dataesr/scientific-paragraphs-categorization huggingface dataset:
Immunofluorescence The cells were grown on glass coverslips, fixed with 2% paraformaldehyde and permeabilized with 0. 5% Triton-X100. After blocking, the cells were incubated with anti-XRCC1 (ab1838, Abcam, Inc. ) or anti-phospho-Histone H2A. X (Ser139) primary antibodies (clone JBW301, Merck-Millipore, USA) diluted in PBS containing 1% BSA and 0. 05% Tween. After washing with PBS containing 1% BSA, the cells were incubated with Alexa 488-conjugated anti-mouse secondary antibodies (Invitrogen, Molecular Probes) and stained with DAPI. Images were captured using a Zeiss motorized Axio Imager Z2 epifluorescence microscope with a ×63/1. 4 NA oil immersion objective equipped with a Hamamatsu camera. Data acquisition was performed using AxioVision (4. 7. 2. ). The number of foci per nucleus was measured with the Image J software.
This work was supported by the  Ligue Nationale contre le Cancer, Institut Nationale du Cancer :  2011-1-RT-01 ,  2011-1-PLBIO-09, 2013-1-PLBIO-14 ,  Agence Nationale de la Recherche :  ANR-14-CE10-0010-02 , and by  AFM-Téléthon. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Amplification specificity was assessed by melting curve analysis. Primers were designed using Primer3 software. Sequences and NCBI references are provided in Additional file 2: Table  S1. Abundance of transcripts of interest was expressed relative to the expression of the reference gene, glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Analyses were performed with the Bio-Rad CFX Manager 2. 1 software.
For confocal imaging, sections were analyzed using a Leica TCS SP8 confocal scanning system (Leica Microsystems, Wetzlar, Germany) equipped with 405-nm diode, 488-nm argon, and 561-nm DPSS lasers. A series of optical sections separated by 0. 3 μm was collected using the ×63 HC PL APO CS2 objective (numerical aperture 1. 40). For each optical section, double-or triple-immunofluorescence images were acquired in sequential mode to avoid potential contamination by fluorescence emission overlap. The orthogonal sectioning and 3D viewing were produced by the Leica Application Suite X-software (Leica Microsystems). Images were equally adjusted for brightness and contrast, and composite illustrations were built in Adobe Photoshop CS3 (Adobe Systems, San Jose, CA).
Statistical analysis Values are expressed as mean ± SD (BF measures and lesion volume) and mean ± SEM (RT-qPCR, immunohistochemistry, and immunofluorescence). BFV and CBF values measured in the different ROIs were compared using repeated measures ANOVA and a post hoc Newman-Keuls test to analyze differences between the two groups. One-way ANOVA followed by a Newman-Keuls post hoc test was used for the difference between two groups (RT-qPCR, immuno-labeled cells, and lesion volumes). Statistical analyses were performed using GraphPad PRISM version 5. 0 (GraphPad Software, San Diego, CA).
) Fig. 5  Gene expression of microglia/macrophage M2-like markers in PBS-and sildenafil (Sil)-treated animals, 72 h and 8 days after pMCAo. M2 markers were measured in the ipsilateral (IL) and contralateral (CL) side in PBS-(plain bars) and sil-10 (hatched bars) animals. Data are mean ± SEM. Data were assessed via an ANOVA, and when significant, the results of the Newman-Keuls post-test are shown; *p < 0. 05, **p < 0. 01, and ***p < 0. 001, compared to PBS  [17, 18]. In contrast, a single pMCAo is sufficient to create ischemic lesions in mice  [19]. Together, this suggests that combined occlusion of carotid and MC arteries is necessary to drop the BF in the ipsilateral hemisphere sufficiently for anastomoses to no longer be efficient despite the circle of Willis and to create a lesion in the rat.
As BF was only measured up to 90 min after pMCAo, we cannot exclude the contribution of late collateral opening and patency. Together, our data suggest that sildenafil, although given shortly after pMCAo, may have other neuroprotective effects that may develop at later time points of recovery. The impact of inflammation on post-injury outcome in the developing brain is increasingly recognized. In our pMCAo model in the P9 mouse, strong astrocytic and microglial responses were detected 72 h after injury and persisted for more than 1 week (personal data). We show that sildenafil potentiates reactive astrogliosis 72 h after pMCAo, in agreement with a previous report following focal cryolesions onto the cortex in adult rats treated with zaprinast and killed 3 days thereafter  [9]. Zaprinast was expected to accelerate the formation of the glial scar and the regeneration of the injured tissue  [10].
RNA quality was assessed using the BioAnalyzer 2100 prior to RT-PCR analysis and all samples with a ratio of 28S/18S < 1. 2 were discarded. In addition, the Tayside Tissue Bank collected and verified the clinico-pathological data established by two anatomo-pathologists. Furthermore Tayside Tissue Bank collected and anonymised all the clinical data (treatment, patient follow-up). The median age at diagnosis of the breast cancer patient cohort was 61. 5 years (range 28. 7 to 89. 1 years) and median follow-up period was 6. 85 years (range 0. 29 to 13. 7 years). Tumor tissues were macro-dissected by a specialist breast pathologist and snap frozen in liquid nitrogen prior to storage at À80ºC. The samples were examined following Local Research Ethics Committee approval under delegated authority by the Tayside Tissue Bank (www.
FACS analysis Cells were transfected with the GFP-tagged isoforms of p53, harvested 24 hr after transfection and then spun down at 1200 rpm for 5 min and fixed by adding 1 mL of 70% EtOH at À20 ˚C. For each condition, propidium iodide staining was performed and the number of GFP-expressing cells was compared to total cells after quantification by FACS analysis using the CellQuest software.
, 2011 (Schleputz et al. , , 2012) )  and mechanical stretch  (Dassow et al. , 2010; Lavoie et al. , 2012; Davidovich et al. , 2013)  have also been ascertained, highlighting the physiological relevance of this system. Biomechanical data from PCLS studies, to date, have largely focused on changes in airway caliber. These datasets, however, contain a rich source of additional dynamic and spatial biomechanical data that heretofore have not been investigated. For example, a limited number of studies have utilized the PCLS to examine the mechanical interdependence between the constricting airway and the surrounding parenchyma  (Adler et al. , 1998; Brook et al. , 2010; Ma et al. , 2013). However, beyond the immediate vicinity of the contracting airway, the parenchyma contains other airways and arterioles which may themselves contract or even passively contribute to the effective material properties of surrounding tissues.
Contraction Studies The response of lung slices were recorded after addition of the contractile agonist methacholine (MCh; 10 -4 M, ICN Biomedicals, Zoetermeer, Netherlands) at t 0 = 0 s, and then addition of the bitter taste receptor agonist chloroquine (ChQ; 10 -3 M, Sigma-Aldrich, Zwijndrecht, Netherlands) to induce relaxation at t 1 = 600 s (in the presence of MCh). As described previously, a nylon mesh and a metal washer were used to keep the lung slice in place. Bright field images of the lung slices were captured in time-lapse (1 frame per 2 s) with a resolution of 1280 × 960 pxl (1. 15 m/pxl) using an inverted microscope (Eclipse, TS100; Nikon). Airway luminal area was quantified using image acquisition software (NIS-elements; Nikon).
Displacement Fields First, the frames were pre-processed with MATLAB to set the length scale in µm and stretch the range of pixel densities so that specific features became more prominent. This preprocessing step gave a list of the frame numbers and a series of images corresponding to adjusted frames. Second, the Farnebäck algorithm  (Farneback, 2003)  as implemented in C++ / OpenCV was used to calculate an estimate of the displacement vector between an initial (or reference) and final image (the frame of interest) for each of the pixels. Then, strain matrices were determined at equally spaced points chosen across the image. To do so, four displacement vectors around the point of interest and central difference methods were used to calculate derivatives in the horizontal and vertical directions from which the major and minor eigenvectors and eigenvalues of the strain matrix were evaluated.
The initial coordinates of the selected points, the components of the displacement vectors, the major and minor strain eigenvalues and the components of the major strain eigenvector were saved to be used in post-processing. This sequence was repeated for each frame of interest. Finally, displacements and strains were displayed with MATLAB and their value was set to zero where there was no tissue. Displacement plots could either show arrows on a bright field image (initial or final) or display the magnitude of the displacements in color maps. Major (radial) and minor (circumferential) strain eigenvalue distributions were also displayed as color maps.
The coordinates of four neighboring points were then determined for each of the points on the spokes. These were selected based on being a specific distance away in the x or y direction. However, the coordinates of these surrounding points were unlikely to be at integer values of pixels, in which case bilinear interpolation of the displacement of the four closest pixels was used first to calculate estimates for the displacements at the surrounding points, then to derive the strain matrix (using central difference methods to calculate derivatives) and finally the mean of the radial and circumferential strain eigenvalues in each section. MATLAB was used to plot graphs of the section-averaged strain as a function of distance from the lumen, which could also be used to show how the time-dependent distribution of average strain alters as the airway contracts.
DISCUSSION To date, most studies using PCLS have simply monitored airway caliber. Although, a few studies have extracted some detailed strain data from PCLS  (Adler et al. , 1998; Brook et al. , 2010; Ma et al. , 2013) , these have been obtained by tracking specific landmarks in the tissue. In this study, by contrast, we present a computational strain-mapping tool that is able to characterize heretofore inaccessible mechanical events that bear directly upon the physiology of airway narrowing. In a representative mouse PCLS, we illustrate how a variety of displacement and strain measures can be visualized dynamically and quantitatively in both the contracting airway and the surrounding parenchymal tissue. Displacements of sub-regions of the slice are tracked on  the phase contrast movies acquired after addition of contractile and/or relaxing drugs to generate maps of displacement across the whole slice.
Sequences of strain maps or maps of normalized deformations are then derived from the displacement maps. With our computational strain-mapping tool, we provide access to the detailed mechanical response data in PCLS in the whole airway-parenchymal tissue both globally and also along local user-specified directions. The strain maps give an overview of the deformations imposed by ASM contraction on the airway wall, the tethers and the alveolar tissue. At maximum contraction, both radial and circumferential strains are higher in the airway wall and on the tethers. However, the maps reveal that these deformations are partly transmitted through the slice and that their distribution in the parenchymal tissue is highly heterogeneous. Strain data are thus treated at two different scales so as to derive global and local behaviors of the tissues in response to ASM contraction.
Astrometric data We measured the relative astrometric orbit of HD 93 129 Aa,Ab using positions from: • One previously published epoch from FGS/HST (Maíz  Apellániz et al. 2008; Benaglía et al. 2015). • Two epochs from the High Resolution Camera (HRC) of the Advanced Camera for Surveys (ACS) onboard HST (Maíz  Apellániz et al. 2008). • Five epochs from the PIONIER four-beam combiner at the Very Large Telescope and Interferometer (VLTI) at the European Southern Observatory (ESO) (Le  Bouquin et al. 2011; Sana et al. 2014). Of those, only the first one had been published before. The measured values are listed in Table  1. The HRC data (from HST GO programs 10 205, 10 602, and 10 898) were processed using a crowded-field photometry package created by the lead author that works on the geometrically distorted (not on the drizzled) exposures  (Anderson & King 2004).
Spectroscopic data We observed HD 93 129 Aa,Ab with the Space Telescope Imaging Spectrograph (STIS) onboard HST using the G430M and G750M gratings in 2010. 264 aligning the slit with the position angle of the system at that time, when the pair was separated by 36 mas, to obtain individually resolved spectra of the two components (Fig. 2 ). The separation between the stars was smaller than the spatial pixel size of the STIS CCD (50 mas). To overcome that, we [a] dithered the exposures spatially with a 2-point pattern in order to decrease the effective pixel size to 25 mas and [b] we used the techiques developed for MULTISPEC  (Maíz Apellániz 2005)  to obtain spatially-resolved spectra for both the Aa and Ab components. We have obtained 42 optical spectra of HD 93 129 Aa,Ab between 2005 and 2016 using the FEROS spectrograph attached at the MPE/ESO-2.
2 m telescope (La Silla Observatory, Chile) and the Échelle spectrograph attached to the du Pont 2. 5 m (Las Campanas Observatory, Chile). The data were obtained within the framework of the OWN Survey  (Barbá et al. 2010). The slit widths used in those observations (2 in FEROS, and 1 in Échelle) do not allow us to spatially resolve the Aa and Ab components. They provide nominal resolving powers of 48 000 and 45 000, respectively. The data were processed using the FEROS Data Reduction System implemented within ESO-MIDAS software, and the échelle package in IRAF. Additional processing such as rectification and telluric corrections were performed using IRAF. The final signal-to-noise ratio of the one-dimensional extracted spectra depends on the wavelength and the observing night, varying between 100 and 400.
We have measured the radial velocity, equivalent width, and full width at half maximum for a number of absorption and emission lines in the spectra in order to determine the behavior of those parameters with time. UVES/VLT observations were obtained on the night of June 27, 2016 with the DIC2 436+760 and 346 + 820 setups, yielding a continuous wavelength coverage from 305 nm to 498 nm and from 570 nm to 945 nm. Two back-to-back exposures of 150 s were obtained in each setup. An entrance slit of 0. 6 was used for both arms, yielding a nominal spectral resolving power of 60 000. The data were processed in the standard way using the ESO CPL pipeline v5. 7. 0 under the REFLEX environment and calibration frames obtained within 12 h of the scientific observations. The extracted 1-dimensional spectra were rectified by fitting a low order polymial through the continuum and show a signalto-noise ratio per resolution element of about 400.
ACKNOWLEDGEMENTS We thank the referee,  Tony Moffat , for insightful comments that helped improve this paper. We also thank  N. R. Walborn  for his inspiration to study HD 93 129 Aa,Ab and  E. P. Nelan  for discussions on the astrometric motion at an early stage of this project. The authors acknowledge the  European Southern Observatory  staff for their support. J. M. A. acknowledges support from the  Spanish Government Ministerio de Economía y Competitividad (MINECO)  through grant  AYA2013-40 611-P  and from  HST GO  programs  10 205 ,  10 602 , and  10 898. R. H. B. acknowledges support from  FONDECYT  Projects  1 140 076  and  11 121 550. The HST data were obtained at the  Space Telescope Science Institute , which is operated by the  Association of Universities for Research in Astronomy, Inc.
Participants Thirty healthy volunteers, divided into 2 groups, participated in the first phase of the study. Group 1 was composed of 16 participants who underwent the Sham-Actual Inhibition protocol applied to the right pSTS (5 women; 22. 1 ± 2. 5 years); Group 2 was composed of 14 participants who underwent the Sham-Sham protocol applied to the right pSTS (3 women; 23. 1 ± 3. 1 years). After analysis comparing these 2 groups, additional data were collected to form a third group (Group 3). Group 3 was composed of 14 participants who underwent the Sham-Actual Inhibition protocol applied to the left pSTS (3 women; 24. 1 ± 3. 4 years). There was no significant age difference between the 3 groups (F 2,41 = 1. 67; P = 0. 20). All participants were right-handed, had normal or corrected-to-normal sight, were free of psychiatric, neurological, and general health problems, and presented no contraindication for the TMS.
Finally, to verify the specificity of the findings for the target area in the right pSTS, subsequently to analysis comparing Groups 1 and 2, additional data were collected in a new experimental set: Sham-Actual Inhibition protocol applied to left pSTS (Group 3; Fig. 1C ) in which actual inhibition was delivered to the left pSTS. All subjects were blinded to the protocol type and to the intervention. In addition, after the experiment subjects were debriefed and did not manifest knowledge regarding sham or active condition. Before the TMS session, an anatomical 3DT1 MRI scan was acquired for all participants. Based on 4 fMRI studies on gaze perception  (Pelphrey, Morris, Michelich, et al. 2005; Hadjikhani et al. 2008; Sato et al. 2008; Nummenmaa et al. 2010) , the precise target location within the pSTS was identified on the individual scans.
A calibration test consisting of 5 registration points was performed before each set of stimuli. The calibration test was repeated if the examiner considered one of the 5 points not valid according to the eye-tracker criteria (recorded gaze extrapolating the limits of the calibration-designed area or the absence of recording for one of the 5 points). All participants matched general recording quality criteria, based on the amount of valid and missing data, as indicated by Tobii Studio™ software. A repeated-measure ANOVA with recoding quality as the dependent variable showed no significant interaction between group and TMS type (F 2,41 = 0. 62; P = 0. 55). The participants were instructed that they would see a sequence of movie fragments and all they had to do was watch them. The stimuli creation, the calibration procedures, and the data acquisition and visualization were performed using the Tobii Studio™ software.
Data Analyses In each movie fragment, the following dynamic areas of interest (AOIs) were selected for analysis: the eyes and mouth of the characters in the social movie fragments and the balloon in the nonsocial movie fragments. Eye-tracking software interpolates the shape and position of the AOI, so that it moves smoothly from one frame to the next. More importantly, AOIs sizes and shapes remained stable across measures. The number of fixations in each AOI was recorded using the Tobii Studio™ software. A fixation event was defined as such by the Tobii fixation filter based on 0. 42 pixels/ms threshold. Number of fixations was selected since it is an absolute variable that informs on exploratory behavior toward a defined region: higher number of fixations indicates that people further explore the region.
Following results from this first analysis, additional data were collected (Group 3) to confirm that the reduction in number of fixations to the eyes was a specific consequence of inhibition of the right pSTS, and further analysis was performed comparing Groups 1, 2, and 3. The average number of fixations after each intervention served as the repeated factor, and the TMS type (sham or actual inhibition) and group (Group 1; Group 2 and Group 3) served as the independent factor. In all analyses, TMS type by group interaction was investigated.
07, P = 0. 80) and the balloon in the nonsocial control scenes (F 1,28 = 0. 05, P = 0. 81). Following results from analysis comparing Groups 1 and 2, additional data on inhibition of the left pSTS were collected (Group 3) to confirm that the reduction in number of fixations to the eyes was a specific consequence of inhibition of the right pSTS. Further analysis comparing the TMS effects on gaze pattern among all 3 groups was performed. Results showed an interaction between TMS type (sham or actual inhibition) and group (Group 1; Group 2 and Group 3) on the number of fixations to the eyes (F 2,41 = 3. 76; P = 0. 03). Indeed, a significant reduction in the number of fixations to the eyes during the visualization of social movies was observed only in the group receiving TMS actual inhibition applied to the right pSTS (F 1,15 = 13.
Funding The study was supported by AP-HP PHRC and Fondation de France grants. A. S. received funding from Fondation Orange. T. P. and J-C. L. received funding from the program "Investissements d'avenir" ANR-10-IAIHU-06, Paris Institute of Translational Neuroscience. Eye-Tracking device was financed by "Les Amis d'Arthur" association. Funding to pay the Open Access publication charges for this article was provided by INSERM U1000.
Methods: aBC patients accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials. gov, NCT01521676). Genomic profiling was established by whole-genome array comparative genomic hybridization (aCGH) and targeted next-generation sequencing (NGS) of 365 candidate cancer genes. For a subset of patients, a sample of fresh tumor was orthotopically implanted in humanized cleared fat pads of NSG mice for establishing PDX. Conclusions: Precision medicine can be implemented in a single center in the context of clinical practice and may allow genomic-driven treatment in approximately 30% of aBC patients. PDX may be obtained in a significant fraction of cases.
Such a low antitumor activity observed in precision medicine strategies, including the present study, may be due to the long, complex and treatmentrich pretreatment history of the disease, the suboptimal efficacy of offered targeted therapies at least as singleagent, rather than to the poor predictive value of detected molecular alterations, predictive value that however might be improved with multigene scores. Another critical limitation to routine implementation of precision medicine strategies remains the relatively low access to molecularly-targeted innovative clinical trials, which are mostly developed in high-volume comprehensive cancer centers, due to the expected low prevalence of the target population. Treating patients with less advanced-stage disease and using more innovative agents is currently tested in the randomized phase 2 trial SAFIR02 (NCT02299999) in which genomics-matched, targeted treatments are used as maintenance after response or stabilization obtained by standard first-or second-line cytotoxic chemotherapy in HER2-negative advanced breast cancer patients.
Patients and samples Between November, 2013 and November, 2014, 34 patients with metastatic or locally-advanced breast cancer accessible to tumor biopsy were prospectively enrolled at the Institut Paoli-Calmettes in the BC-BIO study (ClinicalTrials. gov, NCT01521676). This study is an ongoing institutional clinical study dedicated to molecular characterization of breast cancer, which was approved by our local ethics committee. After giving their informed consent for translational research, including genetic analyses of their germline DNA, tumor biopsy was obtained by any visually-or radiology-guided percutaneous or surgical biopsy. Samples were divided in 3 parts. A first part was fixed and paraffin-embedded for diagnosis and standard immunohistochemistry (IHC). A second part was frozen after control for cellularity and only samples with at least 30% of tumor cells were retained for subsequent genomic analyses.