dataesr/scientific-paragraphs-categorization huggingface dataset:
■ ACKNOWLEDGMENTS The present work is supported by the  Japan Society for the Promotion of Science (JSPS)-French Ministry of Foreign Affairs  ( MAE) Sakura Program  ( 34148TB ). The authors thank  Diamond Light Source  for beamtime (MT11225) on the I13 Diamond- Manchester Branchline  and the staff there for all of the assistance with data collection. This work was made possible by the facilities and support provided by the Diamond-Manchester Collaboration and the  Research Complex at Harwell , funded in part by the  Engineering and Physical Sciences Research Council (EPSRC)  ( EP/I02249X/1  and  EP/ M023877/1 ). Yasuaki Tokudome  appreciates financial support from the  Hosokawa Powder Technology Foundation. The present work is partially supported by  JSPS Grants-in-Aid for Scientific Research (KAKENHI)  and by a research grant from the  Foundation for the Promotion of Ion Engineering.
Acknowledgements We thank the  High Performance Cluster Computing Centre, Hong Kong Baptist University , which receives funding from the  Research Grants Council, University Grants Committee  of the HKSAR and  HKBU. This work was supported in part by project no. 9041650 of the  Research Grants Council of HKSAR  and the  Scientific Research Foundation for the Returned Overseas Chinese Scholars, Ministry of Education of China  (Grant No. [2013]693). MAVH and YLZ were supported in part by the  HKBU Strategic Development Fund. CM acknowledges support from  HKBU's Sabbatical Visitor scheme  and partial support from the  HKBU Strategic Development Fund. KH acknowledges support from  HKBU 's  Distinguished Scholar scheme  and partial support from the  HKBU Strategic Development Fund.
Due to the high NMR relaxation rate of the 81 Br nucleus, its spectrum is significantly distorted by the ringing (electronic and/or electroacoustic) of the probe. 38, 39 In order to overcome this problem we have used a composite pulse sequence,  40, 41  with a 90 degree pulse of 10 µs and a recycling delay of 200 ms. The number of scans ranged from 2048 to 8192 depending on the sample. The spectra were fitted using DMFIT software. 42.
ACKNOWLEDGMENTS This study was supported by the  Slovenian Research Agency fund (ARRS)  through the Program  0103-0201 ,  NIH USA  grant  GM063592. The authors thank  Mojca Seručnik  at the  University of Ljubljana  for help with sample preparation and  Francois Ribot  at the  College de France  for discussions and access to NMR spectrometers. The molecular dynamics calculations were in part performed on clusters of  Ukrainian Academic Grid  and the  Faculty of Chemistry and Chemical Technology of the University of Ljubljana.
Electrochemistry The electrochemical properties of BTBT 8 and of the substituted BTBT derivatives 1a, 2a, 3a, and 4-7 were investigated, in dichloromethane, by cyclic voltammetry (CV). Their electrochemical data are collected in Table  2  together with those of unsubstituted BTBT, for comparison. Cyclic voltammetry curves are given in Supporting Information. All BTBT derivatives investigated in this study present at least one reversible oxidation process which produces radical cation species. However, the substitution of the BTBT core at positions 2 and 7 by electron donating groups such as alkoxy, thioalkyl or amino group, lead to a second oxidation process at higher potential corresponding to the formation of dication species. Unfortunately, this second process is only perfectly reversible for compound 2a.
reagents 2,7-diiodo-[1]benzothieno[3,2-b][1]benzothiophene (9), 58 2,7-dibromo-[1]benzothieno[3,2- b][1]benzothiophene (10), Electrochemistry: Dichloromethane (HPLC grade) and tetra-n-butylammonium hexafluorophosphate (TBAP, electrochemical grade, Fluka was recrystallised from ethanol). Cyclic voltammetry (CV) was performed in a three-electrode cell equipped with a platinum millielectrode, a platinum wire counterelectrode and a silver wire used as a quasi-reference electrode. The electrochemical experiments were carried out under a dry and oxygen-free atmosphere (H 2 O < 1 ppm, O 2 < 1 ppm) in CH 2 Cl 2 with TBAP (0. 1 M) as the support electrolyte. The voltammograms were recorded on a potentiostat/galvanostat (BioLogic -SP150) driven by the EC-Lab software with positive feedback compensation.
Crystal structure: X-ray diffraction data for crystals of compounds 2a, 2c were collected at 123 K with graphite monochromated Cu kα radiation (λ = 1. 5418 Å) using an Oxford Diffraction Gemini S instrument. Data for 2b was collected at DIAMOND synchrotron radiation source by National Crystallographic Service, University of Southampton. All non-hydrogen atoms were refined anisotropically. Hydrogen atoms were included in calculated positions utilizing riding modes. All structures were refined to converge against F2 using the SHELXL-97 program. Detailed crystallographic data with refinement parameters are listed in complete crystallographic information files (CIF) and are available in the Supporting Information. High Performance Liquid Chromatography (HPLC): An Agilent HP 1100 system equipped with a Supelco HPLC column (150 mm x 4.
ACKNOWLEDGEMENTS This work has been financially supported by a concerted research action of the  French Community of Belgian  ( ARC  project  N°20061 ), by the  Walloon Region  ( WCS  project  N°1117306 ), by the  European Commission / Walloon Region (FEDER -Smartfilm   RF  project), by the  Interuniversity Attraction Pole program  of the  Belgian Federal Science Policy Office  ( PAI 7/05 ), the  Programme d'Excellence de la Région Wallonne  ( OPTI2MAT  project), by the  Belgian National Fund for Scientific Research (FNRS ,  POLYGRAD  project  N°22333186 ), by the  ERC  project  SUPRAFUNCTION  ( GA-257305 ), by the  EC Marie-Curie projects IEF-MULTITUDES  ( PIEF-GA-2012-326666 ) and  ITN iSwitch  (GA no. 642196 ), by the  Agence Nationale de la Recherche  through the  LabEx  project  Chemistry of Complex Systems  ( ANR-10-LABX-0026_CSC ), and by the  International Center for Frontier Research in Chemistry  (icFRC).
Raw measurement data are included in the supplementary data (see blinking time trace csv files, available from URL). The laser frequency was chosen to maximise the fluorescence, indicating resonance with the SiV -optical transition. The switching rates (R on , R off ) were determined from the typical durations of "on" and "off" events in these time series. A double-threshold technique was used to identify the "on" and "off" events, since in general the switching contrast was smaller than the noise amplitude as seen in Figure  4(a). In this technique the switch-on threshold was higher than the switch-off threshold. A preliminary threshold T i was manually chosen to start this process, shown by the dashed blue line in Figure  4 (a). The mean I off and standard deviation σ off were Here the first minute of data 30 nW excitation power on a SiV -line at 736.
612 nm is shown as a typical example, with the switching thresholds T on and T off illustrated for k = 2. 5. The raw measurement data are included in the supplementary data (see blinking time trace csv files, available from URL). (b) Histograms of duration for the "on" and "off" intervals gave exponential distributions, from which a characteristic time can be determined (and hence switching rate). The histogram for the "on" events is shown for the 30 nW data and thresholds of k = 2. 5. (c) The "on" and "off" rates (R on and R off ) both increase with excitation laser intensity, with linear and quadratic fits illustrated respectively. The dashed line is the best fit for a constant R on. The horizontal error bars correspond to a 15% uncertainty in determining the laser power applied to the SiV -centre, and the vertical error bars represent the uncertainty in judging a switching event.
Acknowledgements The authors thank  W Gawlik  for helpful discussions. Experiments performed for this work were operated using the Qudi software suite, available from https://github. com/Ulm-IQO/qudi. This work was funded from  ERC project BioQ ,  EU  projects SIQS and EQUAM,  DFG  ( SFB/TR21  and  FOR 1493 ), Volkswagenstiftung and BMBF. ABK and AK acknowledge support of the  Carl-Zeiss Foundation. AK also acknowledges support from  Wissenschaftler-Rückkehrprogramm GSO/CZS ,  IQST , and  DFG. DR acknowledges support of the  NATO 'Science for Peace ' grant ( CBP. MD. SFP 983932 ) and  KNOW  project. VD thanks the  Russian Foundation for Basic Research  (Grant No. 15-03-04490 ) for financial support.
2014; Huo et al. 2010; Zawadzka et al. 2002; Zawadzka et al. 2016; Zawadzka et al. 2013; Zhang et al. 2015; Yuan et al. 2012). In this way, many studies have been published to understand the reactivity of this derivatives in different solvents  (Himmi et al. 2008 ) and to determine the most stable conformation in acidic and alkaline aqueous solutions  (Saylam et al. 2014). But up today only few structural data on 8-hydroxyquinoline derivatives have been published, showing, for example dependence of the molecule structure on the synthesis procedures of 8-hydroxyquinoline derivatives  (Pearson et al. 1967; Gershon et al. 1969; Collis et al. 2003). In this study, we focus on a new one of 8-hydroxyquinoline derivatives named 5-(ethoxymethyl)quinolin-8-ol (5-EMQO) (Scheme 1). This molecule was synthesized and analyzed by different spectroscopic methods.
2a. Relevant crystallographic data are summarized in Table  2. The parameters in the CIF form are available as Electronic Supplementary Information from the Cambridge Crystallographic Database Centre (1029560). The molecule exibited non-planar structure, the dihedral angle calculated between the methylquinolin-8-ol group and other part of the molecule is 77. 08°(Fig. 2b ). The stabilized crystal packing is mainly governed by hydrogen bonds (Fig. 3 ) and p-p stacking interactions (Fig. 4 ). The intramolecular hydrogen bonds observed in the structure involves the OH functional group, this latter presents strong interactions in many solvents, modify physical properties at room temperature  (Kadiri et al. 1994; Cazeau-Dubroca 1991)  and enhancing the biological activity of the molecule. Weak intra and intermolecular hydrogen bonds O-HÁÁÁN and C-HÁÁÁO types are detected in the structure involving adjacent molecules in different plans, with a gap from 0.
Acknowledgments: This work was performed, in partnership with the SAS PIVERT, within the frame of the  French Institute for the Energy Transition (Institut pour la Transition Energétique (ITE) P. I. V. E. R. T. (www. institutpivert. com))selected as an  Investment for the Future ("Investissements d Avenir "). This work was supported, as part of the Investments for the Future, by the  French Government  under the reference  ANR-001-01. Huiling Lu  acknowledges the  Chinese Scholarship Council  for the financial support of her PhD grant.
Computational methods Ab initio calculations have been done with the TURBOMOLE program package (v6. 3) 15 making use of the resolution-of-identity approximation. 16 The equilibrium geometries and the vibrational frequencies in the ground S 0 and excited electronic states (S n , T n ) have been calculated at the coupled-cluster CC2 level  17  with the correlation-consistent polarized valence double-zeta aug-cc-pVDZ basis set augmented with diffuse functions. 18 The Franck-Condon analysis have been performed using PGOPHER software. 19.
Acknowledgments: Financial support of the  Région Champagne-Ardenne  (PhD fellowship for I. A-S. ),  CNRS  and  University of Reims  is gratefully acknowledged. Acknowledgments: Financial support of the  Région Champagne-Ardenne  (PhD fellowship for I. A-S. ),  CNRS  and  University of Reims  is gratefully acknowledged. Acknowledgments: Financial support of the  Région Champagne-Ardenne  (PhD fellowship for I. A-S. ),  CNRS  and  University of Reims  is gratefully acknowledged.
1 vs. 2). TMPLi in hexane and THF (0. 5 eq. wrt Li) was added to CuSCN, allowing the isolation of colourless prismatic crystals (Scheme 3). NMR spectroscopy revealed that, as for 9, these crystals incorporated TMP and Lewis base in a 2 : 1 ratio and a SCN group (δ 141. 5 ppm by  13  C NMR spectroscopy). Corroboration of the last point came from IR spectroscopy, with two peaks seen at 2050. 4 (s) and 1998. 0 (m) cm -1 (Fig. S3 , † cf. 2064. 6 and 1996. 6 cm -1 in 9 2 ), the signals being replaced by a peak at 2105. 7 cm -1 after air exposure for 30 s. X-ray diffraction was undertaken, with data revealing a dimer based on (TMP) 2 Cu(SCN)Li 2 (THF) 10. However, in contrast to the structure of 9 2 , 10 2 exhibited a novel boat conformation (Fig. 4 ) based on the aggregation of two crystallographically independent monomers (of which one will be representatively discussed) and in which the geometry at   sulfur is fundamentally altered relative to that seen in 9 2.
23 Crystallographic data have been deposited with the Cambridge Crystallographic Data Centre as supplementary publications CCDC 1429486 (8 2 ), 1429485 (9 2 ), 1429483 (10 2 ) and 1429484 (11 2 ). Compounds 15c and 16c. Samples were studied using graphite monochromated Mo-Kα radiation (λ = 0. 71073 Å). X-ray diffraction data were collected using an APEXII, Bruker-AXS diffractometer at T = 150(2) K (15c) or a D8 VENTURE Bruker AXS diffractometer at 294(2) K (16c). The structures were solved by direct methods using the SIR97 program,  33  and then refined with full-matrix least-square methods based on F 2 (SHELX-97)  34  with the aid of the WINGX program. 35 Nonhydrogen atoms were refined with anisotropic atomic displacement parameters. H-atoms were finally included in their calculated positions.
Acknowledgements This work was supported by the  U. K. EPSRC  through grant  EP/ J500380/1  (A. P. ) and the  Ministère de l'Enseignement Supérieur et de la Recherche scientifique Algérien  (M. H. ). F. M. thanks the  Institut Universitaire de France  and also  Thermo Fisher  for the generous gift of 2,2,6,6-tetramethylpiperidine. Thanks go also to  Dr Andrew Bond  ( University of Cambridge ) for help with crystallographic analysis. Detailed supporting data for this paper are available at the University of Cambridge data repository (see https://www. repository. cam. ac. uk/handle/ 1810/252480). These include some data in the file formats fid (NMR spectroscopic data) and cif (crystallographic data), which can be opened using the programs TopSpin 3. 2 (or similar) and Mercury CSD 3. 5 (or similar), respectively.
We found that 64 promoters were significantly and differentially expressed during growth in the presence of ampicillin relative to the untreated controls (Table  1 ; Figure  S1 ). We clustered the identified promoters, first as a function of the growth phase in which the specific regulation starts and second according to the regulation type observed, i. e. , higher or lower than the untreated control. Most of these promoters were upregulated, i. e. , 26 of 27 and 21 of 37, during the first and the second growth phases, respectively. The functions of the genes (EcoCyc E. coli database, http:// ecocyc. org/) whose expression was identified as being specifically altered by ampicillin provided information on the temporal changes in the physiological states of the treated cells (Table  1 ). During the first growth phase, the genes that were induced include the mscS gene, which codes for a mechanosensitive channel; the msbB, fabR, pldB and yfeY genes, which are involved in membrane synthesis; and htpX, which is involved in the degradation of misfolded proteins in the periplasm, suggesting that the treated cells attempt to repair the ampicillin-induced damage of the cell wall.
Energy Metabolism and Translation Are Increased in Ampicillin-Treated Cells The gene expression analysis suggests that cells exposed to 50% MIC of ampicillin increased the energy metabolism (Figure  1F ; Table  1 ). We quantified ATP, ADP, and AMP using high-performance liquid chromatography (HPLC) in wildtype (WT) cells during growth with or without ampicillin and calculated the adenylate energy charge (AEC) using the Atkinson equation: ( [ATP] + 1/2[ADP]) / ([ATP] + [ADP] + [AMP]). AEC is a measure of the amount of metabolic energy transiently stored in the adenine nucleotide pool  (Chapman et al. , 1971). The AEC ratio of treated and untreated WT cells increased over time (Figure  1B ; Table  S1 ). This result is consistent with an increase in energy production for treated cells that was suggested by the gene expression data (Figure  1F ; Table  1 ).
ATP, ADP, AMP, ppGpp, and Amino Acid Quantification Overnight cultures were diluted 1/300 in fresh LB medium with or without 1 mg/mL of ampicillin and incubated at 37 C. At different time points, approximately 10 10 cells were harvested. For ATP, ADP, AMP, and ppGpp quantification, the extraction was performed as previously described  (Huang et al. , 2003) , except that trichloroacetic acid (TCA) was replaced by PCA to deproteinize cells. For reversed-phase HPLC (Shimadzu HPLC system interfaced with LabSolution software), samples were injected onto a 250 3 4. 1 mm PRP-1 column (Hamilton) at 50 C. The mobile phase composition for the gradient system was 25 mM KH 2 PO 4 , 25 mM K 2 HPO 4 , and 10 mM tetrabutylammonium hydroxide (pH 7. 0) for mobile phase A and 100% MeOH for mobile phase B. The gradient program was 0-8 min 0% phase B, 8-62 min 0%-30% phase B, and 62-70 min 30% phase B, and the initial conditions (100% phase A) were then maintained for 30 min.
ACKNOWLEDGMENTS We thank  Arnaud Gutierrez  for inspiring discussions;  Odile Bouvet  for helpful advice;  Christophe Herman ,  Martin Ackermann , and  Alejandra Manjarrez  for critical reading of the manuscript;  A. Couve ,  C. Duwat , and  C. Galbert  for technical help;  Linh-Chi Bui  and the technical platform  BioProfiler-UFLC, Paris , for the HPLC analysis; and  Elke Deuerling ,  Kim Lewis , and  Christophe Beloin  for generous gift of strains. This work was supported by grants from  Idex  ( ANR-11-IDEX-0005-01  and  ANR-11-LABX-0071 ),  Idex-Sorbonne Paris Cite , the  AXA Research Fund, Merieux Research, and DIM Malinf-Ile de France. Received: May 2, 2016 Revised: July 18, 2016 Accepted: August 29, 2016 Published: September 27, 2016.
Acknowledgments: This work was funded by grants from the  CNRST-Morocco, CNRS-France , the  University Mohammed V, Rabat and University of Nice Sophia Antipolis. Also, it was supported by  Campus France PHC Toubkal  ( 30330ZF ,  MA/14/304 ). The authors are indebted to  Philippe Belmont  for his invitation to present this work in the Molecules topical issue on Heterocycles. Acknowledgments: This work was funded by grants from the  CNRST-Morocco, CNRS-France , the  University Mohammed V, Rabat and University of Nice Sophia Antipolis. Also, it was supported by  Campus France PHC Toubkal  ( 30330ZF ,  MA/14/304 ). The authors are indebted to  Philippe Belmont  for his invitation to present this work in the Molecules topical issue on Heterocycles.
The STs reside and are strictly organized in the trans-Golgi network of eukaryotic cells as type II transmembrane proteins with a similar topology showing a short N-terminal cytoplasmic tail, a single transmembrane domain, a stem domain and a large C-terminal catalytic domain oriented in the Golgi lumen  [42]. The STs use CMP-β-Neu5Ac, CMP-β-Neu5Gc or CMP-β-Kdn as activated sugar donors for the sialylation at terminal positions of oligosaccharide chains of glycoconjugates. These STs are categorized into 4 families (ST6Gal, ST3Gal, ST6GalNAc and ST8Sia)  [41, 43]  found in the GT-29 of the Carbohydrate-Active enZYme (CAZy) database  [44]  and named according to the glycosidic linkage formed and the monosaccharide acceptor  [45]. Each family catalyzes the formation of different glycosidic linkages, α2-3, or α2-6 to the terminal Gal residue in Nor O-glycans, α2-6 to the terminal GalNAc residue in O-glycans and glycolipids and α2-8 to terminal SA residues in Nor O-glycans or glycolipids).
Genome-Wide Search of STs Genes Decline or Expansion? A general strategy using conventional BLAST search approaches  [54]  was adopted for homologous ST sequences identification in the transcriptomic and genomic databases like NCBI or ENSEMBL to reconstruct the animal ST genes repertoire and assign orthologies  [39]. Although the vertebrate ST amino acid sequences show very limited overall sequence identity (around 20%), conserved peptide motifs have been described within their catalytic domain, which are very useful hallmark for ST identification. Different sets of protein regions considering three levels of amino acid sequence conservation have been described in the past that are retrieved from multiple sequence alignments (MSA) of (1) all animal ST called sialylmotifs L (large), S (small), III and VS (very small); (2) each family of ST, called family motifs a, b, c, d and e; (3) in each vertebrate subfamily  [55].
Molecular Phylogeny of β-Galactoside α2,3/6-Sialyltransferases Molecular phylogeny, with the construction of phylogenetic trees has been used to get further insight into the orthology and structure/function relationships of the identified β-galactoside α2,3/6-sialyltransferase sequences. As a first step, multiple sequence alignments (MSA) using predicted protein sequences, clustal Omega or MUSCLE algorithms evidenced several informative amino acid sites in the catalytic domain of ST to construct phylogenetic trees  [39]. Among these conserved motifs, sialylmotifs and family motifs detection helped establishing the global evolutionary relationships between the identified ST sequences and enabled sequence-based prediction of their molecular function. Phylogeny of β-galactoside α2,3/6-sialyltransferase sequences was reconstructed using various methods implemented in the Molecular Evolutionary Genetics Analysis (MEGA) software and the reliability of the branching pattern was assessed by the bootstrap method  [39, 62].
The topology of the trees indicated that the ST6Gal and ST3Gal sequences identified in invertebrates are orthologous to the common ancestor of vertebrate subfamily members as they branch out from the tree before the split into vertebrate ST subfamilies with the exception of the ST3Gal members of the GRx group, which disappeared during vertebrate evolution  [38, 53]. The molecular phylogeny of β-galactoside α2,3/6-sialyltransferases is displayed in Figure  3  using iTOL  [63]. ). In both cases, the phylogenetic trees were inferred using the Maximum Likelihood method based on the Whelan and Goldman method with options G (gamma distribution) and I (Invariant sites present). Alignments were performed using Clustal Omega, available at the site http://www. ebi. ac. UK/Tools/msa/clustalo/ (Data S1).
Evolutionary analyses were conducted in MEGA6. The trees were re-drawn using iTOL 3. 2  [63]  available at the URL http://itol. embl. de/. (A) ST3Gal tree was obtained from 124 sequences and 228 positions in the final data set; (B) ST6Gal tree was inferred from 50 sequences and 256 positions and 50 sequences in the final data set. ). In both cases, the phylogenetic trees were inferred using the Maximum Likelihood method based on the Whelan and Goldman method with options G (gamma distribution) and I (Invariant sites present). Alignments were performed using Clustal Omega, available at the site http://www. ebi. ac. UK/Tools/msa/clustalo/ (Data S1). Evolutionary analyses were conducted in MEGA6. The trees were re-drawn using iTOL 3. 2  [63]  available at the URL http://itol. embl. de/. (A) ST3Gal tree was obtained from 124 sequences and 228 positions in the final data set; (B) ST6Gal tree was inferred from 50 sequences and 256 positions and 50 sequences in the final data set.