dataesr/scientific-paragraphs-categorization huggingface dataset:
Experimental monitoring of gene expression in real time The expression of the fluorescent reporter genes in different genetic backgrounds and different growth media was monitored in vivo and in real time. About 150 readings each of absorbance (600 nm) and fluorescence (485/520 nm) were obtained during a typical experiment using the Perkin-Elmer microplate reader. In order to compute promoter activities and protein concentrations from these data, data analysis procedures were designed and implemented in MATLAB, completing earlier work  [17, 25]. These data procedures account for the specific half-life of the fluorescent reporter protein and take special care in the subtraction of the autofluorescence background (see Text S3 for details on the data analysis procedures). Denoting by A(t) and I(t) the (background-corrected) time-varying absorbance and fluorescence signals, we computed the reporter concentration r(t) and the promoter activity f(t) by means of the following formulas: rðtÞ ¼ IðtÞ AðtÞ ; ð5Þ f ðtÞ ¼ d dt rðtÞ þ ðg r þ mðtÞÞrðtÞ ¼ d dt IðtÞ AðtÞ þ g r IðtÞ AðtÞ ; ð6Þ where g r [min -1 ] is the degradation constant of the reporter and m(t) [min -1 ] the growth rate of the bacteria.
The half-life of the protein is defined as t 1/2 = ln2/g r. The reporter concentration is expressed in units RFU and the promoter activity in units RFU min -1 , as is usual for this kind of measurements (see  [17]  and Text S3). The growth rate is easily estimated from the time-varying absorbance, using the standard relation m(t) = d lnA(t)/dt. The above equations rely on the use of a kinetic model of the expression of the reporter gene, as explained in Text S2. We used cubic smoothing splines (csaps function in MATLAB) to fit the fluorescence and absorbance data and obtain estimates of A(t), I(t), dA(t)/dt, and dI(t)/dt. The half-life of the GFPmut2 reporter is 19 h (g r = 0. 0006AE0. 0001)). The maturation time of GFPmut2 is so short (4 min,  [65] ) that it can be safely ignored. A similar measurement model was used for the expression of the actual gene of interest, encoding a protein with concentration p(t) [RFU min -1 ]: d dt pðtÞ ¼ f ðtÞ À ðg p þ mðtÞÞ pðtÞ; pð0Þ ¼ p 0 ; ð7Þ where g p [min -1 ] is the degradation constant of the protein.
Usually, the bacteria in the preculture are in stationary phase, so m(T) = 0. Eq. 8 was solved by numerical integration using the quad function in MATLAB. In the case of the motility network there are two complications that slightly modify this general scheme. First, the half-lives of FliA and FlgM are variable over the time-course of the experiment. During exponential growth, when the motility genes are expressed, FliA and FlgM have short half-lives, due to proteolysis and secretion, respectively. During stationary phase, at the end of the preculture, this is no longer the case and FliA and FlgM have longer half-lives (2 h for FliA and 3 h for FlgM  [52, 53] ). As a consequence, when computing the initial protein concentrations from the reporter concentrations at time T, we need to take protein degradation constants g 0 p corresponding to these longer half-lives.
Parameter estimation The promoter activity models we considered in the main text have the form f ðtÞ ¼ f xðtÞ; c ð Þ, where c is a vector of unknown parameters and x is a vector of regressors. The specific form of f xðtÞ; c ð Þis given in Eq. 1 and 3. The regressors take different forms in consecutive sections of this paper, consisting either of the activities f A and f M of the fliA and flgM promoters (x = (f A ,f M )) or the reconstructed concentrations p A and p M of FliA and FlgM (x = (p A ,p M )). In all sections, c = (k 0 ,k 1 ,n,y,K), as defined in the section Identification of gene regulation functions from promoter activities. The superscript symbol s indicates the experimental condition, where s 2 S ¼ fDrpoSÀM9; DcpxRÀM9; DcsgDÀM9; DcsgDÀLB; WT À LBg. Given The solution is found in MATLAB using the multistart global search function gs with standard settings (interior-point method, fmincon for local minimizations).
We tried several other global optimization function available in the MATLAB global search toolbox, but the gs function was found to perform best. The parameter search space C is given by the constraints 0 k 0 maxf f s ðtÞ : t 2 T s ; s 2 S g; 0 k 1 10 Á maxf f s ðtÞ : t 2 T s ; s 2 S g; 1 n 4; 0 y maxf x s 1 ðtÞ : t 2 T s ; s 2 S g; 0 K 20 Á maxf x s 2 ðtÞ : t 2 T s ; s 2 S g: The above procedure applies to the estimation of the regulation function of both tar and flgM. However, for the estimation of the regulation function of flgM, the condition WT-LB is not available and hence excluded from the computation of Q(c). Moreover, in the latter case, K is fixed for biological consistency to the value inferred from the fitting of tar promoter activity. For all parameter fits shown in the main text, we performed a-posteriori identifiability analysis to ensure that no structural or practical identifiability issue affects our results (Text S10).
A region is colored green if the expected regulatory pattern is among the minimal sign patterns returned by the algorithm, and yellow if it is compatible with the returned sign patterns. A region is colored red if none of the returned sign patterns is consistent with the data only. Two examples of inconsistent sign patterns are shown. Note that, for every combination of half-lives, the analysis of the pooled data (results reported as "Intersection") is generally more constraining than the pooling of the results from individual analyses: The expected pattern may be consistent (yellow) with all individual datasets but not minimal (green) for any of them, and turn out to be consistent and minimal (green) when all datasets are analyzed at once (see also Text S5).
Funding: Rhône-Alpes region (cluster ISLE, PhD grant):  DS Investissements d' Avenir Bio-informatique programme , project  RESET  ( ANR-11-BINF-0005 , https://project. inria. fr/reset/):DS, EC, JG, HDJ  INRIA/ INSERM project ColAge  (http://colage. saclay. inria. fr/):JG, HDJ  Agence Nationale de la Recherche , project  GeMCo  ( ANR-2010-BLAN-0201-02 , http://www-sop. inria. fr/members/Madalena. Chaves/ANR-GeMCo/ main. html):EC, JG, HDJ The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data analysis Image analysis was performed at the Cochin Imaging Facility (Institut Cochin, Paris). A 3D image analysis was performed on x, y, and z planes using Imaris 7. 4 (Bitplane AG). First, superficial planes from top of the slice to 15 μm in depth were removed to exclude T cells located near the cut surface. Cellular motility parameters were then calculated using Imaris. Tracks >10% of the total recording time were included in the analysis. The straightness value was calculated as the ratio of the distance from origin to the total distance traveled. To reveal the relationship between CD8 T cell motility and the tumor structure (tumor islets and collagen network), confocal time-lapse images of T cells were superimposed onto the corresponding SHG and EpCAM images. CD8 T cells localized in the stroma were distinguished from those infiltrated in tumor cell nests by looking at individual planes along the z axis.
Videos and images were made by compressing the z information into a single image using Imaris. When a drift in the x, y dimension was noticed, it was corrected using the "Correct 3D Drift" plug-in in ImageJ. For the automated detection of resident CD8 T cells in different tumor areas (stroma, tumor islets, loose, and dense collagen regions identified by visual inspection of SHG images), we used the ImageJ software. First, fluorescent images were thresholded and converted to binary images. Angles between the cell trajectory vectors, which are the connecting lines between starting points and end points of each track, and tumorstroma boundaries were calculated using Image J software. Only the cells positioned within a maximum distance of 100 μm from the tumor-stroma interfaces were included in further analysis.
We then determined the motile behavior of resident CD8 T cells in the stroma and tumor cell regions of slices from ovarian carcinomas. The motility of CD8 T cells localized in the stroma was rather low, with a median of mean velocity of 4. 04 μm/min (Figures  2C, D  and Movie S5 in Supplementary Material). We also quantified the percentage of migrating cells, defined as cells with a mean velocity higher than 5 μm/min during a 20-min recording. Data from nine different ovarian tumors indicated that 37% of CD8 T cells were motile. Large variations were noted from one tumor to the other, with proportion of migrating CD8 T cells ranging from 20 to 60%. Of interest, the few CD8 T cells located in tumor islets migrated more rapidly than those found in the stroma with a median of mean velocity of 5.
acknowledgments We wish to thank Pierre Bourdoncle and Thomas Guilbert of the Cochin Imaging Facility (Institut Cochin, Paris) for advice and assistance with microscopes and help in data analysis; Alain Trautmann and Nadege Bercovici for valuable discussions and critical reading of the manuscript. This study was supported by grants by the French Ligue Nationale contre le Cancer (ED), by the CARPEM (Cancer Research for Personalized Medicine; EP), by the Fondation de France (EP) and by the GamaMabs Pharma (HB).
The nitrocellulose membranes were then incubated with the His-Probe TM -HRP reagent for 1 h at room temperature and washed three times with buffer. After this, the nitrocellulose membranes were developed by incubation with SuperSignalWorking solution containing luminol and peroxide and quantified with ImageJ software. FTIR Difference Spectra-The experimental setup was the same as that described in a previous study  (14, 20). In summary, about 20 l of MelB containing proteoliposome suspension (about 100 g of protein) in 100 mM KCl, 20 mM MES (pH 6. 6) was spread homogeneously on a germanium Attenuated Total Reflectance crystal (Harrick, Ossining, NY; 50 ϫ 10 ϫ 2 mm, yielding 12 internal reflections at the sample side) and dried under a stream of nitrogen. The substrate-containing buffer and the reference buffer were alternatively perfused over the proteoliposome film at a rate of ϳ1.
5 ml/min. The film was exposed to substrate-containing buffer for 4 min and washed with reference buffer for 10 min (or 30 min for the buffer containing 50 mM melibiose). For each cycle, 1000 scans at a resolution of 4 cm Ϫ1 were recorded, and a minimum of 25 spectra were taken and averaged to increase the signal-to-noise ratio (i. e. a total of Ն25,000 scans for every difference spectrum). Spectra were recorded with an FTS6000 Bio-Rad spectrometer equipped with a mercury-cadmium-telluride detector. Data corrections for the difference spectra were carried out following a protocol developed previously  (20). Quantitative Comparison of Intensity and Similarity of FTIR Difference Spectra-Quantitative comparison of the intensity and similarity of IR diff spectra were performed as described pre-viously  (5).
The data were processed with Felix 32 software (Photon Technology International). Trp fluorescence spectra were acquired by setting the excitation wavelength at 290 nm (half-bandwidth of 5 nm) and collecting the emission spectrum in 100 mM KPi buffer (pH 7. 0). Na ϩ -dependent FRET signals ( ex , 290 nm; half-bandwidth, 5 nm) of RSO or ISO membrane vesicles (100 g of protein/ml) or proteoliposomes (30 g of protein/ml) were obtained by incubation with the sugar fluorescent analog D 2 G at a final concentration of 10 M in 100 mM KPi buffer (pH 7. 0) containing 100 mM KCl. Molecular Dynamics Simulations-The starting coordinates where those of molecule A of MelB ST (6) (PDB code 4M64). The CHARMM-GUI server  (21) (22) (23)  was used to mutate the required amino acids to those of MelB. A short energy minimization was performed in vacuo using the Nanoscale Molecular Dynamics program  (24)  to remove any possible steric clash.
This E. coli MelB was inserted into a bilayer of 90 ϫ 90 Å 2 produced using the CHARMM-GUI Membrane Builder (25) consisting of 154 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) molecules by the replacement method. In this step, the protein orientation was calculated from the Orientations of Proteins in Membranes database by minimizing its transfer energy from water to the membrane  (26). The coordinates of this protein-lipid complex were transferred to the Visual Molecular Dynamics (VMD) program (1. 9. 2 version (  27 )) and was complemented with a water layer of 18 Å on top and at the bottom of the bilayer, with water also filling the free space in the protein interior (a total of 13,709 water molecules). NaCl at a concentration of 0. 3 M was finally added randomly with the "Add Ions" extension of VMD (131 Na ϩ and 135 Cl Ϫ per MelB).
The system had a total of 75,800 atoms. The system was energy-minimized, followed by equilibration for 200 ps using an integration step of 1 fs and NVT conditions (constant number of particles, volume, and temperature) using the Nanoscale Molecular Dynamics program. Equilibration was done by slowly heating the system from 0 to 298 K in steps of 2 K. Molecular dynamics were subsequently produced using the ACEMD program  (28)  running on a personal computer with a Graphic Processing Unit graphic card. For protein and lipid atoms, the CHARMM force field parameters  (29, 30)  were used, and, for water, the TIP3P model  (31)  was used. Two different replicas were produced for a minimum of 200 ns at constant pressure and temperature using particle mesh Ewald method full-system periodic electrostatics  (32, 33).
6 ). The binding of substrates was also investigated by measuring FRET directly in RSO and ISO membrane vesicles, which does not involve any solubilization or purification process. Although the MelB protein content of these vesicles detected with the His tag-specific reagent HRP was comparable with C-less, no signal of the sugar analog D 2 G could be detected, a result consistent with the lack of sugar binding concluded from the IR diff and intrinsic fluorescence data (data not shown). Molecular Dynamics Simulations-The MelB ST -A crystal structure (6) was used as a template for E. coli MelB by mutating all side chains of MelB ST that differ from those of MelB (a total of 60 replacements). After a short energy minimization in vacuo to remove steric clashes, the MelB structure was included in a bilayer of POPE because the major head group component of the E.
Acknowledgments-The Nanoscale Molecular Dynamics program was developed by the Theoretical and Computational Biophysics Group in the  Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. We thank  Alex Perálvarez-Marin  and  Arnau Cordomí  for critical reading of the manuscript and  Elodia Serrano  and  Neus Ontiveros  for technical assistance.
2 The Fe 10 Ln 10 compounds are soluble in water  3  and other solvents. Apart from these cyclic coordination clusters there are very few other examples of such d/f systems. 4 n addition to the large number of unpaired electrons in the Fe 10 Ln 10 systems, the molecular tumbling in solution deviates from the usual behaviour of small molecules such as single ion gadolinium complexes. 3 These points are of fundamental interest since these molecules have nanoscale dimensions and are thus expected to behave differently from both single-centre coordination compounds and nanoparticles used as contrast agents. Thus, the first step is to provide a suitable database in order to develop a theoretical model which describes the clusters' properties with respect to PRE. The series of compounds available makes it possible to investigate the individual electronic contributions to the hyperfine relaxation and the parameters that depend on the molecular environment by varying the lanthanide ion and allow us to discover the influence of the time-modulated hyperfine couplings.
The data acquisition software varied from XWINNMR 3. 5 (600 MHz) to TOPSPIN1. 5 (200 MHz) to TOPSPIN2. 1 (400 MHz). T 1 was obtained from mono-exponential fits on data from inversion recovery; T 2 resulted from single echo CPMG measurements as implemented on Bruker high field NMR spectrometers. Data were processed within TOPSPIN. All samples were measured at room temperature. Typical sequence parameters of the measurements are summarized in ref. 3. A Bruker 200 MHz SWB instrument was used for relaxivity measurements, being equipped with a Diff30 probe for 5 mm sample tubes. For imaging, the multi-slice multi-echo sequence was applied on a micro2. 5 set-up with a 25 mm birdcage resonator. Parameters were adjusted such that either dominantly R 1 or R 2 contrast was achieved. Carrier matierials with attached cultivated bioilm were measured first without any relaxation agents, then a time series of images was acquired to detect a possible permeation of the paramagnetic moieties into the biofilm.
As little is known about the details of molecular transport into this technical biofilm matrix, the approach in the present paper is to apply different contrast agents with different mole-cular sizes as well as with different chemo-physical adsorption properties. With 4-Hydroxy-TEMPO, a small and hydrophilic molecule, a contrast agent is available, which does not agglomerate nor shows a pronounced surface activity (images not shown). Conventional Gadovist was applied, being well known as a medical relaxation agent, which can pass through tissue. The axial images obtained from long-term experiments after the injection of a bolus are compared with those obtained when applying the mentioned Fe 10 Gd 10 clusters. The slice thickness was chosen to be 0. 7 mm, the spatial resolution in the image plane is 80 µm × 80 µm, acquiring 256 data points in each direction for T 1 weighted images.
Acknowledgements Our work was funded by the  German State of Baden-Württemberg , the  Karlsruhe Institute of Technology (KIT)  and the  Deutsche Forschungsgemeinschaft as administrated through the Center for Functional Nanostructures (CFN)  and within the  DFG-instrumental facility center Pro 2 NMR. LNCMI Grenoble  is member of the  European Magnetic Field Laboratory (EMFL) , and part of this work there has been supported by  EuroMagNET  under the  EU  contract no. 228043. Financial support of  Julyana R. Machado  was provided by  Csf/CNPq-Conselho Nacional de Desenvolvimento Científico e Tecnológico , of the  Ministry of Science, Technology and Innovation from Brazil , which is kindly acknowledged. Maria P. Herrling  thanks the  German Carl-Zeiss Foundation  for financial support. Special thanks to  Dr Jochen Junker  for helpful discussions, to  Dr Mladen Horvatić  and  Dr Hadrien Mayaffre  for assistance at the LNCMI, and to  Vanessa Grande  for laboratory support.
Acknowledgments We gratefully thank  Christin Hong  ( Harvard University ) for constructive comments and the  Swiss National Science Foundation  ( PZ00P3-131945  to MI), the  Marie Curie Actions (Career Integration Grants ,  CIG_SIGnEPI4Tol_618541  to MI), the  ARC Foundation  ( PJA 20131200238  to AS), and the  Institut National de la Santé et de la Recherche Médicale (INSERM). We acknowledge American Journal Experts for editorial assistance.
It is however expected that fast, low-cost and accurate full genome sequencing and analysis (of bacteriophages) will replace routine microbial genotyping techniques in the near future c In some cases (e. g. , novel bacteriophages with no homology in databases), electron microscopy could provide important information and could thus be warranted d In general, it is recommended to only use lytic phages (and no temperate phages) in phage therapy. Lytic phages are more potent killers of host bacteria, making them more effective in therapy than temperate phages. Following lysogenic induction, temperate phages may transfer fragments of host bacterial DNA into nontargeted bacteria (possibly belonging to other species). This phenomenon is called transduction or phage-mediated horizontal gene transfer (HGT).
ACKNOWLEDGMENTS AND DISCLOSURES We would like to thank  Marc Struelens  [ European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden ] for his critical comments. Several authors are employed by Small and Medium Enterprises that are developing phage therapy products. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
Acknowledgments We thank  Irene Vila  and  Peggy Dartigues  from the pathology platform of IGR. We thank  Dr. Benoit Couturaud  and  Dr. Angelique Girod  for surgery of the SLN and  Deborah Rechard ,  Christelle Auger  ( URC Paris centre ) and  Isabelle Scheer-Senyarich  for their contribution to the data management.
This makes a precision confrontation of lattice data with our planar equivalence predictions difficult. An exception is the recent work of Engel et al. [15]  and the ALPHA lattice collaboration  [16]  in which they quote self-consistent evaluations of both the RG-invariant condensate Σ 1/3 RGI and the scale parameter Λ (2) M S for n f = 2. The condensate is determined by studying the rate of condensation of the low eigenvalues of the Dirac operator near the limit of vanishing quark mass. For the ratio, they quote 6 Σ 1/3 RGI /Λ (2) M S = 0. 77 (4) (2. 5) Comparing with eq. (2. 2) for n f = 2, this is in quite remarkable agreement with our K F = 1 prediction of 0. 763. To illustrate this further, in Figure  5  we restrict the plot of Σ 1/3 RGI /Λ (2) M S (see Figure  1 ) to n f = 2 and superimpose our prediction for the condensate as a function of K F with the one-sigma error band of the lattice result (2.
Promoting European conservation strategies and assembling conservation data The dynamic conservation of elm genetic resources was promoted by EUFORGEN through a dedicated Ulmus species strategy (Collin 2002) and a "Technical Guidelines" six-page leaflet devoted to the conservation of Ulmus laevis Pall. (Collin 2003). More generally, EUFORGEN has defined methods and created a geo-referenced database to monitor the progress of dynamic conservation of FGR in Europe. Before 2011, it was difficult to pool information Minimum requirements for DCUs include various criteria: biological (a minimum number of reproducing trees), legal (have a designated status as an FGR conservation area at national level) and management (be managed for the genetic conservation of one or several target tree species, be monitored regularly -  Koskela et al.
2013). Whereas the static preservation of elm clones has already been carried out in many European countries, the low number of DCUs entered by the National Focal Points in the EUFGIS database shows that efforts are still needed for successful dynamic conservation. In September 2013, the number of DCUs was 27 in seven countries for the wych elm (Ulmus glabra Huds. ), 17 in six countries for the European white elm and only two in two countries for the field elm.
Two DCUs of U. laevis have been approved by the CRGF commission and entered into the EUFGIS database: the "Val d'Allier" DCU in the Loire basin, and the "Ramier de Bigorre" DCU in the Garonne valley. The former was preferred to other candidate DCU populations because its whole area is state owned and managed for nature conservation. The latter was the only large population inventoried in the Garonne valley, and its management and monitoring are also very good. Its autochthony is not consistent with Atlas Florae Europaeae  (Jalas & Suominen 1976 ), but seems possible according to  Schmucker (1942). Moreover, a study of chloroplast DNA markers carried out with B. Demesure-Musch (Office National des Forêts, Orleans) on 67 leaf samples originating from southwest France showed that 10 samples had a rare cpDNA type which was found neither in the rest of France, nor in Belgium and Germany (Cemagref, Final report DERF 02/98, 2000).