dataesr/scientific-paragraphs-categorization huggingface dataset:
All wells then received a further 25 ll of lysis buffer followed by 25 ll of mixed beads. After overnight incubation at 4 °C with continuous orbital shaking, the plate was washed two times with wash buffer. After washing, 25 ll of detection antibodies were then added to each well and incubated for 1 h at room temperature with orbital shaking. Subsequently, 25 ll of streptavidin-phycoerythrin solution was added to each well and incubated for an additional 30 min at room temperature with orbital shaking. Wells were washed two times with 1• wash buffer, re-suspended in 150 ll of sheath buffer, and read on a LuminexÒ 200 machine with Milliplex Analyst software (Millipore, Billerica, MA).
Following incubation, the plate was washed three times with 1 • wash buffer. After washing, 50 ll of detection antibodies were added to each well and incubated for 1 h at room temperature with orbital shaking. Wells were once again washed three times with 1 • wash buffer. Subsequently, 50 ll of streptavidin-phycoerythrin solution was added and the plate was incubated for an additional 30 min at room temperature with orbital shaking. Wells were washed three times with 1 • wash buffer, and then magnetic beads were re-suspended in 100 ll of sheath buffer and read on a LuminexÒ 200 machine with Milliplex Analyst software (Millipore, Billerica, MA).
Acknowledgments We thank  Janet M. Storey  for editorial review of the manuscript and  L. Haro  and  P. Guesnet  for technical and material assistance in the preparation of the lemur tissue samples. This work was supported by a  Discovery grant  from the  Natural Sciences and Engineering Research Council (NSERC) of Canada  (Grant No. 6793 ) and a grant from the  Heart and Stroke Foundation of Canada  (Grant No. G-14-0005874 ) to KBS. KBS holds the  Canada Research Chair in Molecular Physiology ; SNT held a  NSERC  postgraduate scholarship and BAK held a  NSERC postdoctoral fellowship.
Quantitative RT-PCR analyses. For gene expression analyses, mRNAs obtained from FACS-sorted tanycytes were reverse transcribed using SuperScript III Reverse Transcriptase (Life Technologies) and a linear preamplification step was performed using the TaqMan PreAmp Master Mix Kit protocol (P/N 4366128, Applied Biosystems). Real-time PCR was carried out on an Applied Biosystems 7900HT Fast Real-Time PCR System, using exon-boundary-specific TaqMan Gene Expression Assays (Applied Biosystems) as follows: DARPP32 (Ppp1r1b: Mm00454892_m1), ERa (Esr1: Mm00433149_m1), ERb (Esr2: Mm00599821_m1), PR-A/B (Pgr: Mm00435628_m1), TGF-b1 (Tgfb1: Mm01178820_m1) and Sema7a (Sema7a: Mm01171202_m1). Control housekeeping genes were r18S (18S: Hs99999901_s1) and ACTB (Actb: Mm00607939_s1). Gene expression data were analysed using SDS 2.
Short hairpin RNA for PlexinC1 and Rap1-V12 plasmids, employed for GnV3 transfections, were produced by Dr Tamagnone (Institute for Cancer Research at Candiolo, University of Torino, Italy). GnV3 morphological analysis. Changes in GnV3 cell morphology were evaluated by staining the cells with Alexa 588-X phalloidin (Molecular Probes, Eugene, OR) to visualize cytoskeletal actin. GnV3 cells were incubated overnight with or without a recombinant human Semaphorin-7A/Fc chimera (100-250 ng ml À 1 ; 1835-S3, R&D Systems). Quantification of GnRH fibre length was performed by an experimentator, blind to culture treatments on digitized photomicrographs using the NeuronJ plugin of ImageJ software (National Institute of Health, Bethesda, USA). Immunoblotting. Female rats (n ¼ 4 independent experiments per oestrous cycle phase; 3-4 months old) were decapitated at 1600 h on the day of diestrus II (Di16h) or on proestrus or estrus at the same time (Pro16h).
03 ng ml À 1 and 7% intra-assay and 10% inter-assay coefficients of variance. Statistics. All analyses were performed using Prism 5 (GraphPad Software) and assessed for normality (Shapiro-Wilk test) and variance, when appropriate. Sample sizes were chosen according to the standard practice in the field. Data were compared by a two-tailed unpaired Student's t-test, one-way ANOVA for multiple comparisons or by two-way repeated-measures ANOVA. A Tukey's post-hoc test was performed when appropriate. The significance level was set at Po0. 05. For comparison between two or multiple groups not having a normal distribution, the non-parametric tests unpaired test (Wilcoxon-Mann-Whitney) and Kruskal-Wallis, respectively, were used. A P-valueo0. 05 was considered to indicate a significant difference.
Acknowledgements This paper is dedicated to the memory of the late  Professor Aldo Fasolo , to whose scientific mentorship, guide and sincere friendship we will always be deeply grateful. This work was supported by the  Institut National de la Sante et de la Recherche Medicale, Inserm, France  (grant number  U837 ),  Agence Nationale de la Recherche ,  ANR, France  (grant numbers  ANR-2010-JCJC-1404-01  and  ANR-14-CE12-0015-01  RoSes and GnRH to P. G. ;  ANR-09-BLAN-0267  to V. P. ), the  Fondation pour la Recherche Medicale  (Equipe FRM 2005 & DEQ20130326524, France, to V. P), the  Institut de Medecine Predictive et de Recherche  Therapeutique (IMPRT-IFR114, France; electron microscopy core facility), the  University of Lille 2, Lille, France (Appel aProjets du Conseil Scientifique de l'Universite Lille 2  to P.
The very small source enables diffusion characteristics to be determined in a volume of tissue with a characteristic length of ~100 μm and in periods of 30-90 s. Analysis of studies of diffusion of molecules in the ECS has thrown light on this most inaccessible brain compartment. Today the interpretation of the data often involves computer models. For example it was thought for a long time that the typical value of λ = 1. 5-1. 6 for 'point' molecules could be accounted for by the extra distance a diffusing molecule had to travel as it navigated around cellular profiles. Detailed Monte Carlo modeling using the MCell program (www. mcell. org) showed, however, that the increase in tortuosity attributable to this mechanism was generally less than or equal to 1. 225  [32, 33]. Experiments by Hrabětová and Nicholson  [24]  and further application of Monte Carlo simulation showed that one way to increase the tortuosity was to incorporate so-called dead-spaces into the description of the ECS to elevate the tortuosity to the measured values.
Stroke studies: CBF measurements using MRI One of the first major undertakings was to compare two MRI arterial spin tagging (AST) methods for estimating CBF with the classic IAP-based QAR technique  [92]. A rat ischemic stroke model with suture occlusion of the middle cerebral artery for 2 h was employed in these studies. This model had the advantage of producing an extended range of CBF rates for testing the sensitivity of the measurements and a normal contralateral side for comparison in the same rat. Two MRI approaches were used: spin echo (SE) and variable tip angle gradient echo (VTA-GE) readouts. Despite the widespread use of AST-MRI techniques to estimate CBF, very few studies were done till then to compare the MRI data with established terminal tracer studies. For instance, single-coil AST has been used in the laboratory as an imaging technique for assessing the state of cerebral perfusion in a variety of rat models of ischemia.
With Gd-BSA as the paramagnetic agent, RISA was employed for QAR. Look-Locker MRI estimates of T 1 followed Gd-BSA blood (sagittal sinus) and tissue (ROI) concentration. QAR and MRI maps of K trans were co-registered, an ROI that included the tumor and its surrounding brain tissue was selected, and the two estimates of K trans from the ROI on QAR and MRI maps were compared by either mean per animal ROI or on pixel-bypixel data using a generalized estimating equation. Good correlation was observed between end-point QAR values and MR parameters whether calculated as mean values per ROI or as pixel-by-pixel values within each ROI  [106].
Gadomer-17 was used for CE-MRI and a single, high dose of dexamethasone (8 mg/kg) was used to achieve quick therapeutic effects. The dose of dexamethasone was chosen based on previous work on animal brain tumor models in which between 3 and 30 mg/kg of dexamethasone was shown to be effective in lowering the interstitial tumor pressures and reducing edema. After the first MRI estimate of permeability ('Test'), dexamethasone was administered intravenously. A second permeability study ('Retest') was performed 90 min after the administration of dexamethasone. Results demonstrated that model selection effectively captured the effect of dexamethasone on tumor vasculature  [109]. Using significantly fewer rats the data also confirmed an earlier work of Fenstermacher and his colleagues  [108].
As an additional confirmation, the cell density data were also compared with ADC values from these experiments. The results demonstrated that the Logan plot-estimated V D correlated with the Standard Model's v p + v e  [112]. In addition, the parameters v e and V D significantly and negatively correlated with tumor cellularity. A significant correlation of cell density with ADC values was also observed, although this relationship was not as strong as those with DCE-MRI measures  [112]. An interesting feature of these studies was the adaptation of the AIF from the previous radiotracer experiments. An accurate determination of the AIF is essential for precise calculation of permeability parameters. Because of the difficulty in directly estimating the AIF from the MRI data, a radiotracer assay-based input function obtained from the previous investigation  [94]  was used in the dynamic MRI studies.
This demonstrated that, starting at about two minutes after injection of CA, the radiotracer and MRI measures of blood concentrations of CA track each other very well. It was assumed for this adaptation that: (1) no vascular leakage of CA occurred in the contralateral striatum, and (2) the plasma volume of the caudate putamen was 1%. The integrated area of the radiotracer AIF was scaled so that its area was 100 times that of the integrated area of the average value of ΔR 1 (t) in the caudate putamen of the opposite hemisphere. Using the criteria established by such investigations, the acute effects of cilengitide, an anti-angiogenic agent, on tumor vascular permeability kinetics were measured. These data showed that cilengitde had a vascular normalizing effect at about 8 h after administration.
Acknowledgements We thank  Dr. Nathalie Strazielle  for her critical review of the manuscript. We also thank  Julie Sarri  for her secretarial assistance. This work was supported by funds from the  Department of Emergency Medicine at the Alpert Medical School of Brown University  and by a fund from  D. N. Weiss  (to AC and JSC); by  ANR-10-IBHU-0003 ,  Cesame grant  (to JFGE), by the  NIH/NINDS  grant  NS028642  (to CN); by an  American   Heart Association Scientist Development Grant   0635403N  and the  Henry Ford Health System research funds  (to TNN).
Acknowledgments MVP is supported by the  NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)  grant  R01-AR067273  and  Edward Mallinckrodt Jr Foundation  grant. XW is supported by the  Canadian Institutes of Health Research (CIHR)  postdoctoral fellowship. CFG-J is supported by the  NSF   Graduate Research Fellowship Program (NSF GRFP)  grant  DGE-1321846. CDM is supported by a  Postdoctoral Fellowship  from the  American Cancer Society  ( PF-12-145-01-DDC ). DG is supported by  INSERM  and  ANR  funding. The authors thank  Dr David M. Gardiner  for his helpful discussions on the topic of blastema.
, 2011). The LifeAct Venus construct was obtained by replacing GFP by Venus sequence from a pCMV LifeAct-GFP2 construct  (Gauvain et al. , 2011). mCherry-tCaMKII was obtained by replacing GFP by mCherry from GFP-tCaMKII plasmid from the Malinow laboratory. mCherry-tCaMKII was then cloned into a pCMV-Tet3G-TRE vector (Clontech) to allow for doxycycline-induced expression (TET-ON system). For rescue experiments, recombinant KCC2 4904 -4924 nucleotide sequence AAC GAG GTC ATC GTG AAT AAA TCC was replaced with AAT GAA GTT ATT GTT AAC AAG TCT to preserve amino acid sequence. Rescue efficacy was verified both by KCC2 immunocytochemistry and in electrophysiological assays of chloride extrusion (data not shown). Cell culture and transfection. Hippocampal neurons were prepared as described previously  (Gauvain et al.
4. For miniature EPSC (mEPSC) recordings, neurons were recorded in whole-cell configuration with borosilicate glass micropipettes filled with a solution containing (in mM) the following: 110 CsMeSO 4 , 20 CsCl, 10 HEPES, 10 EGTA, 4 MgATP, and 0. 4 Na 3 GTP, pH 7. 4. Cells were held at Ϫ70 mV, and mEPSCs were isolated by adding TTX (1 M) and bicuculline methochloride (20 M) to the extracellular solution. Currents were recorded with a Multiclamp 700B amplifier (Molecular Devices), filtered at 2 kHz, and digitized at 20 kHz. Access and input resistance were regularly monitored with Ϫ5 mV voltage steps. mEPSCs were detected and analyzed offline using Detectivent software. Chemical LTP (cLTP) was induced as described previously  (Kopec et al. , 2006)  by switching extracellular solution for 16 min to a nominally Mg-free solution containing (in mM) the following: 125 NaCl, 20 D-glucose, 10 HEPES, 2 KCl, 5 CaCl 2 , pH 7.
A recording borosilicate glass pipette (2-4 M⍀) filled with B-ACSF was inserted in the molecular layer of a densely infected dentate gyrus area, and a tungsten bipolar electrode (0. 5 M⍀) was used to stimulate the perforant pathway. fEPSPs were recorded in the presence of the GABAA receptor antagonist bicuculline methochloride (20 M), using a Multiclamp 700B amplifier (Molecular Devices) low-pass filtered at 5 kHz, and digitized at 20 kHz. fEPSP slopes were analyzed offline using Clampfit software (Molecular Devices). Briefly, baseline potential was set to zero, and recordings were low-pass filtered at 1 kHz using a Bessel filter. The initial slope of the fEPSP was then automatically measured using a 1 ms time-window manually positioned at the onset of the fEPSP. Data were acquired and analyzed blind to the experimental condition.
Normalization of SEP intensity was performed for each cell by dividing the mean fluorescence intensity by the average of fluorescence intensities of the three time points before cLTP induction. In experiments using NH 4 Cl application to collapse transmembrane pH gradients  (Ashby et al. , 2006 ) (see Fig. 3 ), rapid alkalization of intracellular compartments due to passive NH 3 diffusion through membranes was followed by a delayed, rebound acidification, likely reflecting KCC2mediated ammonium transport  (Tietz et al. , 1999). Accordingly, this rebound acidification was not observed in neurons with suppressed KCC2 expression, whereas the initial alkalization was unaffected (data not shown). We therefore always measured SEP fluorescence before the onset of the rebound acidification (Ͻ7 min).
Several spine head parameters were also computed: mean and variance of LifeAct-Venus fluorescence intensity and geometric center of the spine. Spine heads were then realigned using a line originating from the attachment point of the spine neck to the head (manually determined) and passing through the geometric center. For spatial autocorrelation analysis of LifeAct-Venus signal (see Fig. 5 ), data from isolated spine heads were first normalized. The degree of clustering in each dataset was assessed using Moran's index analysis  (Moran, 1948). This index ranges values from Ϫ1 (complete dispersion) to 1 (complete clustering), with 0 representing random distribution. For each pixel i, local Moran's index (I i ) was computed as follows: I i ϭ z i ⅐ j W i, j ⅐ z j where z i is the value of the pixel i and W represents the matrix of neighboring weights.
For quantification, all data were normalized to internal Tuj1 control signals. For coimmunoprecipitation, neurons were homogenized in modified RIPA buffer (50 mM Tris-HCl, pH 7. 4, 150 mM NaCl, 1 mM EDTA, 1% Nonidet P-40, 0. 1% SDS, 0. 5% DOC, and protease inhibitors; Roche). Lysed cells were kept on ice for 20 min and then centrifuged at 14,000 ϫ g for 10 min. Lysates were then incubated with KCC2 (Millipore) or ␤PIX IgG (Millipore, 2 g)  (Smith et al. , 2014)  overnight at 4°C. The pulldown was performed using Protein G Magnetic beads (Invitrogen) for 2 h at 4°C. The beads were washed 3 times in RIPA buffer and one time in RIPA buffer without detergents. Bound proteins were eluted in SDS sample and separated by SDS-PAGE. Rac1 and RhoA activity was measured using effector pulldown assays.
Blots were probed with mouse monoclonal anti-Rac1 (1:1000, BD Transduction Laboratory) or anti-RhoA (1:200, Santa Cruz Biotechnology), as described previously  (Causeret et al. , 2004; Backer et al. , 2007). Band densities were quantified by Fusion software (Vilber Lourmat). The relative densities of pulled down activated Rac1 and RhoA were normalized to the maximal Rac1 or RhoA in the same samples incubated with 200 M GTP-␥S for 15 min at room temperature, according to the manufacturer's instructions. Biochemical assays were repeated at least 3-4 times on independent cultures, and data were compared using Student's t test, after testing normality and equal variance of the data with SigmaPlot 12. 5 (SPSS). In all other experiments, data were compared using nonparametric paired (Wilcoxon) or unpaired (Mann-Whitney) tests.
57 Ϯ 0. 02 vs 0. 60 Ϯ 0. 02, n ϭ 149 and 85 spines, from 19 and 20 neurons, respectively, p ϭ 0. 13; Fig. 6E-G ). To compare the spatial distribution of F-actin within spines, we performed spatial autocorrelation analysis of LifeAct-Venus signal using Moran's index  (Moran, 1948)  (see Materials and Methods; Fig. 6F ). Again, we found no significant difference in the proportion of high-intensity clustered pixels (Moran's index p value Ͻ0. 05) between neurons expressing nontarget or KCC2-directed shRNA (23. 0 Ϯ 0. 3% vs 23. 1 Ϯ 0. 4%, same dataset as above, p ϭ 1. 0; Fig. 6F-H ). Together, our results show that suppression of KCC2 results in a net increase in F-actin accumulation within dendritic spines with no substantial subspine redistribution.
E, Pseudocolored averages of 149 and 85 individual spine images from 19 and 20 neurons, respectively, as in D, aligned as described in Materials and Methods to show the mean distribution of LifeAct-Venus fluorescence within spine heads. Scale bar, 500 nm. F, Schematic representation of spine heads (yellow) isolated from the micrographs shown in D with high-intensity clustered pixels (orange), as derived from spatial autocorrelation analysis using Moran's index (for details, see Materials and Methods). G, H, Summary graphs of the mean coefficient of variation (CV) of LifeAct-Venus fluorescence (G) and the mean percentage of high-intensity clustered pixels (H ) in spine heads of neurons expressing nontarget or KCC2-directed shRNA (same dataset as in E). n. s. , Nonsignificant difference.
Program Research Grant  ( RGP0022/2013 ) to J. C. P. ,  Institut National de la Santeet de la Recherche Medicale, Ville de Paris Biomedical and Health Research Program  to J. C. P. ,  Federation pour la Recherche sur le Cerveau  to J. C. P. ,  Fondation pour la Recherche Medicale  ( DEQ20140329539 ) to J. C. P. , and  PICPEN (Center for Psychiatry and Neuroscience, Paris). Q. C. was the recipient of doctoral fellowships from  UniversitePierre and Marie Curie and Fondation pour la Recherche Medicale. We thank  Ingrid Chamma  for the quantitative analysis of phalloidin staining data;  Theano Irinopoulou  for support with spinning disc and confocal imaging;.
Scale bar, 500 nm. E, Pseudocolored averages of 149 and 85 individual spine images from 19 and 20 neurons, respectively, as in D, aligned as described in Materials and Methods to show the mean distribution of LifeAct-Venus fluorescence within spine heads. Scale bar, 500 nm. F, Schematic representation of spine heads (yellow) isolated from the micrographs shown in D with high-intensity clustered pixels (orange), as derived from spatial autocorrelation analysis using Moran's index (for details, see Materials and Methods). G, H, Summary graphs of the mean coefficient of variation (CV) of LifeAct-Venus fluorescence (G) and the mean percentage of high-intensity clustered pixels (H ) in spine heads of neurons expressing nontarget or KCC2-directed shRNA (same dataset as in E). n. s. , Nonsignificant difference.
More specifically, we propose an egocentric view of the system and assess whether and to what extent the node's tendency of repeating already established contacts is correlated with its probability of being reached by the infection. Findings obtained on past available contact data are then used to predict the infection risk in the current unknown epidemic situation. We apply this risk assessment analysis to two large-scale empirical datasets of temporal contact networks -cattle displacements between premises in Italy  [19, 36] , and sexual contacts in high-end prostitution  [16]  -and evaluate its performance through epidemic spreading simulations. We also introduce a model to generate synthetic time-varying networks retaining the basic mechanisms observed in the empirical networks considered, in order to explain the results obtained by the proposed risk assessment strategy within a general theoretical framework.
Results and Discussion The cattle trade network is extracted from the complete dataset reporting on timeresolved bovine displacements among animal holdings in Italy  [19, 36]  for the period 2006-2010, and it represents the time-varying contact pattern among the 215, 264 premises composing the system. The sexual contact network represents the connectivity pattern of sexual encounters extracted from a Web-based Brazilian community where sex buyers provide time-stamped rating and comments on their experiences with escorts  [16]. The five-years data of the livestock trade network show that stationary properties at the global level co-exist with an active non-trivial local dynamics. The probability distributions of several quantities measured on the different yearly networks are considerably stable over time, as e.
The distributions of loyalty values, though of different shapes across the two datasets, display no considerable variation moving along consecutive pairs of configurations of each dataset (Fig  2A-B  and Supplementary Material), once again indicating the overall global stability of system's properties in time and confirming the results observed for the degree. A diverse range of behaviors in establishing new connections vs. repeating existing ones is observed, similarly to the stable or exploratory strategies found in human communication  [42]. Two pronounced peaks are observed for θ = 0 and θ = 1, both dominated by low degree nodes for which few loyalty values are allowed, given the definition of Eq. (  1 ) (see Supplementary Material for the dependence of θ on nodes' degree and its analytical understanding).
The exact preservation of the neighborhood structure (θ = 1) is more probable in the cattle trade network than in the sexual contact network (P (θ = 1) being one order of magnitude larger), in agreement with the findings of a higher system-wide memory reported in Fig 1. Moreover, the cattle trade network exhibits the presence of high loyalty values (in the range θ ∈ [0. 7, 0. 9]), differently from the sexual contact network where P (θ) is always equal to zero in that range except for one pair of consecutive configurations giving a positive probability for θ = 0. 8. Farmers in the cattle trade network thus display a more loyal behavior in purchasing cattle batches from other farmers with respect to how sex buyers establish their sexual encounters in the analyzed sexual contact dataset. For the sake of simplification, we divide the set of nodes composing each system into the subset of loyal nodes having θ greater than a given threshold , and the subset of disloyal nodes if instead θ <.