dataesr/scientific-paragraphs-categorization huggingface dataset:
Rapid prototyping tool: from Simulink to Gumstix The novel fast prototyping tool we have developed can be used to automatically and easily download a Simulink model (containing the controllers and the observers in our case) onto the autopilot board. This development toolchain uses a user friendly interface, such as Matlab Simulink, to execute in real-time digital controllers designed in the Simulink environment. This novel automatic code generation tool makes the implementation of a digital control system considerably easier and faster because: • it generates and compiles a bug-free C code • it gives block-level access to on-chip peripherals (wifi, serial connections, etc. ) • it can be used to directly design systems using floating-point system design, simulation and scaling procedures thanks to the 32-bit FPU of the Gumstix (it also handles all the fixed-point data).
When the operator wants to make the robot change target, he/she just needs to send the robot the target coordinates, expressed in the inertial frame ( T I X k ). Once the target's new coordinates have been specified, the robot immediately changes its eye orientation and re-positions itself appropriately with respect to the reference R T X ⋆. A simulation of the robot's target-jumping behaviour is illustrated in the figures 7, 8 and 9. Remark 2: These simulations were performed with the Processor-In-the-Loop (PIL) environment described in the section 2. 1, with the set of parameters given in table  1. The whole control strategy presented in section 3 was developed under Matlab/Simulink and the computations were performed at a frequency of 400Hz (except for the VFR which was computed at only 40 Hz by considering a realistic refresh rate of the visual sensor).
Acknowledgements The authors would like  Jessica Blanc  for correcting the English manuscript. This work was supported by  CNRS ,  Aix-Marseille University  and the  French National Research Agency (ANR)  with the EVA,  IRIS  and  Equipex/Robotex  projects ( EVA  project and  IRIS  project under ANR grant numbers  ANR608-CORD-007-04  and  ANR-12-INSE-0009 , respectively).
While an overestimation was observed, the simplified quantification based on target ROI to cerebellum ratio at equilibrium (DVR-1) was highly correlated with the 5 studied kinetic models. The present data suggest that short imaging times (10-20 minutes) for imaging conducted less than 30 minutes after the administration of [ 18 F]LBT-999 are feasible for small animals. High reproducibility and reliability are prerequisites for the use of a PET tracer in the evaluation of DAT in pharmacological challenges and/or animal models of brain disorders. In this study, the non-invasive DAT quantification using [ 18 F]LBT-999 in the striatum assessed by the BP ND was reproducible with low variability ranging from 8 to 14%, depending on the model used. The reliability of DAT quantification was high in this region, reaching for example an ICC of 0.
Synaptic responses were recorded using an Axoclamp 900A amplifier and digitized using Digidata 1440A (Molecular Devices) with WinWCP software (John Dempster, University of Strathclyde, United Kingdom). To prevent muscle contractions, -conotoxin GIIIB (2 M; Peptide) was used. To evaluate the threshold of nerve-evoked action potentials (APs), muscle preparations were incubated in 0. 5 M D-tubocurarine (dTC) for 60 min and then continuously perfused by 3 M neostigmine and 0. 2 M dTC throughout the recording period  (Wood and Slater, 1995). The low concentration of dTC and the inhibition of cholinesterase allowed the recovery of the muscle AP generation in part of the muscle fibers. Contractions of diaphragm in these conditions remained very weak, which made possible intracellular recording by microelectrodes.
Images were collected using an oil-immersion objective [Plan-Apochromat ϫ63/1. 2 numerical aperture (NA)]. The pinhole aperture was set to 1 Airy unit. Images were digitized at 12-or 16-bit resolution into 512 ϫ 512 or 1024 ϫ 1024 pixel arrays. Data were analyzed using Zen 2008 software on a series of "lookthrough" projections of average intensity. Immunolocalization by EM. After perfusion-fixation, as described in Immunolocalization at light microscopy, muscle fibers were incubated in 4% normal horse serum (NHS) for 30 min and then with 4H1 antibody (0. 5 g/ml) supplemented or with 30 nM biotinylated ␣-BTX (Invitrogen) with 1% NHS at room temperature overnight. After washing, biotin was detected using streptavidin coupled to gold particles (1. 4 nm in diameter, 1:100 in PBS/BSA; Nanoprobes) for 2 h.
Signals from the force sensor were recorded and analyzed digitally, using PowerLab system and LabChart 6 software (ADInstruments). MG animal model. An experimental autoimmune model of MG was produced according to the following protocol  (Baggi et al. , 2003). Female rats 6 -8 weeks of age were immunized twice (1 month intervals) by subcutaneous administration of the peptide (DGDFAIVKFT-KVLLDYTGHI) mixed in Freund's complete adjuvant (first injection) and incomplete (second injection). The development of muscle weakness was diagnosed in vivo by the marked decrement of surface electromyogram amplitude (i. e. , integral AP) of hindlimb muscles. Under urethane anesthesia (1. 2 g/kg, i. p. ), the sciatic nerve was stimulated (40 Hz, train of 200 stimuli) in the femoral part and the integral muscle action potential from posterior surface of the lower leg was recorded by skin electrodes.
F intensity was measured over the area of the TSC cell body and the relative changes in F intensity were evaluated as a percentage as follows: ⌬F/F ϭ (F Ϫ F 0 )/F 0 ϫ 100. Stimulation of the distal end of the cut motor nerve (20 Hz, 120 s) was achieved using a suction electrode. To prevent muscle contractions evoked by transmitter release, we used -conotoxin GIIIB (2 M; Peptide). If the calcium waves were triggered in a TSC by a burst of nerve stimulations (20 Hz, 120 s), the preparations were allowed to rest for 30 min for recovery with or without methyllycaconitine (MLA) (10 nM) to specifically block ␣7 nAChR); then, a second burst of nerve stimulations (20 Hz, 120 s) was applied and the F intensity was measured. Data analysis. In all cases, data are reported as mean Ϯ SEM and n indicates the number of end plates measured in each group.
SERT cre and ePet-cre mouse lines demonstrate similar selectively for expression in serotonergic neurons, as 90. 3% of 651 total eYFP-positive cells from five SERT cre mice injected with cre-ON eYFP virus were found to double label with tryptophan hydroxylase. However, preliminary results in TdTomato reporter mice suggested greater penetrance of expression in serotonergic populations with the SERT cre line (data not shown), therefore we used these mice in electrophysiology experiments to ensure that cre-OFF viral expression was limited to nonserotonergic neurons. We obtained whole-cell patch clamp recordings in horizontal slices containing VTA tissue beginning 12 weeks after surgery. Stimulation of the non-serotonin pathway produced excitatory post-synaptic currents (EPSCs) in 34 out of 43 cells tested (79.
Optogenetic real-time place preference Mice were placed in a 24 × 36 cm plastic chamber with walls of opposite halves identified by horizontal or vertical stripes, and a small 0. 5 cm barrier on the floor at the division site. A cohort of naïve wild-type mice tested in these chambers did not display a preference for either side (51. 8 ±2. 6% preference for horizontally-striped half; n=6). Mouse movement was tracked with Ethovision computer software (Noldus; Wageningen, Netherlands) and presence in the randomly-assigned laser-paired half resulted in 15 mW 473nm laser stimulation at 20 Hz, with 5 ms pulses. Mice remained in the chamber for 12 minutes. Electrical self-stimulation studies indicate that the reward substrate within the DRN is increasingly responsive to higher stimulation frequencies, with reward thresholds occurring within the range of 13-40 Hz, depending on electrode placement  (Rompre and Miliaressis, 1985).
Acknowledgments This research was supported by the  Intramural Research Program  of the  National Institute on Drug Abuse. We are grateful to  Dr. Karl Deisseroth  for providing cre-ON ChR2 plasmid DNA,  Dr. Zheng-Xiong Xi  for assistance with mouse self-administration,  Dr. Francois Vautier  and  Joni McKenzie  for assistance with transgenic mouse colonies,  Zachary Fusfeld ,  Christina Hatch ,  India J. Kawata , and  Martha Zemen  for assistance with surgery and behavioral testing,  Doug Howard  and  Lowella Fortuno  for assistance with cre-OFF vector preparation, and the  NIDA Optogenetic and Transgenic Technology Core  for production of other vectors.
S5 ). These data confirmed that PPAR-d activity determines C1q transcription in AM. There was no striking difference in transcript and total protein levels of PPAR-d between WT and Trem-2 2/2 AM, suggesting that the ability of TREM-2 to regulate C1q via PPAR-d was not due to enhanced PPAR-d levels (Fig. S6 ). To demonstrate that TREM-2 itself downregulates PPAR-d activity, we made use of TREM-2 over-expressing HEK cells and quantified PPAR-d activation using a reporter system. Over-expression of TREM-2 was able to lower both basal and ligand-induced PPAR-d reporter activity (Fig. 4G ). To rule out differences between HEK cells and macrophages, and to further confirm the reporter gene experiments, we next stimulated TREM-2 or GFP control overexpressing RAW264. 7 macrophages with GW0742 or DMSO control and monitored nuclear PPAR-d levels.
TREM-2 is deleterious during pneumococcal pneumonia The enhanced bacterial phagocytosis of S. pneumoniae in Trem-2 2/2 mice finally led us to monitor the survival of WT and Trem-2 2/2 mice during pneumonia. Ninety five hours post infection, before the first Trem-2 2/2 mouse succumbed, 60% of WT mice were dead, demonstrating conclusively that WT mice displayed enhanced mortality compared to their TREM-2 deficient counterparts during pneumococcal pneumonia (Fig. 6A ). To determine the reasons for this effect, we evaluated pulmonary bacterial loads and bacteremia shortly before the first mouse succumbed. TREM-2 deficient mice exhibited a thousand fold decrease in S. pneumoniae burden in lungs 48 h post infection (Fig. 6B ). These data corroborated our earlier time points of infection (Fig. 3M ).
(E) Representative H/E staining of lungs 48 h post infection. (F) Lung inflammation score, as described in the Methods section. (G) Levels of lung cytokines were evaluated using ELISA. (H-J) Representative Ly6G (H), active caspase 3 (I) and TUNEL (J) staining of lungs 48 h post infection. Magnification depicted for TUNEL stains is 206 and arrows indicate caspase 3 positive cells. (K-L) Thymocytes (n = 4) were treated with 1 mM dexamethasone and apoptosis was evaluated using DNA laddering (K) or Annexin-V/7-AAD positivity (L). (M) WT and Trem-2 2/2 AM (n = 8 per genotype and condition), were fed CFSE labeled apoptotic cells and efferocytosis was assessed 1 h later using FACS. Data in B, D, F, G and M are presented as mean 6 SEM, WT versus TREM-2 2/2. Data in A-G are representative of two independent experiments.
Microarray Isolated total RNA was purified using the RNeasy kit per manufacturer's instructions (Qiagen). Total RNA (200 ng) was then used for GeneChip analysis. Preparation of terminal-labeled cDNA, hybridization to genome-wide murine GeneLevel 1. 0 ST GeneChips (Affymetrix), and scanning of the arrays were carried out according to manufacturer's protocols. Affymetrix microarray cell intensity files were combined, and expression was normalized using the robust multi-array average algorithm  [71] , generating an expression matrix. Identification of differentially regulated genes was performed with significance analysis of microarrays as described previously  [72] ; a false-discovery rate of 5% was imposed. All data are deposited at Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) and the accession ID is GSE51378.
(K-L) Thymocytes (n = 4) were treated with 1 mM dexamethasone and apoptosis was evaluated using DNA laddering (K) or Annexin-V/7-AAD positivity (L). (M) WT and Trem-2 2/2 AM (n = 8 per genotype and condition), were fed CFSE labeled apoptotic cells and efferocytosis was assessed 1 h later using FACS. Data in B, D, F, G and M are presented as mean 6 SEM, WT versus TREM-2 2/2. Data in A-G are representative of two independent experiments. Data in M is pooled data from 2 independent experiments; * p = ,0. 05, ** p = 0. 005. doi:10. 1371/journal. ppat. 1004167. g006.
Magnification depicted for TUNEL stains is 206 and arrows indicate caspase 3 positive cells. (K-L) Thymocytes (n = 4) were treated with 1 mM dexamethasone and apoptosis was evaluated using DNA laddering (K) or Annexin-V/7-AAD positivity (L). (M) WT and Trem-2 2/2 AM (n = 8 per genotype and condition), were fed CFSE labeled apoptotic cells and efferocytosis was assessed 1 h later using FACS. Data in B, D, F, G and M are presented as mean 6 SEM, WT versus TREM-2 2/2. Data in A-G are representative of two independent experiments. Data in M is pooled data from 2 independent experiments; * p = ,0. 05, ** p = 0. 005. doi:10. 1371/journal. ppat. 1004167. g006.
Statistical analysis PET/CT assessment and the standard procedure (surgical biopsy and clinical monitoring) were compared for sensitivity, specificity, positive and negative predictive values (PPV and NPV), and positive and negative likelihood ratios (PLR and NLR). The distribution of T/L ratios between benign and malignant tumors was assessed using a non-parametric test (Mann-Whitney test). Only p-values ,0. 05 were considered statistically significant. All statistical analyses were performed with SPSS v. 17 (IBM).
Beginning of the thesis La Pallière's dyke is one of our test site, on which we will conduct regular acquisitions. This 1100m section is interesting because previous land surveys have shown for many years that it is not perfectly stable. As a first test site, we set up 50 ground control points (GCP) to be sure we have enough data to analyse the results. As we are concerned about the accuracy on the Z-axis, we surveyed those points using precision levelling techniques, while XY were determined by RTK GPS. Setting up points that way is time consuming, as two days were needed to complete the full operation. Even though some improvements are expected very soon to embark RTK GPS on UAV  (Stempfhuber 2013 , Piksi 2013) , we do not think it will yet be accurate enough on the altitude, and so a precision levelling might still be necessary in the future for that range of accuracies.
Bundle adjustment residuals We refined the existing ENSG calibration polygon by adding new targets. With the help of the last year student from ENSG, these have been determined from 5 different stations. Using IGN's Comp3d calculation software, we were able to get coordinates with a submillimetric accuracy. From a set of 8 pictures made with various angles of view, we have computed 4 calibration models. The mean absolute errors of these residuals are listed in Table  2. Note that we used the same image measures for each computation. Using the RadialStd model we get the best residuals, while the RadialBasic does not seem to be very adapted to the situation. On the other way, the most complex models give residuals between these. We then used these calibration models on our UAV pictures, and computed the bundle adjustments following two different strategies :.
X (mm) Y (mm) Z (mm) Image (pixel) • "Figee" : Freeze the calibration parameters in the bundle adjustment • "AutoCal" : Re-evalutes the calibration parameters, which are released in the bundle adjustment. For the AutoCal process, we tried to firstly adapt it on a central subsample from our dataset -20 pictures at the middle of the dyke -and then used that new calibration on the entire dataset. That step finaly proved to be pointless, as we obtained similar results while working directly on the full dataset. Table  3  lists the different results we had for these models. It seems to indicate that the calibration made on the polygon should not remain frozen, although we noticed some slight improvement while using Figee with the FraserBasic model. The 5 coefficients distortion model applied on RadialExtended leads to the best residuals, while adding an affine and a decentric part  (Fraser)  leads to the worst one.
The camera was sliding on a "perfectly straight" rail (supposed to be the UAV), on which we measured the displacements between each pictures. To simulate faithfully the conditions required on the field, the accuracy of the GCP had to be improved from the same rate. We set up on the wall a network of 75 targets that we surveyed with metrological methods. Each target has been measured 8 to 14 times, resulting on RMSE around 0,2mm. The position of the camera has been measured using a Renishaw XL-80 interferometer, assuring a 0,5 ppm accuracy. Navigating between 0 and 50 meters, the accuracy on the positions should not exceed 25 microns. We hope to be able to use these data to get a clear idea on how the bundle adjustment results influence the position and orientation results. We believe that the tie points detection applied on the textured wall delivered many tie points, but their quality and repartition could be improved to approach the centimetric accuracy required.
II. METHODS Molecular dynamics (MD) simulations of various ZIF frameworks, empty and with CH 4 molecules loaded in their pores, were performed in the isostress-isothermal ensemble (N , σ , T) using the NAMD 2. 9 software package. 23 The temperature was fixed using Langevin dynamics on the heavy atoms, with a damping coefficient of 10 ps -1. The pressure was fixed by a modified Nosé-Hoover method, which is a combination of the constant pressure algorithm proposed by Martyna et al. 24  with piston fluctuation control implemented using Langevin dynamics. 25 We used a piston oscillation period of 0. 2 ps and a piston decay time of 0. 1 ps. Though the stress considered in this work corresponded to isotropic compression, the simulation was performed in the (N , σ , T) ensemble, and not the (N , P, T) ensemble, by allowing full flexibility of the unit cell.
The NAMD source code for the barostat was patched in order to allow the unit cell to be fully flexible, with random variations of all components of the unit cell vectors (rather than the 3 vector lengths as implemented in NAMD version 2. 9). The patch is available as supplementary material. 26  integration time step of 1. 0 fs was used, and each MD simulation was run for 5 ns, of which the first 1 ns was discarded as an equilibration period and not used for the calculation of averages and time correlations. Checks performed with longer simulations showed that calculation of elastic constants from 4 ns of unit cell fluctuations in the (N , σ , T) ensemble yielded elastic constants with an uncertainty of ±0. 03 GPa. In all cases, we checked that the elastic tensor is definite positive, and thus fulfills the Born elastic stability criterion.
However, prerequisites for this to materialize are: (1) that such models are developed, something that initiatives like the Virtual Physiological Human (VPH) strongly support  [1, 2] , and  (2)  that appropriate model identification methods are developed, whose function is to estimate the various model parameters from the specific patient multimodal image data. In this context, an important issue remains: how to validate such models and associated identification methods? Medical image simulation appears as an interesting approach to this problem. It has undergone significant progress in the last ten years, with simulators being developed for many imaging modalities, e. g. SINDBAD  [3]  in CT, SIMRI  [4] , BrainWeb  [5]  in MR, SORTEO  [6] , GATE  [7]  in PET and FIELD-II  [8]  in US. This allows addressing a number of needs related both to the design and optimization of imaging equipment and the validation of image processing software.
Use of a foundational ontology 1 http://www. creatis. insa-lyon. fr/vip/ontologies. html 2 http://bioportal. bioontology. org/ontologies/OntoVIP In this interdisciplinary context it is also important to ensure that the resulting application ontology will be consistent. Therefore, we chose to rely on a common integration framework provided by a foundational ontology called DOLCE (Descriptive Ontology for Language and Cognitive Engineering)  [11]. This choice is based on our important experience of this framework gained in the context of the NeuroLOG project  [12, 13]. DOLCE was produced during the WonderWeb project  (2001) (2002) (2003). It is an ontology of particulars and defines some 40 basic concepts such as for example endurant, perdurant, quality, abstract, and about 50 relations  3. DOLCE is foundational in the sense that it provides entities and relations that are relevant for many kinds of application domains.
Ontology module extraction approach An ontology module can be an entire ontology or a subset of an ontology containing the knowledge needed for a certain application. There are many advantages in extracting modules as a subset of an existing ontology rather than importing them entirely. Particularly, it helps to clearly define the scope of the application and avoids overwhelming the application ontology with numerous entities not directly linked to the application. Indeed, by importing several existing ontologies, the size of the ontology importing the modules could increase dramatically, which could be a problem for reasoning since the current reasoners are particularly sensitive to the size of the ontology. All extractions were made using the vSPARQL  [16]  and Gleen software  [17] , both developed by University of Washington in Seattle (more details are provided in Appendix A).
Ontologies modularization in VIP In the VIP project, we selected several existing ontologies, namely the Foundational Model of Anatomy (FMA), the Mouse Pathology ontology (MPATH), the Phenotypic Attribute and Trait Ontology (PATO), the Radiology Lexicon (RadLex) and the Chemical Entities of Biological Interest ontology (ChEBI), and extracted modules containing the knowledge needed for our application (Table  1 ). They all were widely recognized ontologies, built according to the Open Biomedical Ontologies (OBO) Foundry principles  [18]  (especially they are orthogonal, i. e. do not overlap), and available from the NCBO BioPortal. By reusing existing ontologies, we increase the compatibility with existing software and platforms. Furthermore, we ease the construction of our ontology as we can focus on modeling the concepts specific to our application.
II. 3. Creation of new ontology modules Several aspects of the domain of discourse of medical image simulation were not covered by existing ontologies. So we had to develop the corresponding modules, following the OntoSpec methodology. OntoSpec assists the ontological knowledge modeling step, "upstream of the formal representation and knowledge implementation steps"  [29]. According to this methodology each new ontology component is first defined as a textual document of semi-formal nature, capturing rich semantics. In particular, each new conceptual entity (concept or relation) is characterized by its essential properties, such as its subsumption link with parent concepts or relations, or "existential restrictions" involving some relations and classes of the ontology. This semi-formal part is usually completed by an informal definition and together with relevant examples, citations or references to external documentation.