful to  Dr. Rüdiger Bertermann  for the fruitful discussion on NMR spectroscopy of paramagnetic compounds. Open Access funding enabled and organized by Projekt DEAL.
28). Full experimental details can be found in the supplementary information. Dye adsorption experiments 10 mg/L of aqueous Methylene Blue (MB) and Methyl Orange (MO) solutions were prepared by dissolving the dyes in ultrapure water. The synthesized MOFs were dried overnight in vacuum oven at 100°C and left in the desiccator until used. For the adsorption kinetics study, exactly 10 mg of absorbent was mixed with 10 mg/L dye solution (50 mL) in the orbital shaker at 160 rpm in dark environment. After the desired adsorption time, the resultant solutions were ltered through syringe lter (PESO, 0. 45 µm) to obtain clear ltrates for UV-vis measurements. The kinetics data are tted to pseudo rst-order and pseudo second-order. Maximum adsorption capacity was determined through undergoing dye adsorption in 50 mL solutions at varying concentration solutions (5, 10, 25, 50, 100, 150 mg/L) for 24 hours.
Acknowledgements This work has been partially supported by  University of Rouen Normandy ,  INSA Rouen Normandy , the  Centre National de la Recherche Scientifique (CNRS) ,  European Regional Development Fund (ERDF) ,  Labex SynOrg  ( ANR-11-LABX-0029 ),  Carnot Institute I2 C, the graduate school for research XL-Chem  ( ANR-18-EURE-0020 XL CHEM ), and  Region Normandie. F. P. -C. , L. R. and T. B. thank the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation programme  (grant agreement no. 758710 ). F. P. -C. thanks the  Region Normandy for a doctoral fellowship  ( RIN 50% program ).
995. Carryover was evaluated for both methods by injection of two consecutive solvent blanks after the most concentrated calibration level and was <5% for all analytes in the LC method and below detection in the SFC method (data not shown). The carryover of internal standards was evaluated by injection of a solvent blank after the lowest calibration level in both techniques. For both methods, no signal from the internal standards was detected. Instrumental accuracy showed good results at all tested concentration levels in both methods, with only a few compounds exceeding the acceptable limits in the LC method. Notably, 9-and 13-HODE, 11(E)-10-KOME, 11(E)-10-HOME, and 9-OH-12,13-EpOME had high deviation from the theoretical concentration value at both low and medium concentrations (300-800%, Table  S13 ).
No significant difference was observed with the exception of 5,6-EpODEs, which had a 12-25% degradation after 24 h. The stability of IS was evaluated by area comparison, showing 11-31% signal enhancement at 48-96 h, compatible with day-byday variability in ESI and observed also for the analytes at the same time points (Table  S16  for internal standards, data not shown for analytes). Analysis of Octadecanoids in Human Plasma. To evaluate the stability and precision of the complete analytical procedure over the course of analysis in a typical study, 12 replicates of spiked plasma reference material were injected at regular intervals during a longer sequence consisting of 151 mouse plasma samples. All target octadecanoids were quantified by SFC-MS/MS and LC-MS/MS to evaluate the stability of the obtained concentration values and the precision of the two methods.
■ ACKNOWLEDGMENTS This article is dedicated to  Dr. Bruce Hammock , whose pioneering work in leukotoxins set the stage for this study of octadecanoids. We acknowledge support from the  Swedish Heart Lung Foundation  ( HLF 20190017 ,  HLF 20190421 ,  HLF 20200693 , and  HLF 20210519 ) and the  Swedish Research Council  ( 2016-02798  and  2018-00520 ). B. Z. acknowledges the  H2020 ITN consortium ArthritisHeal  (grant agreement no. 812890 ) for funding. C. E. R. and G. S. K. were supported by the intramural programs of the  National Institute on Aging (NIA)  and  National Institute on Alcohol Abuse and Alcoholism (NIAAA) ,  National Institutes of Health (NIH).
Funding Our work was supported by the Société Francophone du Diabète (SFD-2013, SFD 2022), the Fondation pour la Recherche Médicale (FRM-DEQ20130326518 and FRM-DEQ20150331744) and by the Programme Inter-Cochin (Institut Cochin, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Paris). Hasanain Al-Mukh held a PhD grant from the CORDDIM-Région Ile-de-France and was also funded by the Fondation pour la Recherche Médicale.
162 These copolymers formed cylindrical micelles by CDSA, with the shortest cylinders being obtained for the most hydrophilic corona (PDMA) as predicted by the software Molinspiration. When applied to PDMAEMA, a charged polymer with antimicrobial activity, spherical or platelet morphologies of different sizes were obtained. It was found that small platelets showed the highest antibacterial activity compared with larger platelets or spherical morphologies. 163 PLLA-b-PDMAEMA nanoparticles with different shapes were also exploited to tune the adhesion properties of nanocomposite hydrogels. 164 It was shown that loading nanoparticles with platelet morphology into In most examples of CDSA, a water-miscible organic solvent is necessary to induce the living growth of nano-objects. Solvent switch or evaporation is therefore required to obtain aqueous suspensions of the nano-objects, which may limit their controlled growth and affect their morphology.
Using this selection criteria, a total of 842 proteins were identified (Fig. 2a ). Of these, 50% (409) had a known (339) or predicted (70) mitochondrial status in the Mitominer database  19  , while the remaining were nonmitochondrial (322), or had an unspecified status (111), which can be expected given that crude mitochondrial fractions were used for this analysis. Since these likely contained residual amounts of ncOGT and fOGA outside mitochondria, we sought to determine whether the impact of NButGT on protein O-GlcNAcylation varied according to the localization of these proteins. As shown in Fig. 2b , treatment with NButGT predominantly increased O-GlcNAcylation of mitochondrial proteins (i. e. known + predicted mitochondrial status) compared to non-mitochondrial proteins, indicating that the reconstitution assay was effective at targeting the intra-mitochondrial O-GlcNAcylation system.