dataesr/scientific-paragraphs-categorization huggingface dataset:
These specific fluorescence coefficients describe only the part of the fluorescence that changes due to DNA binding. The software performs numerical integration of a system of ordinary differential equations with subsequent nonlinear least-squares regression analysis. In the fits, we optimized all relevant rate constants for the forward and reverse reactions as well as the specific molar response factors for all the intermediate complexes. During the data processing, the kinetic information was obtained from temporal behavior of the fluorescence intensity, not from the amplitudes of the specific signal contributions. The response factors for different conformers resulting from the fits were not used for determination of the equilibrium constants but rather provided additional information on the fluorescence intensity variations in different complexes and conformers.
Homology modeling and sequence alignment A model of the structure of hSMUG1 was built by homology modelling in the SWISS-MODEL environment using the structurebased alignment (http://swissmodel. expasy. org). 27 Structures of GmeSMUG1 from Geobacter metallireducens (Protein Data Bank codes 5H98 and 5H9I)  28  and xSMUG1 from Xenopus laevis (Protein Data Bank codes 1OE4 and 1OE5) 5 served as templates. For each model generated based on the selected templates SWISS-MODEL provides the model coordinates along with relevant information to assess the modelling process and to expect the accuracy of the model: the target-template alignment, a step-by-step modelling log, information about the oligomeric state, binding the ligands and cofactors, as well as QMEAN model quality estimation. The ''good'' models, which are comparable to the experimental structure, reach QMEAN value À0.
For this purpose, the intrinsic protein fluorescence from tryptophan residues and DNA fluorescence from the incorporated reporters were recorded by the stoppedflow technique. The hSMUG1 molecule contains four Trp residues: Trp62, Trp107, Trp142, and Trp251. Because no structure of hSMUG1 is available, we used the high sequence homology among hSMUG1, xSMUG1, and GmeSMUG1 (Fig. 1A ) to obtain a structure of the hSMUG1-DNA complex by homology modelling. It follows from the structures of the xSMUG1-DNA complex  5  that the enzyme bound the ends of the DNA duplex. Therefore, these data do not elucidate the lesion recognition state of the enzyme and DNA. Nevertheless crystal-soak experiments with free Ura bases indicate the possible position of the damaged base in the active site of the enzyme. Structural superposition of the noncovalent complex of xSMUG1 with a Ura base (Protein Data Bank code 1OE5)  5  and the model structure of hSMUG1 revealed that Trp62, Trp107, and Trp142 are located inside the protein globule and far away (at least 11.
Interaction of hSMUG1 with undamaged DNA The parameters for binding of hSMUG1 to undamaged DNA were obtained by recording the changes of Trp fluorescence and FRET signals using the C-ligand and C-FRET-ligand, respectively. When the C-aPu-ligand was studied, the changes of aPu fluorescence were not observed, indicating the absence of DNA double helix distortion near the aPu residue. In the kinetic curves obtained during the interaction of hSMUG1 with the undamaged C-ligand, a fast single phase of an increase in the Trp fluorescence intensity up to 5 ms is seen (Fig. 2A ). When hSMUG1 interacts with the C-FRET-ligand (Fig. 2B ), a fast increase in the FRET signal is observed. These data most likely correspond to collisional nonspecific binding of the enzyme to DNA, resulting in the movement of the intercalating loop (239-249) with a change of the Trp251 environment and shielding of FAM fluorescence from the quenching with BHQ1.
Acknowledgements This work was supported partially by a  Russian Governmentfunded project  (No. VI. 57. 1. 2 , 0309-2016-0001 ),  SB RAS Comprehensive Scientific Program  (No. II. 2P/VI. 57-6 , 0309-2015-0025 ), and grants from the  Russian Foundation of Basic Research  (numbers  16-04-00037  and  15-04-00467 ). The part of the work with Trp, aPu, and FRET detection combined with stopped-flow kinetics was specifically funded by  Russian Science Foundation  grant  16-14-10038.
gondii, 1 for H. pylori, 2 for HSV-1, 2 for HSV-2, and 2 for VZV; (ii) 5 lysates: CMV, T. gondii, H. pylori, HSV-1, and HSV-2; (iii) 2 mixes: one of 5 CMV Ags and one of 2 B. burgdorferi Ags; (iv) 2 negative controls: PBS, and PBS with 0. 1% bovine serum albumin (BSA). For hybridization, IgG concentrations were adjusted to 400 µg/mL for serum and from 50 to 200 µg/mL for purified mc IgG. 80 µL of samples were incubated for 2 h at RT. After washing, slides were incubated with a labeled secondary Ab (0. 2 µg/mL DylightTM 680 Labeled Goat antihuman IgG (H + L), from SeraCare, Milford, MA, USA; Ref. 5230-0342). Fluorescence signal, detected with the Odyssey infrared imaging system scanner at 21 µm resolution (LI-COR Biosciences, NE, USA) was quantified using the GenePix ® Pro 4 Microarray Acquisition & Analysis Software (Molecular Devices, Sunnyvale, CA, USA).
statistics Data analysis was performed by GraphPad Prism 6. 01 software. Patient parameters were expressed as medians and ranges, or/ and means ± SEM. The chi-2 test was used for categorical variables. For continuous variables (n ≥ 30) the Student t-test or the one-way ANOVA followed by Tukey's post hoc test were used. For continuous variables (n < 30), a normality test was systematically performed for each group. When parametric conditions were fulfilled, a Student's t-test or a one-way ANOVA followed by Tukey's post hoc test was performed. For non-parametric conditions, a Mann-Whitney U test or a Kruskal-Wallis test followed by Dunn's post hoc test was performed. The tests used are indicated in Figure and Table legends. A P value below 0. 05 was considered statistically significant.
Purification of mc and pc iggs According to the patients' data, in the present cohort the mc IgG represented 40. 8-87. 7% (median: 70. 8%) of total IgGs in MGUS, and 49. 7-95. 5% (median: 86. 3%) in MM. These percentages represent estimations, since mc IgGs and total IgGs are not measured by the same techniques. However, the data indicated that almost all MGUS and MM patients in the cohort produced some level of pc IgGs, estimated to represent ~30 and ~14% (medians) of total IgGs in MGUS and in MM, respectively. After electrophoresis of the 148 sera on agarose gel, mc IgGs and pc IgGs from each patient were separated. The relevant bands were collected, and proteins were eluted from the gel (Figure  1A ). The purity of IgGs was confirmed by immunoblotting after isoelectophoresis. Examples of the efficiency of this method are illustrated in Figure  1B  and Figure  S1  in Supplementary Material.
characteristics of Patients In this retrospective study, we analyzed 148 patients presenting with mc IgG and diagnosed with MGUS (n = 68), SM (n = 6) or MM (n = 74). Clinical data were available for 133/148 patients (59 MGUS, 6 SM, 68 MM). The biological and clinical characteristics of the 133 patients are shown in Table  1. The median age for MGUS, SM, and MM patients at the time of diagnosis was similar, 67. 0, 67. 1, and 63. 6, respectively. The male/female ratio was 55. 9% for MGUS, and higher for SM and MM patients: 83. 3 and 60. 3%, respectively (differences not significant, Chi-2 test). The International Staging System (ISS) and Durie-Salmon Staging (DSS) scores indicated that 32. 7% of MM patients presented with ISS stage III at the time of diagnosis (DSS stage III: 44. 6%). In MM, mc IgG were studied either at the time of diagnosis (17 patients; 23%), or during or after treatment (40 patients; 54%); for 17 patients (23%), information was not available.
Simulation Results The MIMO-OFDM system described in Chapter 8 forms the basis of the system simulations. 1296 subcarriers are used in the frequency range from 4 to 30 MHz. Each subcarrier is adaptively modulated, according to the adaptive modulation algorithm described in Section 9. 3. 1. The target average BER of the uncoded system is adjusted to 10 -3. An additional FEC might easily reduce this BER. The bitrate is obtained as the sum of the number of bits assigned to all subcarriers divided by the OFDM symbol length. This bitrate describes the raw physical layer bitrate without considering the guard interval length, training data or FEC overhead. The basic system parameters are summarised in Table  9. 3. The noise is modelled by AWGN with zero mean, and it is assumed that the noise is uncorrelated and that the noise power is the same for all receive ports.
Fatty acid composition Total lipid was extracted from diets, whole fish and tissue pates by homogenisation in chloroform/methanol (2:1, v/v)  (44). Fatty acid methyl esters (FAME) were prepared from total lipid by acid-catalysed transesterification at 50°C for 16 h  (45)  , and FAME extracted and purified as described previously  (46). FAME were separated and quantified by GLC using a Fisons GC-8160 (Thermo Scientific) equipped with a 30 m × 0•32 mm internal diameter × 0•25 μm ZB-wax column (Phenomenex), on-column injector and a flame ionisation detector. Data were collected and processed using Chromcard for Windows (version 2. 01; Thermoquest Italia S. p. A. ). Individual FAME were identified by comparison to known standards and published data  (46).
Statistical analysis Minitab 17 Statistical Software (2010) was used for all statistical analyses. After confirming normality and homogeneity of variance in the data using the Kolmogorov-Smirnov test and Levene's test, a two-way ANOVA was performed on independent parameters considering nutritional history (NH, Diet M stimulus and Diet V stimulus ), ploidy (2 N and 3 N), and their interaction. Percentage data were transformed using the arcsine square root function. Significance was accepted at P < 0•05 and Tukey's post hoc test was used to compare significantly different means. To investigate solely nutritional influence, differences shown within a given ploidy were analysed using a Kruskal-Wallis test. Histological scores were analysed statistically using a Kruskal-Wallis test followed by Dunn's post hoc test for non-parametric, categorical comparison.
Acknowledgements This study received funding (including fellowships for JFT, CM and LMV) from the  European Union   Seventh Framework Program  ( FP7/2007-2013 ) under the grant agreement no. 288925 ,  Advanced Research Initiatives for Nutrition & Aquaculture (ARRAINA). The funders had no role in the design, analysis or writing of the article. Additional funding for M. C. was provided by a  Biotechnology and Biological Sciences Research Council (BBSRC)  grant ( BB/M013049/1 ,  SALMOTRIP + : Optimisation and implementation of sterile triploid salmon in Scotland ).
Histological analyses Tissues (liver and inguinal adipose tissue) were collected from WT and Tg(Gasp-1) mice at different ages and fixed in formol for 3 days. Then, tissues were embedded in paraffin and sectioned with microtome in 4 µm thickness. The sections were stained with hematoxylin and eosin. Measurements of area/size and quantification of adipocytes were realized with ImageJ software (http://rsbweb. nih. gov/ij/). Oil Red O solution was prepared in propylene glycol (5 g. l -1 ) and heated at 100°C for 10 min. Frozen liver were sectioned with a cryostat (8 µm thick) and dried for 15 min at 37°C. Sections were then fixed for 10 min in 10% formol /PBS (v/v). To detect neutral lipid accumulation, sections were stained with Oil Red O for 10 min at RT and counterstained with hematoxylin for 2 min at RT.
Following primary antibody incubation, sections were washed 3 times for 5 min in Tween-20 1%/PBS. Secondary antibodies were applied to sections for 30 min at 37°C at a dilution of 1:2000 in PBS. GLUT-4 antibody was targeted with goat anti-rabbit IgG 488 (Invitrogen). DAPI (Sigma Aldrich) staining for cell nuclei was added to the secondary antibody at a 0. 5 μg•mL -1 concentration. After secondary antibody incubation, sections were washed 3 times for 5 min in Tween-20 1%/PBS. We used the MetaMorph software (Molecular Devices, Sunnyvale, USA) to acquire images with a Leica DMI6000B inverted epifluorescence microscope and to determine the total intensity of GLUT-4 fluorescence for each image.
Metabolic analyses For intraperitoneal glucose tolerance tests (IPGTTs), overnight-fasted mice were injected with 20% D-glucose (2 mg. g -1 body weight). Blood glucose levels were monitored using a glucose meter (Roche Applied Science) from 2. 5 μl of tail blood at 0, 15, 30, 60 and 120 min after glucose injection. Serum insulin levels were also measured after glucose injection in 10 μl of serum from blood collected from the tip of the tail vein by sandwich ELISA (Rat/Mouse Insulin ELISA kit, Millipore). All measurements were performed in triplicate and data for the standard curve were fitted to a logistic plot with the MARS Data Analysis Software (BMG Labtech) to determine the levels of insulin.
Enzyme-linked immunosorbent assay (ELISA) of myostatin and insulin Myostatin and insulin concentrations for mouse plasmas were determined in a sandwich ELISA (GDF8/ Myostatin ELISA kit, R&D Systems) and (RAT/Mouse Insulin Elisa, Millipore) as previously described  [31]. All measurements were performed in triplicate and data for the standard curve were fitted to a logistic plot with the MARS Data Analysis Software (BMG Labtech) to determine the levels of myostatin and insulin.
Cytokines and adipokines antibodies array Mouse cytokine array (Proteome Profiler Mouse Cytokine Array Kit, R&D Systems) were used following the manufacturer's instructions on mouse tibialis anterior. Mouse Adipokine Array (Proteome Profiler Mouse Adipokine Array Kit, R&D Systems) were used following the manufacturer's instructions on mouse inguinal adipose tissue. The arrays were incubated overnight at 4°C on a rocking platform shaker. The blots were detected using an enhanced chemiluminescence (BM Chemiluminescence Western Blotting Substrate (POD)) (Roche Applied Science) and exposed to a film (GE Healthcare Hyperfilm ECL, GE Healthcare). Densitometric analysis of the array image files were performed using ImageQuant TL software (GE Healthcare).
These data confirmed an alteration of muscle metabolism. To go further, we decided to test if Pgc1α and FoxO1, potent actors of muscle metabolism, were also altered by the insulin resistance. Thus, we quantified the expression level of these two genes. Pgc1α expression was increased in young Tg(Gasp-1) mice compared to WT (Fig. 7A ). In Tg(Gasp-1) mice, Pgc1α expression was decreased at 16 months of age compared to young mice while no variation of FoxO1 expression was observed (Fig. 7A ). Moreover, Pgc1α and FoxO1 genes are essentially expressed in slow-type and fast-type myofibers respectively. The slow-type myofibers mostly express Myh7 and the fasttype myofibers express Myh2, Myh1 and Myh4. Q-PCR analyses on tibialis anterior show that young Tg(Gasp-1) mice present an upregulation of Myh7 compared to WT (Fig.
Acknowledgements We are indebted to  Dr. Brigitte Picard  and  Dr. Isabelle Cassar Malek  for access to the EchoRMI-500TM analyzer. We also thank  Karine Pasquier  from the animal facility (SCA) for her technical help with animals. All animal experiments were performed according to European directives ( 86/609/ CEE  and  2010/63/UE ) and approved by the  Committee on Ethics of Animal Experiments  from the  Author's Institution, "Comité Régional d'Ethique de l'Expérimentation Animale" of the Limousin region  (n°  11-2014-11 ). According to the European Directive 210-63-EU, mice were observed daily for the general health status and mortality scoring. This project was co-financed by the  European Union , the  Limousin Regional Council  and the  French National Institute for Agricultural Research.
ACKNOWLEDGMENTS This work was supported by the  Program of Visiting Research Scientist of the Chinese Academy of Sciences  (Grant No. Y3KY02013L ) and  PIFI project of Chinese Academy of Science  (Grant No. 2016VBC077 ). Authors are also thankful to  Key Laboratory of Environmental Corrosion and Biofouling, Institute of Oceanology, Chinese Academy of Science Qingdao, China  for providing facility, space, and resources for this work.
Analysis of Nanoclusters and Trajectories We used the SLIMfast MATLAB code  (Normanno et al. , 2015)  to recover single-molecule localizations and DBSCAN to identify nanoclusters. Trajectories were reconstructed by finding the optimal global assignment between points in consecutive frames using an inference approach. The mapping of diffusivities in single cells was achieved using a maximum likelihood approach. Single-cell maps were averaged using custom-built MATLAB routines. All these procedures are detailed in the Supplemental Information.
ACKNOWLEDGMENTS We thank  Leo Valon  for designing and making the TIAM_linker_CRY2_IRFP optogenetic plasmid. We thank  Fred Etoc  for the initial mEOS2-Rac1 construction and for preliminary experiments. M. C. acknowledges financial support from  French National Research Agency  ( LICOP  grant  ANR-12-JSV5-0002-01 ). M. C. and M. D. acknowledge funding from  French National Research Agency (ANR) Paris-Science-Lettres Program  (grant  ANR-10-IDEX-0001-02 PSL ),  Labex CelTisPhyBio  (grant  ANR-10-LBX-0038 ), and  France-BioImaging infrastructure supported by ANR  grant  ANR-10-INSB-04  (Investments for the Future). M. C. and M. C. P. acknowledge  INSERM ITMO Plan Cancer   2014-2018  ( PC201530 ).
ACKNOWLEDGMENTS We thank  Premal Shah ,  Joshua Plotkin  and  Luca Ciandrini  for useful discussions. GC was funded by the  Human Frontier Science Program  ( LT000873/2011-L ). We acknowledge financial support by the  Synthetic Biology Engineering Research Center (SynBERC). This work used the  Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley  ( NIH S10  Instrumentation Grants  S10RR029668  and  S10RR027303 ).
All NMR experiments were recorded at submillimolar concentrations and showed total complex formation, and total disappearance of uncomplexed species signals, at an approximate molar ratio of 1-to-1 in LptC-and LptA m. Since LptC is stabilized in a dimeric form, the NMR data support the formation of a LptC-LptA m 2:2 complex. When LptC-LptA m complexes are subjected to SEC-MALLS analysis, dilution during the course of the SEC allows complexes to dissociate(Figure  S1 ). Even in a presence of a two-times molar excess of LptA m , we observe a complex of 54-kDa, not fully assembled that corresponds to a 2:1 LptC-LptA m stoechiometry. LptC and LptA m do not form a highly stable complex and partly dissociate in the course of the SEC, consistent with the estimated LptC-LptA Kd of ~4 µM  26. C-(A β I δ1 L δ1 V γ1 )]-LptC-[ 1 H, Comparison of the LptC or LptA m resonances chemical shift in the free protein forms and in the LptC-LptA m complex (Fig.
SEC-MALLS data and SAXS recorded on LptA m confirm a monomeric behavior for this protein in solution. Interestingly, this monomeric LptA m is still able to support cell growth in vivo revealing that the property of LptA to multimerize in solution is not strictly required to accomplish LPS transport to the OM. This result, in complement with the lack of stability observed for the wild type LptA-LptA complex by EPR  26  , supports the idea that a multimeric LptA bridge is not always strongly assembled. The proposed stable bridge, connecting the 21-nm-wide periplasm  30  , could dynamically assemble, potentially depending on the presence of LPS and on the local periplasm width. The length of the periplasmic Lpt machinery formed only with a monomeric LptA, one LptC, and the two periplasmic parts of LptF-LptG and LptD-E complexes can be approximated to 16 nm.
In the LptC-LptA m complex, several residues forming crosslinks with LPS delimit a 429 Å 3 cavity located at the LptC-LptA m interface identified in our model (Fig. 8 ). In particular Y182 crosslink in LptC clusters at the interface with T32, I36, L116, Y114 crosslinks in LptA. Analysis of the size of this second cavity (Fig. 8 ) shows a volume of only 429 Å 3 versus 720 Å 3 for the LptC-LptC interface. This area will thus have to undergo significant opening to adapt to the LPS molecule. On the contrary, in the LptA-LptA complex structures solved by X-ray (PDB:2R1A), a third cavity of 1140 Å 3 is present at the molecular interface, which could be used to receive the lipidic part of the LPS during the transfer. Altogether the determination of a LptC-LptA model, LPS binding experiments and analysis of structures suggest that the three intermolecular cavities LptC-LptC, LptC-LptA and LptA-LptA are important sites for LPS binding.
SEC-MALLS. Protein samples (40 µl) are injected in buffer B at 25 °C on a Superdex S200(10/300GL) connected to an HPLC system with on-line Multi Angle light scattering (DynaPro Nanostar), refraction index (Optilab rex) and Optical density detectors (SPD-M20A). Data analysis is performed with ASTRA 5. 4. 3. 20 software (WYATT) using theoretical dn/dc values of 0. 188 and 0. 187 ml/g and massic extinction coefficients of 1206 (theoretical protparam (http://web. expasy. org/protparam/) and 466 (obtained experimentally by aminoacid analysis) ml. g -1. cm -  for LptC and LptA m , respectively. Two-component analysis with the protein conjugate method was used for the LptC-LptA m complex mass and stoichiometry determination. Small Angle X-ray Scattering. SAXS data were collected on beamline BM29 from the European Synchrotron Radiation Facility in Grenoble (France) on samples at concentrations of 1.
6 and 2. 4 mg/ml for LptA m , 1, 2 and 3 mg/ml for LptC and 3. 6 and 5. 4 mg/ml of a LptA m :LptC 1:1 molar ratio in the same buffer as for the NMR experiments, at 20 °C, and supplemented with 0. 5% w/v sucrose to avoid radiation damage. Ten frames of 1 second each were recorded on each sample, positioned at 2. 86 m from a Pilatus detector, at a wavelength of 0. 99 Å. For each sample, frames were normalized to the intensity of the transmitted beam before being merged. Buffer's contribution to the scattering was subtracted automatically by ISPYB  42. Data were, for each sample type, extrapolated to zero dilution using the PRIMUS software from the ATSAS 2. 5. 1 software package  43. Radius of gyration, Rg, forward scattering intensity, I(0), maximum particle dimension, D max , and distance distribution function, P(r), were calculated with GNOM from the same program suite.
Dammif  44  in slow mode calculated 20 bead-model envelopes from the SAXS data, models were averaged and filtered (with damaver and damfilt, respectively  43  ) to obtain the final ab-initio envelopes. Dammif was executed with a P2 symmetry for LptC and LptC-LptA m complex. Back-calculated diffusion data were calculated with Crysol  45  with a modified solvent density to account for the buffer composition and systematic buffer substraction. Superimposition of molecular structures and envelopes was done with supcomb  46. LptC N-and C-termini and LptA m C-termini and 78-83 loop, missing from their respective crystal structures (3MY2 and 2R1A chain B, respectively) were added with XPLOR-NIH and minimized with simulated annealing protocol. The obtained structures were used in the figures showing the LptA m monomer or LptC dimer in the current study, as well as inputs for the HADDOCK software  47  used for data-driven docking.
Data-driven docking (HADDOCK). LptC-LptA m docking was performed for half of the complex (1xLPtC + 1xLptA m ) to speed-up calculations and the full complex was rebuilt according to the LptC dimer symmetry. Residues used to established Ambiguous Interaction Restraints (AIR) in HADDOCK were LptC residues from methyl titration experiments (A119, L151, L174, I175, V178, I184) with a Relative Surface Accessibility (RSA) superior to 10% (as calculated with the NACCESS software). LptA m residues for which NH resonances could not be followed upon LptC interaction and with a RSA superior to 40% were considered active, as well as residues 32, 40 and 115, which experience high CSP. HADDOCK 2. 2 online (http://haddock. science. uu. nl/ services/HADDOCK2. 2/) was run with 2000 rigid body structures, 400 structures refined and water refined, automatic passive residues definition, and clustering by default.