dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments This study is part of the  OPTIFEL  project that received funding from the  European Union 's  Seventh Framework Program  for research, technological development and demonstration under grant agreement n°  311754. AG PhD grant is also from the  EU   Optifel  project. We are grateful to  Riantsoa Ratsimamanga  for technical assistance. 2011. Proteomic analysis reveals the strategies of Bacillus thuringiensis YBT-1520 for survival under long-term heat stress. Proteomics 11,  2580-2591. 10. 1002/pmic. 201000392. Zhao, Y. H. , Li, H. M. , Qin, L. F. , Wang, H. H. , Chen, G. Q. , 2007. Disruption of the polyhydroxyalkanoate synthase gene in Aeromonas hydrophila reduces its survival ability under stress conditions. Fems Microbiol. Lett. 276,  34-41. 10. 1111Lett. 276 ,  34-41. 10.
Cell viability Cell viability was measured by flow cytometry using the FITC Annexin-V Apoptosis Detection Kit I (BD Biosciences, Le Pont de Claix, France) according to the manufacturer's instructions. Briefly, adherent and floating cells were harvested and centrifuged at 600 g for 5 min at room temperature. Macrophages were detached with Accutase TM (Biolegends, London, UK), washed with cold PBS and suspended in binding buffer (PBS, 2 % FBS). Cells (100,000) were placed in a flow cytometer tube and incubated with FITC Annexin-V (A5) and propidium iodide (PI) for 15 min. Stained cells were analyzed in an LSR II cytometer with FACSDiva software (BD Biosciences, Le Pont de Claix, France). Viable cells were defined as A5-and PI-negative cells.
The blocked membranes were incubated overnight at 4°C with the appropriate primary Abs (1/1000), then with horseradish peroxidase-conjugated secondary Abs (1/2000), and the visualised bands analysed by densitometry (Image Lab™ Software for total protein normalization; BioRad, Marnes-la-Coquette, France). The clone and reference of all Abs used for Western blot analysis are summarized in the Table  S1.
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) Total RNA was extracted from cells with the Trizol reagent (Thermo Fisher Scientific, France) and was submitted to reverse transcription using the High Capacity cDNA Reverse Transcription kit from Applied Biosystems (Thermo Fisher Scientific, France). Quantitative PCR were performed with the fluorescent dye SYBR Green methodology and a CFX384 real-time PCR system (BioRad)  [21]. Primers for gene expression analysis were purchased from Sigma-Aldrich. The specificity of gene amplification was checked at the end of PCR by analyzing amplification curves using the comparative cycle threshold method (CFX Manager™ Software). This software automatically sets the fluorescence baseline for each well and computes the optimal quantification cycle (Cq) with a multivariate, nonlinear regression model.
Acknowledgements This work was supported by the  Institut National de la Santé et de la Recherche Médicale (INSERM) , the  Université de Rennes  ( Univ Rennes ) and  Boehringer Ingelheim Pharma GmbH. Nessrine Bellamri  holds a fellowship funded by the  University of Rennes. We thank the  Rennes Biosit platform  for flow cytometry and  Professor Olivier Fardel  for helpful comments and critically reading the manuscript. Dr Owen Parkes  edited the English text.
Data acquisition The positions of the ant and its tarsi were estimated for each frame with the ImageJ software. The position of the ant was represented by the centroid of its body, i. e. , the ant without its legs and antennae (Fig. 1E ). The body was selected by a semiautomatic method applied to all or parts of each film, with the same set of values (a detailed description of the method can be found in Appendix A. 1). The positions of the tarsi were identified by eye, by defining the center of a circle fitting the extremity of a tarsus. This method gave a more accurate estimation of the position of the tarsi than the selection of a single point. These points were used in all analyses that required the recording of the position of legs. The extent of a leg in contact with sand is highly variable; it is at least the tip of the tarsus and never more than the entire tarsus.
Data acquisition and analysis Depending on the granulometry and on the inclination, ants exhibit more or less difficulty to move. In order to quantify this apparent difficulty, we introduce an abnormality index which is determined through the analysis of the position and orientation of the ants during locomotion. The position of the ant [x(t), y(t)] was represented by the center of its body (green cross in Fig. 1E ), while the orientation was determined by the angle b, which describes the tilt of the main axis of the body (with positive direction toward the head, see Fig. 1E ) with respect to the vertical direction. We also defined an angle a ¼ arctanðdy s =dx s Þ that measures the inclination of velocity with respect to the vertical direction (blue arrow in Fig. 1E ). The image treatment used to estimate the positions and orientations is described in Appendix A.
Introduction: The World Health Organization recommends vaccination of health workers (HWs) against influenza, but low uptake is intransigent. We conducted a Rapid Evidence Appraisal on: the risk of influenza in HWs, transmission risk from HWs to patients, the benefit of HW vaccination, and strategies for improving uptake. We aimed to capture a 'whole-of-system' perspective to consider possible benefits for HWs, employers and patients. Methods: We executed a comprehensive search of the available literature published from 2006 to 2018 in the English language. We developed search terms for seven separate questions following the PICO framework (population, intervention, comparators, outcomes) and queried nine databases. Results: Of 3784 publications identified, 52 met inclusion criteria. Seven addressed HW influenza risk, of which four found increased risk; 15 addressed influenza vaccine benefit to HWs or their employers, of which 10 found benefit; 11 addressed influenza transmission from HWs to patients, of which 6 found evidence for transmission; 12 unique studies addressed whether vaccinating HWs produced patient benefit, of which 9 concluded benefits accrued.
Systematic literature search General Search Approach: The search objective was to examine the evidence under three topics using a Rapid Evidence Appraisal approach. Each topic gave rise to 2 or 3 questions for query (see Table  1 ). Evidence was queried from MEDLINE, EMBASE, CINAHL, Cochrane CENTRAL, Cochrane Reviews, WHO Global Index Medicus, National Health Service (NHS) Evidence, NHS HTA database, and multiple international clinical trials' registries. We executed three independent searches by topic with distinct search terms to capture literature for all topic questions. Search terms followed the PICO framework (population, intervention, comparators, outcomes) and studies were selected based on pre-determined criteria. Study Types varied by review topic and question but generally included experimental or observational studies, systematic reviews, controlled observational studies, and randomized controlled trials (RCTs).
Conclusion (see summary of findings Table 5) In recent years, several comprehensive reviews have attempted to rigorously address different aspects of influenza vaccination in health workers. Paradoxically, the number of reviews far outweighs the number of studies that are of high quality or give definitive answers. Similarly, our review included only RCTs that have not already been evaluated as part of a more updated systematic review. It is therefore hardly surprising that it has proved difficult to draw universal and emphatic conclusions for policy makers, government leaders, and healthcare managers; and that implementation is poor and acceptance low. Nevertheless: Nosocomial influenza is a recognized problem and it is clear there is a problem to solve or a case to answer. There is adequate evidence that HWs contract influenza and data suggests they are at risk of continuing to work whilst infected.
Preoperative evaluation of endoscopic resection EMR or ESD is indicated based on the following contents (1) Histological type: Histopathological type is usually determined by the histopathological examination of the specimen. Although it has been reported that histopathological types can be predicted by endoscopy to some extent, there is still insufficient evidence. (2) Size: Final size data ought to be obtained from the measurement after resection and pathological examination, instead of measuring by conventional endoscopic examination, because measuring the size of lesions by conventional endoscopic examination is easy to make mistakes and difficult to accurately measure preoperatively. (3) Ulcerative findings: Pay attention to the presence of ulcers in the lesions. If ulcers present, check whether it is an active ulcer or an ulcer scar.
III. MONTE CARLO SIMULATION The existing SNOMAN Monte Carlo and analysis code  [16]  incorporates a detailed, high-precision model of the SNO detector, including geometry, material and optical properties, and the response of the PMTs and electronic readout system. This model was based on measurements of microphysical parameters, and tuned and verified using calibration data from deployed radioactive and optical sources in the context of previous neutrino analyses  [17] [18] [19] [20] [21] [22] [23] [24] [25] [26]. However, the code relevant to the production and propagation of muons and neutrons evolved to become a compilation of algorithms from various sources. In particular, neutron propagation was based principally on the MCNP package  [27] , which in SNOMAN is applicable only for neutron energies below 20 MeV.
IV. ANALYSIS There are two goals of this study. The first is to provide a detailed comparison of the data to model predictions across a number of observables, including the capture time and the reconstructed position of the captured neutrons, offering validation of the models implemented in GEANT4. The second goal is a measurement of the neutron yield, defined as the number of neutrons produced per unit muon track length per unit target material, in the D 2 O target. Use of a heavy water target in SNO offered a higher energy signature for neutron capture than the morecommonly used light water and liquid scintillator: neutron capture on the deuteron results in a 6. 25-MeV gamma, in comparison to the 2. 2-MeV gamma from capture on hydrogen. As a result the efficiency for detecting neutron capture events is greater than 95% in the data set under consideration (Sec.
B. Data selection The data used in this analysis was taken during Phases I and II, with the AV filled with pure heavy water and salt-loaded heavy water, respectively. It is thus a subset of the data used in the SNO cosmic muon flux measurement  [25] , which also considered data taken during Phase III, and the 13-day period between Phases II and III when the detector contained pure heavy water. Phase I data was collected between November 2, 1999 and May 28, 2001, and Phase II data was collected between July 26, 2001 and August 28, 2003, for a combined livetime of 836. 7 ± 0. 03 days. The selection criteria for muon events are designed to select through-going muons and reject instrumental backgrounds. Specifically, to qualify as a muon, events must have had at least 500 calibrated PMTs fired, with fewer than three of them in the neck of the AV, which is a characteristic of external light entering from the top of the detector.
Neutron events are selected by requiring 4. 0 MeV < E eff < 20. 0 MeV and r < 550. 0 cm. These high-level selection criteria differ from previous neutron selection in using a widened energy window consistent between the two phases, compared to the 6-10 MeV window used previously for Phase II data  [18] , intended to maximize neutron acceptance. Table  II  shows the number of muons accepted for the cosmogenic neutron search, and the percentages for which a follower was detected in both the data and Monte Carlo. The scarcity of neutron followers as shown in the table results in fewer than 3000 muons with detected neutron followers across both phases.
C. Tests of model predictions In order to validate the models of cosmogenic neutron production and propagation in the GEANT4 Shielding physics list at SNO depth and muon energies, we compare the data with model predictions for a number of observable distributions, including the properties of muons after which neutrons were observed, detected neutron multiplicity, neutron capture position, capture distance from the muon track, clustering of capture positions, and capture time. These quantities offer benchmarks of different aspects of the models implemented in GEANT4, and unique measurements of the physics involved in neutron production. For example, measurement of the per-muon neutron multiplicity yields insight into the validity of the cross sections of different neutron-producing reactions, while the capture time is sensitive to different neutron energies.
B. Follower multiplicity The distributions of the number of neutron-like events following a muon are shown in Figure  8. Muons with hundreds of followers were observed in each phase; indeed, events of such high multiplicity are reproduced using existing simulation tools. The potential disagreement in the number of high-multiplicity events in Phase II, however, may indicate that some reactions on chlorine are mismodeled. This could be attributed to incorrect cross sections for the dominant, low-multiplicity, neutron-producing processes, i. e. photonuclear and neutron inelastic scattering, or incorrect final-state generation after near-complete nuclear breakup at high energies. Distinct identification of cosmic muons as showering either electromagnetically or hadronically has been demonstrated by studying the distribution of multiplicities of neutron followers in high energy (> 90 GeV) muon-induced showers in liquid scintillator detectors  [35].
VII. CONCLUSIONS Although the production and propagation of cosmogenic neutrons are modeled in publicly available software, such as GEANT4  [28] , these models have not been exhaustively tested, particularly at the depth of SNO, due to the scarcity of experimental data. Extrapolations from more shallow experimental sites are not well understood. SNO offers a unique opportunity to test models at this depth, and in this muon energy regime, as well as to understand this source of background events for other experiments at SNOLAB. Community-standard simulation tools are seen to reproduce many characteristic observables of muon-induced neutrons in the SNO detector. However, some discrepancies indicate that these tools may be improved, particularly in the high energy regime. Using these simulation tools, the cosmogenic neutron yield at a depth of 5890 km.
ACKNOWLEDGMENTS This research was supported by:  Canada: Natural Sciences and Engineering Research Council, Industry Canada, National Research Council, Northern Ontario Heritage Fund ,  Atomic Energy of Canada, Ltd. , Ontario Power Generation, High Performance Computing Virtual Laboratory ,  Canada Foundation for Innovation ,  Canada  Research Chairs program; US:  Department of Energy Office of Nuclear Physics, National Energy Research Scientific Computing Center, Alfred P. Sloan Foundation ,  National Science Foundation , the  Queen's Breakthrough Fund, Department of Energy National Nuclear Security Administration  through the  Nuclear Science and Security Consortium; UK: Science and Technology Facilities Council (formerly Particle Physics and Astronomy Research Council ); Portugal: Fundação para a Ciência e a Tecnologia.
This may be possible only if the studied animals are followed individually over years, accurately noting all the manipulations to which each individual underwent. In this case, a capture-recapture (CR) approach  (Lebreton, Burnham, Clobert, & Anderson, 1992 ) would be possible. For our study, we used the data from a long-term behavioural study focused on behaviour (mainly orientation mechanisms and communication among individuals) of blue petrels (Halobaena caerulea) during the incubation period in Kerguelen archipelago (southern Indian Ocean). From the beginning of the long-term study in 2006 researchers noted which individual bird participated in a given experiment, and all birds were followed along the study period checking their presence, absence, and breeding each year. We used classical CR approach and adapted it to our dataset and our field-work protocols.
A1 , transition probabilities). In this model, there are nine possible states that change over time according to a Markov process and seven possible events that are generated from the states on each occasion (Fig. 1 ). Because capture is modelled in transition probability, then, event probabilities were degenerated and fixed to 1  Choquet, Rouan, & Pradel, 2009)  for parameter estimation and model. (see model 1 in Appendix Fig. A1, event probabilities). We used program E-SURGE 2. 2 (R Goodness-of-fit (GOF) tests for multistate model were performed with program U-CARE 2. 3. 4 (R. Choquet, Lebreton, Gimenez, Reboulet, & Pradel, 2009). These tests were based on the JollyMove model  (Brownie et al. , 1993)  with the assumptions that survival, transition between states and encounter probabilities were homogeneous among individuals (R  Pradel, Gimenez, & Lebreton, 2005).
Model 2: Cumulative effect of manipulations With the first model, we tested for a one-year effect of experimental manipulations on survival and reproduction. However, experimental manipulations may have a long-term impact. Therefore, we tested for a potential cumulative effect of the experimental manipulations over years to understand how experiments may impact an individual when it is manipulated several years in a row. -9 -We used the same dataset of 501 individuals as in the first model except that all experimental manipulations were gathered in one class. The general approach was similar to the first model except that survival, breeding and capture probabilities at time t might be conditional to have been already manipulated at least two times in a row. In this second model we consider nine states: 'alive non-breeder not caught', 'alive non-breeder and caught', 'alive breeder and not caught', 'alive as breeder', 'caught and not manipulated', 'alive as breeder', 'manipulated the last year but not caught', 'alive as breeder', 'caught and manipulated one year', 'alive as breeder', 'manipulated two years in a row but not caught', 'alive as breeder', 'caught and manipulated two or more years in a row' and 'dead' (Fig.
Discussion We measured short and long term impact of experimental manipulations on a small colony of blue petrels. To that purpose, we first developed a new multi-event model that allowed us to account for different severity classes of experimental manipulations and to measure their potential impacts independently. Secondly, we developed a model that allowed us to consider cumulative impact over years of these experimental manipulations. Applying those models to our blue petrels' data set, contrarily to our predictions, we found no evidence that the experimental manipulations performed have short or long term impact on both survival and breeding probabilities. In addition, similarly to other studies on undisturbed blue petrels, the survival was shown to be dependent on the bird experience and the breeding probability to be dependent on time  (Barbraud & Weimerskirch, 2003 , 2005; Chastel et al.
Acknowledgements This work was financed by the  French Polar Institute (IPEV) : project  ETHOTAAF 354  to FB. We want to thank all the volunteers, students, and colleagues that worked with us on different subjects since 2006. We thank the  Institut Polaire Français Paul-Emile VICTOR (IPEV)  for logistic support. We also thank  Nigel Gilles Yoccoz  and two anonymous reviewers for improving the manuscript with their suggestions. Bibliography Ackerman , J. T. , Adams, J. , Takekawa, J. Y. , Carter, H. R. , Whitworth, D. L. , Newman, S. H. ,. Orthmeyer, D. L. (2004). Effects of radiotransmitters on the reproductive performance of Cassin's auklets. Wildlife Society Bulletin, 32(4),  1229-1241. doi:  Doi 10. 2193/0091-7648(2004)032[1229:Eorotr]2. 0. Co;2.
Blood flow measurement with FFOCT For our in vivo blood flow dataset, automated methods based on optical flow failed to extract a velocity map due to the speckle pattern of the images inside vessels. Motion no longer corresponded to a diffeomorphism field, especially locally, leading to a complete divergence of the previous algorithm even with smaller α. Nonetheless we succeeded in extracting a velocity profile inside a vessel using a kymograph plot, i. e. plotting the vessel curvilinear abscissa against time. On such a plot, each event (i. e. a passing particle, such as a blood cell) produces a line, and the slope of this line corresponds to the speed. Using a custom segmentation algorithm, we automatically fit these lines and extracted the speed for each event at a given vessel cross-position.
Towards real time dynamic FFOCT Currently each dynamic image is computed in approximately 10 seconds on a GPU (NVidia Titan Xp). Most of this time is dedicated to memory management. In the original D-FFOCT configuration  [7] , images were computed using the CPU so the frame grabber was configured to save data directly on the computer Random Access Memory (RAM). The difficulty for real-time applications is the data transfer bottleneck. Indeed, a GPU can process data only as fast as the data can be transferred to it. In traditional system memory models, each device has access only to its own memory so that a frame grabber acquires to its own set of system buffers. Meanwhile, the GPU has a completely separate set of system buffers, so any transfer between the two must be performed by the CPU, which take times if the amount of data is important.
Acknowledgments The authors would like to thank  Valérie Fradot  and  Djida Ghoubay  at the  Vision Institute  for sample preparation, and helpful advice and discussion on biology aspects, and  Michel Paques  and  Vincent Borderie  at the  Quinze Vingts Hospital  for helpful discussions Disclosures CB: LLTech SAS (I),  K. Groux: LLTech SAS  (E), others: none.
Dynamic light scattering measurements The average particle size and zeta potential (z) of the CDs were measured by dynamic light scattering (DLS) using a Zetasizer NanoZS apparatus (Malvern Instruments, Paris, France). All measurements were performed on 1. 0 mg mL À1 samples in 1. 5 mM NaCl, pH 7. 4, at 25 C and in triplicate. Data were analyzed using the multimodal number distribution soware supplied with the instrument and expressed as mean (AESD).
Furthermore, KRAS mutations appear to affect an heterogeneous population with different prognostic/predictive values depending on the type of nucleotide base substitution, regarding EGFR-TKI treatment. 13, 14   inally, several studies have distinguished patients with EGFR mutations from those with non-EGFR mutated tumors, yet including KRAS-mutated tumors. In our study, we evaluated what impact the mutation detection threshold has on prognostic value of erlotinib efficacy. The ERMETIC (Evaluation of EGFR Mutation status for the administration of EGFR-TKIs in non-small cell lung Carcinoma) study, designed and supported by the French Collaborative Thoracic Cancer Intergroup (IFCT), funded by the French NCI (INCa), reported that formaldehyde-fixed paraffin-embedded (FFPE) specimens may be suitable sources for DNA analysis by means of genomic Sanger sequencing, providing rigorous pre-analytical quality control standards are respected.