dataesr/scientific-paragraphs-categorization huggingface dataset:
2c ) thus constituting the minimal signature discriminating mice fed a MCDD. The hepatic lipid signature of NASH was constituted by cholesterol and 2 cholesterol esters, 7 fatty acids and 11 phospholipids (Fig. 2d ). Then, this statistical approach was validated by using unsupervised clustering DIANA (dendrogram with Euclidean distance) based on the 21 lipids identified. Indeed, the heat map showed that the groups of mice including mice fed a MCDD were well clustered (see Supplementary Fig. S2d ). Altogether, these results demonstrated that comprehensive lipidomic analysis combined to data learning approaches succeeded to characterize a specific hepatic lipid signature of the grades of fatty liver diseases, in particular of NASH. Serum lipid signature of nonalcoholic steatohepatitis. A specific lipid signature of NASH in the serum was we further investigated from the same series of animals described previously.
This opens new avenues for non-invasive early diagnosis of NASH and follow-up of patients with NAFLD. 5% kcal from fat; 3. 1 kcal/g), HFD (n = 5; 13 weeks on diet, Research Diet D12492i; 60% kcal from fat; 5. 24 kcal/g) and MCDD (n = 5; 5 weeks on diet, Teklad, Ref# TD. 90262). Mice fed HFD and MCDD developed NAFL and NASH, respectively  69, 70. Mice were housed at room temperature (22-24 °C) with a 12-hour light/12-hour dark cycle. Food and water were provided ad libitum. Body weight of each mouse was recorded every week. The optimal number of animal per study group (n = 5) was calculated using t-test with 0. 05 α error-set, 0. 9 for the power (1-β ) and based on lipidomic data already published  24. Then, based on our lipidomic data using total TG in the liver assessed in the three groups of mice, the calculated power was 0.
Quantitative real time PCR was performed by using LightCycler ® 96 Instrument (Roche, Life Science) machine. Gene expression levels were normalized to actin RNA levels and data analyzed with LightCycler ® 96 SW 1. 1 software (Roche, Life Science). For each sample, the gene to Gadph ratio was calculated based on an arbitrary value of copies determined by the standard curve for each gene, as described before  72.
Oven temperature was programmed from 200 °C to 350 °C at a rate of 5 °C per min and the carrier gas was hydrogen (0. 5 bar). The injector and the detector were at 315 °C and 345 °C respectively. Phospholipids for relative quantification were extracted as neutral lipids but with 2% acetic acid in the presence of the internals standards (Cer(d18:1/15:0) 16 ng; PE(12:0/12:0) 180 ng; PC(13:0/13:0) 16 ng; SM(d18:1/12:0) 16 ng; PI(16:0/17:0) 30 ng; PS(12:0/12:0) 156. 25 ng). After centrifugation the organic phase was collected and dried under azote, then dissolved in 50 μ L of methanol. Sample solutions were analysed using an Agilent 1290 UPLC system coupled to a G6460 triple quadripole spectrometer (Agilent Technologies) and using MassHunter software (Agilent Technologies) for data acquisition and analysis.
The collision energy optimums for Cer, PE, PC, SM, PI, PS were 2 eV, 2 eV, 30 eV, 25 eV, 45 eV, and 22 eV respectively. Then the corresponding SRM transitions were used in order to quantify different PL species for each class. Data were treated using QqQ Quantitative (version B. 05. 00) and Qualitative analysis software (version B. 04. 00). For Fatty Acid Methyl Ester (FAME) analysis, liver tissues (the equivalent of 1 mg) or serum (10 μ l) were extracted as neutral lipids in the presence of the internal standards glyceryl triheptadecanoate (2 μ g) and transmethylated 1 h in boron trifluoride methanol solution 10% at 55 °C. After addition of water (1 ml) to the crude, FAMEs were extracted with hexane (3 ml), evaporated to dryness and dissolved in ethyl acetate (20 μ l). FAME (1 μ l) was analysed by gas-liquid chromatography on a Clarus 600 Perkin Elmer system using Famewax RESTEK fused silica capillary columns (30 m × 0.
After drying under vacuum system, lipids were eluted with 2 mL of MeOH. Prior to LC-MS/MS analysis, samples were evaporated under nitrogen gas and reconstituted in 10 μ L of MeOH. LC-MS/MS analyses of eicosanoids were performed as previously described  76. Briefly, lipids were separated on a ZorBAX SB-C18 column (2. 1 mm, 50 mm, 1. 8 μ m; Agilent Technologies) using 1290 Infinity HPLC system (Agilent Technologies) coupled to an ESI-triple quadruple G6460 mass spectrometer (Agilent Technologies). Data were acquired in multiple reaction monitoring mode with optimized conditions (ion optics and collision energy). Peak detection, integration and quantitative analysis were done using Mass Hunter Quantitative analysis software (Agilent Technologies) based on calibration lines built with commercially available eicosanoids standards (Cayman Chemicals)  76.
Statistical Analysis. All calculations are performed using R v. 3. 2. 2  77. To avoid any bias due to animal experiment procedure, prediction analysis for microarrays was used on lipids identified from liver and serum between the four groups of mice define as a control group fed normal diet for mice fed HFD (n = 5), mice fed HFD (n = 5), a control group fed normal diet for mice fed MCDD (n = 5) and mice fed MCDD (n = 5) and including heterogeneity analysis, accurate and fast classifier for discriminating the diseased group mice fed MCDD to the others using "pamr" package  78. The maximum of misclassification error was set-up at 20% for both liver and serum analysis to determine the best threshold for the minimum of lipids discriminating the three groups of mice. Then, in order to identify the specific lipids that contributed to the significant overall effect between the different groups of mice, random forests was used with "randomForest" and "varSelRF" packages leading to obtain a narrow numbers of markers  38, 40.
To determine the best number of predictors (mtry) was used for each split of the tree and tuneRF() function was used to determine the lowest mtry for to the lowest out-of-bag (OOB) error data that was used to get a running unbiased estimate of the classification error as trees were added to the forest. Also ntree (number of trees to be built) was set up at 1490 and 1550 for liver and serum, respectively, corresponding to the number of the columns (variable) of the matrix multiply by ten. Indeed, with small sample sizes or even "small n large p" problems, growing large trees usually does lead to the best performance as demonstrated before  39. During the analysis, the mean decreased accuracy (MDA) and the mean decreased Giny (MDG) were determined. MDA was determined during the OOB error calculation phase and lipids with a large MDA were more important for classification of the data (data not shown).
In addition, MDG that was a measure of how each variable contributes to the homogeneity of the nodes and leaves in the resulting random forests was assessed. Lipids that resulted in nodes with higher purity have a higher MDG. Therefore, data were classified based on their variable of importance score. Principal component analysis (PCA), 95% confident ellipse centre to the mean and lipids of interest were computed and extracted using "FactoMinR" package. The global p-value was calculated using the critical probability associated with the F-test of the analysis of variance along the axes of the first and the second dimensions (α = 0. 05). Heat map using unsupervised clustering DIvisive ANAlysis (DIANA dendrogram) with Euclidean distance was built based on the lipids identified in the liver and the serum using heatmap.
Population monitoring We took advantage of a systematic monitoring scheme, involving ringing and a survey of reproduction, starting in 1990. Each spring, all known territorial pairs were closely monitored, and historicallyoccupied sites (including some abandoned before 1990) were checked for possible re-colonization  (Burger et al. , 2013). We defined this count of territorial pairs as population size. Repeated visits at occupied sites from mating to fledging periods were made to record the number of fledgling produced per pair (from 0 to 2), hereafter referred as fecundity. Capture-Resighting data were collected from 1990 to 2013. During this period, 524 out of 540 chicks (97%) born in the population have been ringed at the nest before fledging with a conventional metal ring and a Darvic plastic ring with a short alphanumeric code that can be read using a telescope at a distance up to 200 m  (Chevallier et al.
, 2015). Resighting data (212 events from 80 different individuals) consisted in resightings across the study area which was intensively monitored by different organizations, mostly in occupied territories but also within key areas used in winter or by non-breeding birds (e. g. Camargue, plain of la Crau). A total of 56 marked birds were recovered dead within the study area and then used to improve survival estimation  (Burnham, 1993). As a consequence of Darvic ring loss, an intensive survey was implemented so as to read metal rings, and a majority of individuals having lost their Darvic ring were actually identified  (Chevallier et al. , 2015). However, and so as to remove any potential bias in the survival estimation, ring loss has been included as a state process in the capture-recapture model (see below).
These eagles could have been observed as fledgling, floater with or without Darvic ring, territorial with or without Darvic ring or recovered dead (see the state-transition and observation matrices in Supplementary material A). The parameterisation of such a model for the French population of Bonelli's eagle has been recently performed with a model selection approach using data collected between 1990 and 2009  (Chevallier et al. , 2015). We used the same model structure, assuming this structure was not affected by additional data (dataset spanning up to 2013). More specifically, we parameterized survival probabilities according to the age of the birds (age 1, 2-3, 4 +), with no difference between sexes  (Hernandez-Matias et al. , 2011). Resighting probabilities were age-dependent (age 1, 2, 3 +) and accounted for the loss of the Darvic ring (for birds aged 3 +, i.
2. 2  (Choquet et al. , 2009). As lower survival of young individuals may generate spurious transience, we removed the first encounter in capture-recapture histories and accounted for agespecific survival in all models. The umbrella model adequately fitted the data (GOF tests: χ 48 2 = 26. 1, P = 0. 99). Fecundity of Bonelli's eagles, expressed as the number of fledgling per territorial female, was modelled using a Poisson distribution of error including a random variation around the mean as well as the age and experience of the breeding females involved (four classes: inexperienced and experienced young females [b 4 year old], inexperienced and experienced old females [≥ 4 years old]; Supplementary material C). Finally, we built a matrix population model (post-breeding census) including six different stages (Supplementary material D; Caswell 2001).
Because all previous parameter estimations in the literature were extracted from the same data set, we could not use them as informative priors in our model. Therefore, we checked the sensitivity of each parameter only by changing uninformative priors. The priors for effect size of the different covariates (power lines retrofitting on survival and temporal trends of immigration) were centred on 0. These effects were considered significant when the 95% of their posterior distribution did not overlap zero  (Grosbois et al. , 2008). We applied the Markov Chain Monte Carlo (MCMC) method to simulate observations from the posterior distributions in WinBUGS  (Lunn et al. , 2000)  which was run from R (package R2WinBUGS;  Sturtz et al. , 2005). We specified a burn-in of 40 000 and simulated 90 000 samples that were thinned by a factor 10 and ran 2 chains with different starting values.
2 ). The combination of different sources of demographic data into a unique IPM allowed us to explain the divergence between projections and observations by the occurrence of immigration at a rate of about 11%. Thus, a sustained immigration rescued the population by slowing down the decline before the main campaign of power lines' retrofitting took place from 1998. Thereafter, immigrant recruits reinforced a roughly stable local demography and allowed the population to actually increase. Our results indicated that about three immigrant females (most likely from Spain) were recruited each year in the French population. Note that this result entails an equal number of immigrant males to be recruited as we assumed similar demographic rates for either sex. This level of demographic connection between Spanish and French populations of Bonelli's eagle is actually in line with field data.
Given that residual humaninduced mortality sources have been identified (electrocution, illegal killing;  Burger et al. , 2013) , the studied population has the potential to become a source provided that appropriate conservation actions will be undertaken. Specifically, an absolute increase of 3% in adult survival (or of 14% in immature survival) would make the population selfsustainable  (Chevallier et al. , 2015). Second, emigration have also been documented with recruitments of birds born in France recorded in Catalonia (authors' unpublished data). Yet, data on emigration were too scarce for testing the occurrence of a relationship between immigration and emigration processes, potentially compensating each other  (Doncaster et al. , 1997; Runge et al. , 2006). Interestingly, the Catalan population actually underwent a trajectory similar to the French population, with a strong decline until 2000 followed by a recovery  (Real et al.
Acknowledgements We are grateful to the local network of volunteers and collaborators helping in monitoring the Bonelli's eagle population since 1990. The ringing programme is ethically approved by CRBPO. This study was funded by two species action plan between 1999 and 2009, and otherwise by DREAL-LR and DREAL-PACA. NL received a PhD grant from  Ecole Normale Supérieure  throught the  ED Sciences de l'Environnement (Aix Marseille Université ). Thank you to  G. Astruc  for her help with GIS.
The leakage of fluorescein into the other compartment was evaluated by fluorescence microscopy after 24 h of incubation at room temperature while maintaining the microfilament in place. To investigate the diffusion of fluorescein triggered by microfilament removal, the filament was removed from a glass-bottom device under fluorescence microscopy observation 10 min after filling the reservoirs. A numerical simulation of fluorescein diffusion was performed using COMSOL Multiphysics software.
Acknowledgements We thank  Floriane Cohen ,  Guillaume Laffite ,  Fanny Cayrac , and  Anne-Christine Brunet  for their help with our experiments. We thank  Caterina Tomba  for providing the protocol for glial cell culture. We thank  Danijela Vignjevic  for providing the tdTomato mice,  Pablo Vargas  and  Ana-Maria Lennon  for providing the GFP-LifeAct mice,  Isabelle Grandjean  and  Manon Chartier  from the  Animal Facility of Institut Curie  for their crucial support for mice. This work was performed in part in the technology platform of  Institut Pierre-Gilles de Gennes , in UMR 168 microfabrication cleanroom, and in Bio-Imaging Cell and  Tissue Core Facility (PICT-IBiSA) of Institut Curie. This work was supported by  ANR  " Investissements d'Avenir" for Labex and Equipex IPGG  ( ANR-10-LABX-31  and  ANR-10-IDEX-0001-02-PSL ), and grants from the  European Commission: MicroDEG, ERA-NET Neuron   JTC2012  "Novel Methods", http://www.
Cadaveric hip specimens and acetabular cup implant Six cadavers were used in this study, which was approved by the ethical committee of the Surgery School of the Fer à Moulin (Paris, France), which is a French institution who handles cadavers for research and education purposes. None of the authors had access to patient data identifications. The Ethics committee did not ask for any consent of the next kin in the present case. Both hips of each cadaver were tested, resulting in a total of 12 hips studied herein. The surgery was then realized similarly as in clinical conditions. All cadavers were placed in lateral decubitus position. A posterior approach to the hip joint was performed in all cadaveric specimens. After opening and exposing the joint capsule, the femoral neck was osteotomized and the femoral head was removed.
Acknowledgments This work has been supported by  French National Research Agency (ANR)  through the  PRTS program  (project OsseoWave  n˚ANR-13-PRTS-0015-02 ). This work has been realized thanks to the support of l 'Ecole de Chirurgie du Fer à Moulin (Paris, FRANCE). This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  682001 , project  ERC  Consolidator Grant 2015 BoneImplant).
This work has been supported by  French National Research Agency (ANR)  through the  PRTS program  (project OsseoWave  n˚ANR-13-PRTS-0015-02 ). This work has been realized thanks to the support of l 'Ecole de Chirurgie du Fer à Moulin (Paris, FRANCE). This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No  682001 , project  ERC  Consolidator Grant 2015 BoneImplant). The funders had no role Conclusion in the development of a medical device that could be used in the future in the operative room to help orthopedic surgeons adapt the surgical protocol in a patient specific manner. in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data analysis Each of the following clinical data was collected: age, gender, weight, BMI, histological type of cancer, number of previous chemotherapy lines, ongoing chemotherapy during biopsy. An enhanced-CT scan was performed less than one month before biopsy for each patient which underwent a CT-guided biopsy. A radiologist with 4 years of experience blinded to the clinical data reviewed the CT images in random order on a PACS workstation to collect target lesion characteristics (Carestream Health, Version 11. 4, Mountain View, CA). Patients' identities were removed from the images. CT data included the biopsied organ, the target lesion size (largest diameter) and the enhancement of the lesion. A 20 mm diameter ROI was drawn at the distal end of the co-axial needle in the axis of the cutting needle on the non-enhanced image.
The prognostic value of the ∆HU to identify successful biopsies was assessed by the receiver operating characteristic (ROC) curve. Cutoff values were further derived to by maximizing the Youden index (sum of the sensitivity plus specificity minus one). Tests were two-sided, with a level of significance set at P < 0. 05. All analyses were performed using Statistical Analysis Software (SAS) (version 9. 4, SAS Insitute Inc. , Cary, NC).
Background: Locomotor disorders and infections by Escherichia coli represent major concerns to the poultry industry worldwide. Avian pathogenic E. coli (APEC) is associated with extraintestinal infections leading to respiratory or systemic disease known as colibacillosis. The most common lesions seen in cases of colibacillosis are perihepatitis, airsacculitis, pericarditis, peritonitis/salpingitis and arthritis. These diseases are responsible for significant economic losses in the poultry industry worldwide. E. coli has been recently isolated from vertebral osteomyelitis cases in Brazil and there are no data on molecular and phenotypic characteristics of E. coli strains isolated from lesions in the locomotor system of broilers. This raised the question whether specific E. coli strains could be responsible for bone lesions in broilers.
For digestion, plugs were equilibrated in incubation buffer containing XbaI restriction enzyme (Takara) overnight. Pulsed-field gel electrophoresis was conducted in a CHEF-DRIII apparatus (Bio-Rad). Gels (1 % agarose) were run at 14 °C for 24 h in TBE buffer (4 mM Tris, 4 mM borate, 1 mM EDTA, pH 8. 3) at 6 V cm -1. Pulse times were increased from 10 to 30 s. XbaI restriction fragments of Salmonella enterica serovar Braenderup H9812 were used as size markers. Cluster analysis using Dice similarity indices was done in BioNumerics 6. 6 software (at 0. 5 % tolerance and 0. 5 % optimization) (Applied Maths, Ghent, Belgium) to generate a dendrogram describing the relationships among PFGE profiles.
Its rapid emergence and successful spread is strongly associated with antibiotic resistance  [31] [32] [33]. One O25:H4-B2-ST131 E. coli strain was detected in a broiler joint with arthritis in this study. In Brazil, this clone was previously detected in APEC strains recovered from broilers with different visceral lesions  [34]  and from APEC and human ExPEC collections  [25]. Although few data are available on this clonal group from poultry, Mora et al. [35]  reported an increasing presence of clonal group O25b:H4-ST131 in retail chickens. Interestingly, a retail chicken sample revealed macrorestriction profile indistinguishable from an E. coli strain isolated from a human with urinary tract infection  [36]. High percentage of multidrug resistant E. coli was detected in this study. It is known that E.
In the state of Minas Gerais, where samples were collected, tetracycline use has no longer being recommended by poultry veterinarians due to its prohibition and bacterial resistance (personal information). These data suggest that the discontinued use of tetracycline in poultry in the region may have provided an increase in the number of E. coli strains susceptible to this drug, as described for Salmonella strains in USA, where it was observed significant reduction of humans and swine strains resistant to tetracycline after its prohibition as prophylactic drug in animal feed  [42]. All 15 E. coli strains studied were isolated from the exudate of osteomyelitis or arthritis lesions. The strains EC11 and EC18 classified as non-pathogenic were also isolated from broilers with vertebral osteomyelitis and arthritis, respectively.
Acknowledgments The authors thank  Nathalie Lallier  for her valuable technical assistance on PFGE and lethality tests, and the personnel from the experimental unit  PFIE (Plateforme d'Infectiologie Expérimentale ) at the  INRA-Centre Val de Loire, Nouzilly (France). We also thank  Jorge Blanco  and  Ghizlane Dahbi  from  Laboratorio de Referencia de E. coli (LREC)  of the  University of Santiago de Compostela (Spain)  for kindly providing the antisera.
In the present paper, we seek to overcome this shortcoming and propose an a posteriori construction of a kinematically admissible displacement field. The proposed method applies to any UGPLS solver (regardless of the discretization strategy and the linear solver). The ideas underlying the construction are described now. Let ε N denote the discrete strain field resulting from a UGPLS analysis, where the supscript 'N' is a discretization parameter which relates to the fineness of the grid (see Sec. 3. 1). In a Galerkin setting, ε N can be considered as a cell-wise constant estimate of the true strain ε  [12]. From Eq. (3c), the discrete stress polarization τ N is evaluated. Likewise, it is seen as a cell-wise constant estimate of the true stress polarization τ. If the true stress polarization τ were known exactly, then the displacement u would be the periodic solution to Eq.