dataesr/scientific-paragraphs-categorization huggingface dataset:
In the near term, comprehensive testing of actionable mutations will be accomplished via NGS-based CDx assays and used to match patients with appropriate targeted therapies. Longer term, the utility of NGS to predict responders to immunotherapy, either through RNA-Seq based gene expression or mutational burden, could also drive significant clinical uptake of clinical NGS testing. Recent data suggest that NGS may be broadly applicable to ctDNA, which can be safely and repeatedly obtained through a "liquid biopsy" and may actually be more representative of tumor heterogeneity than a single biopsy. Pending further clinical validation, this approach could open entire new avenues, including detection of early-stage cancers, determination of residual disease, and longitudinal monitoring for resistance mechanisms.
Methods: The study used bibliometrics to undertake a quantitative analysis of research output in the 24 leading countries in cancer research internationally on the basis of articles and reviews in the Web of Science (WoS) database. Results: A total of 32,161 lung cancer research articles from 2085 different journals were analyzed. Lung cancer research represented only 5. 6% of overall cancer research in 2013, a 1. 2% increase since 2004. The commitment to lung cancer research has fallen in most countries apart from China and shows no correlation with lung cancer burden. A review of key research types demonstrated that diagnostics, screening, and quality of life research represent 4. 3%, 1. 8%, and 0. 3% of total lung cancer research, respectively. The leading research types were genetics (20%), systemic therapies (17%), and prognostic biomarkers (16%).
Methods We performed a bibliometric analysis of research outputs during 2004 to 2013 on the basis of articles and reviews in the Web of Science (WoS) database. This analysis contains full bibliographic information about the articles, including all addresses and the numbers of citations received by each article. The WoS is considered the optimum database for undertaking this type of evaluation as the use of additional biomedical databases does not significantly increase the yield of relevant journals. We identified the lung cancer articles by means of a specially developed algorithm formed by the intersection of two filters. Each filter consisted of lists of specialist journals for cancer (185 journals) and lung disease (11 journals), as well as specific title words relating to both subjects.
However, fractional counts alone do not give us specific information on the predominant focus of lung cancer research in each individual country, as otherwise, countries producing the largest volume of research within a specific category would appear to have the greatest commitment. Outputs of articles in lung cancer and all oncology research in two quinquennia and relative commitments to the subject area within cancer research. Cells tinted pale green indicate values greater than 1. 41, those tinted yellow indicate values less than 0. 71, and those tinted pink indicate values less than 0. 50. database, the largest research type (genetics) accounted for 20% of the articles, and the smallest (QoL) just 0. 3%. Research on systemic therapies, which included articles in the chemotherapy (11. 6%) and targeted agents (5.
Acknowledgements The authors thank  Dr Akansha Ashvani Sehgal ,  Dr Fatiha Kateb  and  Dr Roberto Buratto  for valuable assistance. This work was supported by the  Swiss National Science Foundation (SNSF) , the  Ecole Polytechnique Federale de Lausanne (EPFL) , the  Swiss Commission for Technology and Innovation (CTI) , the  French CNRS , and the  European Research Council  ( ERC  contract 'Dilute para-water').
29 At the same time, this surge of interest also contributed to digitization campaigns of visual archives,  30  which provides researchers access to very useful databases, such as the European Film Gateway project devoted to archival images about the First World War,  31  or DVD compilations such as the one made by the Belgian Film Archives. 32 wadays, most of the SCAB productions available at the audio-visual service of the Belgian Ministry of Defense and at the Belgian Film Archives are post-war productions (1918-1922), among which some yser journal newsreels and many post-war anniversary films and compilations put together by the SCAB. However, all of them used original footage shot by the SCAB at the Yser front during the conflict. They are now often considered as the only remaining window on the original footage of the Great War, which has probably disappeared forever.
However, as early as the 1920s, it became apparent that this outburst of national fervour would not last". 52  fact, the 'Belgian feeling' deteriorated during the conflict. In the post-war years, the Flemish-nationalist movements blossomed. The Northern and Southern parts of the country each took divergent paths and adopted distinct ideological causes. This fracture was also reflected in documentaries because the SCAB records  53  were recycled by different ideological groups, each with a particular 'war culture'. These documentaries exploited the SCAB footage to serve their own purposes. On the one hand, the SCAB, which had a large supply of visual material of the front at its disposal, used this material when it considered it fit and edited documentaries that combined archive footage and re-enactments.
Acknowledgments Studies in the  Center for Epigenetics and Metabolism  are supported by the  National Institute of Health , Merieux Research Grants, and  INSERM (Institut National de la Sante et Recherche Medicale, France). Open Access This chapter is distributed under the terms of the Creative Commons Attribution-Noncommercial 2. 5 License (http://creativecommons. org/licenses/by-nc/2. 5/)which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. The images or other third party material in this chapter are included in the work's Creative Commons license, unless indicated otherwise in the credit line; if such material is not included in the work's Creative Commons license and the respective action is not permitted by statutory regulation, users will need to obtain permission from the license holder to duplicate, adapt or reproduce the material.
Three cases of C. celerecrescens infections were also described including an osteomyelitis, an abscess secondary to an open fracture and a post traumatic wound infection  [7, 8, 17]  (see table  2  for details). Here we report the first case of osteitis related to C. indolis identified by MALDI-TOF MS using Biotyper database. The recent spread of new identification tools in routine such as MALDI-TOF MS allows an accurate identification of bacterial species that were previously underestimated. Nevertheless, there is only one reference spectrum of C. indolis, C. sphenoides and C. celerecrescens included in the Bruker database (Biotyper v2. 3) and there is still no reference for C. methoxybenzovorans and D. guttoideum. These limits may lead to an underestimation of these species. Hopefully, new reference spectra will be soon included in the upcoming databases.
In this study, we further attempted to identify the patient strain (Strain 570. 15) using Rapid ID 32A strips (BioMérieux, Marcy-l'E l , F c ) that is still widely used in routine microbiological diagnosis. The test misidentified the strain as C. clostridioforme with an acceptable significance (biochemical API profile: 45362000, 99,4% T=0. 77) except for a positive reaction for indole production. Interestingly, Bouvet et al. reported the misidentification of C. celerecrescens as C. clostridioforme using RAPID ID 32A strips  [17]. This type of mistakes pinpoints the need to integrate new strains to refine biochemical databases. In order to help identifying these phylogenetically related anaerobic species in routine diagnosis, and waiting for enlarged databases, we provide a summary of the main biochemical characteristics of C.
Gram staining showed large spore-forming Gram-variable bacilli. Subculture performed on blood agar plates under anaerobic conditions grew with medium size mucoid colonies surrounded by a single zone of beta-hemolysis (two out of three samples). MALDI-TOF mass spectrometry (MS) performed directly on the colonies identified Clostridium indolis (Log score value of 2. 19 matching Clostridium indolis reference strain DSM755T; MALDI Biotyper v2. 3). This identification was confirmed by the National Reference Center of Anaerobic Bacteria and Botulism (Institut Pasteur, Paris, France) by 16S rDNA gene sequencing using forward AAGGAGGTGATCCAGCCGCA and reverse primers AGAGTTTGATCATGGCTCAG, (99,6% of identity with the sequence of Clostridium indolis type strain DSM755T, GenBank accession number Y18184) (Strain 570.
Scrapie-infected sheep brain This was either a classical scrapie PG127-infected VRQ/VRQ sheep brain stem sample that has been endpoint titrated by intracerebral inoculation in tg338 mice and has a titre of 10 6. 6 ID 50 /g  [30] , or cerebral cortex brain material from a confirmed scrapie-positive VRQ/VRQ sheep (SE1848/0005)  [31]. Plasma samples from scrapie-infected sheep: these were obtained from classical scrapie-positive VRQ/VRQ sheep. Plasma samples from sheep experimentally infected with classical scrapie were prepared from animals challenged by oral inoculation with PG127-infected sheep brain homogenate as previously described  [19]. Plasma samples from sheep naturally infected with classical scrapie were prepared from animals born and maintained in a flock endemic with the disease  [32]  and that were confirmed positive for PrPSc through routine statutory surveillance (data not shown).
Sensitivity of PrP transgenic Drosophila to ovine prions We first established the sensitivity of ovine PrP transgenic Drosophila to ovine scrapie prion infectivity. To do so, PrP transgenic Drosophila at the larval stage were exposed to a dilution series of PG127 scrapie-infected sheep brain homogenate. The locomotor ability of prion-exposed Drosophila was assessed, after hatching from the larval stage, by a negative-geotaxis climbing assay and the data were expressed as a PI. Supplementary Data S1 shows that PrP transgenic Drosophila demonstrated an accelerated decline in locomotor ability after hatching following exposure to scrapie prions at the larval stage compared with the response seen after exposure to scrapie-free sheep brain material. This accelerated decline, which became apparent ∼10 days after hatching, diminished upon exposure to increasing dilution of scrapie-infected brain homogenate.
This titration effect was evident over the duration of the assay and was most clearly shown during the first half of the time course when the climbing ability of flies was assessed. Accordingly, the data in Figure  1  show linear regression analysis of the PI from Supplementary Data S1 for each fly line from day 1 to day 22 after hatching. These data demonstrate that VRQ(GPI) (Figure  1A ) and VRQ(cyt) (Figure  1B ) PrP transgenic Drosophila both showed a similar sensitivity to all dilutions of scrapie-infected sheep brain material, although the magnitude of the response by the VRQ(cyt) fly line was somewhat greater than that of VRQ(GPI) flies. Supplementary Data S2 shows P-values for the statistical analysis of the PI for each fly line in response to dilutions of scrapie-infected sheep brain material compared with the response induced by the control sheep brain sample.
The data given in Figure  3  show that adult VRQ(cyt) Drosophila displayed an accelerated decline in locomotor activity, after exposure at the larval stage, to plasma isolated from PG127-infected donor sheep compared with similar flies exposed to control scrapie-free sheep plasma. The decline in locomotor activity induced by plasma prepared from sheep 30 days post-PG127 challenge (Figure  3A ) was less marked than that seen in response to plasma isolated from the same sheep at the clinical stage of scrapie disease (Figure  3B ). The locomotor activity of VRQ(cyt) Drosophila was also assessed after exposure to plasma isolated from sheep at 60, 90 and 120 days post-PG127 challenge. Analyses of these additional time points provided further evidence that plasma isolated later in the time course of PG127-induced non-prion-exposed tg338 mouse brain (negative control); Tracks 3-8: brain samples from prion disease-positive tg338 mice in Table  1.
The locomotor ability of plasma-exposed Drosophila was assessed, after hatching from the larval stage, by a negative-geotaxis climbing assay and the data were expressed as a PI. Supplementary Data S4 shows that PrP transgenic Drosophila demonstrated an accelerated decline in locomotor ability soon after hatching following exposure to PG127-infected sheep plasma at the larval stage compared with the response seen after exposure to scrapie-free sheep plasma. The rate of decline in locomotor ability diminished with exposure to increasing dilution of scrapie-infected plasma, indicative of titration of a particulate transmissible moiety, a characteristic feature of the infectious scrapie agent  [36]. The accelerated decline in locomotor ability became apparent <10 days after hatching and was most evident during the first half of the time course when the fly climbing ability was assessed, in a similar manner to that seen in response to PG127 scrapie-infected sheep brain material.
Detection of pre-clinical natural scrapie blood plasma by PrP transgenic Drosophila We next investigated whether PrP transgenic Drosophila could detect plasma from sheep with natural scrapie. The donor animals were VRQ/VRQ sheep born and maintained in a flock endemic for natural classical scrapie  [32]. Blood samples were collected from sheep shortly after birth and then at regular intervals until the animals showed clinical signs of terminal scrapie disease when they were killed. All of the killed blood donor sheep were shown to be positive for scrapie disease by routine testing for disease-associated PrP (data not shown), and the mean survival time of the animals was 695 ± 25 days. PrP transgenic Drosophila, at the larval stage, were exposed to plasma from sheep with natural scrapie and the locomotor ability of adult flies was assessed by a negative-geotaxis climbing assay with the data expressed as a PI.
The locomotor ability of adult VRQ(cyt) PrP transgenic Drosophila was also assessed after exposure at the larval stage to plasma prepared at regular intervals during the time course of natural scrapie in sheep. The data given in Figure  6  show that plasma from sheep with natural scrapie aged ≥6 months induced a statistically accelerated decline in locomotor ability compared with that seen with control scrapie-free plasma. The decline in locomotor activity of VRQ(cyt) PrP transgenic Drosophila became more pronounced when exposed to plasma samples isolated during the later stages of the time course for natural scrapie disease in sheep. These observations demonstrated the ability of PrP transgenic Drosophila to respond to plasma samples from asymptomatic scrapie-infected individuals since clinical signs of the disease were not evident until these sheep were ≥20 months of age.
We next investigated whether the neurotoxic fly phenotype induced by pre-clinical natural scrapie plasma was transmissible through fly-to-fly transmission. Accordingly, we prepared head homogenate from 30-day-old VRQ(cyt) PrP transgenic Drosophila that had been exposed at the larval stage to plasma isolated from sheep with pre-clinical or clinical natural scrapie. These head homogenates were subsequently used to inoculate fresh batches of recipient VRQ(cyt) PrP transgenic Drosophila larvae. After hatching, the locomotor ability of fly head homogenate-exposed Drosophila was assessed by a negative-geotaxis climbing assay. The PI data in Figure  7  show that head homogenate from natural scrapie plasma-exposed VRQ(cyt) PrP transgenic Drosophila induced a significantly accelerated decline in locomotor ability in recipient flies compared with similar flies exposed to control scrapie-free plasma.
Mapping forest aboveground biomass (AGB) has become an important task, particularly for the reporting of carbon stocks and changes. AGB can be mapped using synthetic aperture radar data (SAR) or passive optical data. However, these data are insensitive to high AGB levels (>150 Mg/ha, and >300 Mg/ha for P-band), which are commonly found in tropical forests. Studies have mapped the rough variations in AGB by combining optical and environmental data at regional and global scales. Nevertheless, these maps cannot represent local variations in AGB in tropical forests. In this paper, we hypothesize that the problem of misrepresenting local variations in AGB and AGB estimation with good precision occurs because of both methodological limits (signal saturation or dilution bias) and a lack of adequate calibration data in this range of AGB values.
We test this hypothesis by developing a calibrated regression model to predict variations in high AGB values (mean >300 Mg/ha) in French Guiana by a methodological approach for spatial extrapolation with data from the optical geoscience laser altimeter system (GLAS), forest inventories, radar, optics, and environmental variables for spatial inter-and extrapolation. Given their higher point count, GLAS data allow a wider coverage of AGB values. We find that the metrics from GLAS footprints are correlated with field AGB estimations (R 2 =0. 54, RMSE=48. 3 Mg/ha) with no bias for high values. First, predictive models, including remote-sensing, environmental variables and spatial correlation functions, allow us to obtain "wall-to-wall" AGB maps over French Guiana with an RMSE for the in situ AGB estimates of ~51 Mg/ha and R²=0.
GLAS dataset LiDAR data were acquired from GLAS on board the Ice, Cloud, and Land Elevation Satellite The data were acquired during 18 missions by using three on-board lasers with orbit cycles that repeated between 57 and 197 days. The horizontal geolocation error of the ground footprints is less than 5 m on average for all ICESat missions (http://nsidc. org/data/icesat/laser_op_periods. html). Several studies (e. g. ,  Carabajal and Harding, 2006; Huang et al. , 2011)  have estimated the vertical accuracy of the GLAS to be between 0 and 3. 2 cm on average over flat surfaces. The GLA01 and GLA14 data products that were available for ICESat/GLAS were used in this study. GLA01 comprises the full waveform data, and GLA14 comprises the global land surface altimetry data. Over flat terrain, the waveforms that were acquired over vegetated areas are bimodal distributions and represent the different layers (top of canopy, branches, ground, etc.
, 2014). From the original database of 101312 footprints, 39856 footprints that satisfied the three filter conditions were kept. Some metrics were derived from the GLAS waveforms to reflect the canopy's vertical variables. First, the waveform extent (Figure  1 , Wext), which is defined as the difference between the signal's end and beginning, was calculated for each GLAS waveform. A signal's beginning and end (Figure  1 ) are defined as the first and last locations where the waveform intensity exceeds a noise threshold that equals 4. 5 times the standard deviation of the background noise  (Lefsky et al. , 2007). In addition, Gaussian peaks from the decomposition of each GLAS waveform, which represent canopy features such as the canopy top (position of the first Gaussian peak, Figure  1 ), canopy trunks, ground or a mix of these elements, were identified.
MODerate-resolution Imaging Spectroradiometer (MODIS) data The MODIS sensors mounted on the Terra and Aqua satellites possess a total of 36 spectral bands, seven of which are designed specifically for land applications with spatial resolutions that range from 250 m to 1 km. The MODIS dataset (MOD13A1c5) that was used in this study includes ten years (January 1 st , 2003 to December 31 st , 2012) of enhanced vegetation index (EVI) time series data with a resolution of 250 m. These EVI data effectively characterize biophysical and biochemical states and processes from vegetated surfaces. Freitas, Mello and Cruz, 2005 and Pascual et al. , 2010  found a strong relationship between forest structures (forest height and biomass) and vegetation indices. This 10-year period was synchronized with the GLAS data (from 2003 to 2009).
SRTM digital elevation model data The Shuttle Radar Topography Mission (SRTM) digital elevation model, which has a resolution of 90 m, was used in this study. This SRTM DEM dataset and its derived maps were considered because the local topography and drainage are important for tree anchorage and forest dynamics both directly and through soil types. Three derivative maps were created from these SRTM DEM data: (1) a slope map (Slope); (2) a surface roughness map (Rug), which was defined as the standard deviation of the elevation in a 3x3 moving window; and (3) a map of the heights above the nearest drainage (HAND). The HAND normalizes the topography according to the local relative heights along the drainage network and thus presents the topology of the relative soil gravitational potentials or local draining potentials  (Nobre et al.
In situ AGB dataset Two different forest inventories were used as field biomass estimates in this study  ( Guitet et al. , 2015). The first dataset was acquired by the CTFT ("Centre Technique Forestier Tropical") between 1974 and 1976 for 14 blocks, which covered 547 000 ha in the northern part of the French Guiana (FG) territory  (Baccini et al. , 2008). To remove uncertainties from the CTFT dataset, we excluded plots with partial inventories (pre-census DBH equal to 40 cm) or containing several forest types (i. e. mixed terra firme and seasonally flooded forest). Plots located in areas affected by forest harvesting or gold mining between 1974 and 2007 were also eliminated. The second inventory was campaigned between 2006 and 2013 on behalf of the ONF ("Office National des Forêts": the French national forest agency) to complete the regional coverage and better sample the environmental variability  (Clark et al.
The confidence interval of mean AGB estimates at 95% at the plot scale did not exceed 6 Mg/ha at the worst case. Moreover, the monitored permanent plots in French Guiana (on Paracou for the last 30 years) showed no significant trend in the evolution of biomass (increase in general but not significant if one takes into account the few events of death). Therefore, we can hypothesize that the old inventory reflects correctly the mean variations of biomass linked to environmental and spatial effects. The in situ AGB dataset was randomly divided into two datasets with 1253 plots each. One dataset was used for model building and the other to validate the wall-to-wall AGB maps.
Materials and methods Our methodology to map the aboveground biomass (AGB) consisted of four steps of spatial modelling within the Kriging regression framework  (Hengl, Heuvelink and Stein, 2004). (i) Finding the best regression between GLAS waveform-derived metrics and in situ AGB, with additional GLAS-derived estimates used as additional AGB data. (ii) Mapping AGB at several grid sizes (500 m, 1000 m, and 2000 m) by developing a trend model of AGB data from GLAS estimates with predictors that are derived from optical, radar, and environmental maps. (iii) Improving the AGB map's precision by adding the kriged residuals to the AGB map from step (ii). (iv) Finally, estimating the map's efficiency by using the validation dataset.