dataesr/scientific-paragraphs-categorization huggingface dataset:
It is important to note that the statistically established cut-points used to identify positive samples are bioanalytical cut-points that reflect the analytical variability of the assay and biological variability of the treatment-naive study population. Therefore, they are not 'clinically relevant' , in the sense that identifying a sample as positive for ADA is not an indicator that the level of ADA present in the sample is sufficient to cause a biologically or clinically meaningful effect (e. g. alter PK, efficacy or cause adverse effects). However, sensitive assays capable of detecting all ADA present help establish definitively whether there are any relationships between clinical effects and the measured ADA when initially studying the immunogenicity profile in clinical studies. Where sufficient clinical data demonstrating a clear relationship between ADA positivity or titres, and clinical effect are available, it may be possible to establish a 'biological' or 'clinical' for subsequent use to distinguish clinically relevant from irrelevant ADA responses.
Sensitive ADA assays are also needed to correlate ADA development with underlying causes of immunogenicity and identify markers of immune response; e. g. markers of early events in triggering an immune response to the BP or indications of incomplete activation of the immune system that could lead to immune tolerance by the BP. Other assays may be developed to characterize ADApositive samples further and provide additional data to understand and interpret more extensively the clinical relevance of the ADA response to a BP. For example, an assay that specifically measures ADA that neutralize the Fig. 1. Typical tiered testing scheme for anti-drug antibody (ADA) testing and characterization. In the first tier, all evaluable samples are run in the screen assay. Samples that score positive in the screen assay are then analysed in a confirmatory assay (tier 2).
Because of the potential for BP, BP target or serum component interferences, ABIRISK includes the definition of an 'inconclusive' sample: 'for which the assay result cannot be reported as incontrovertibly negative or positive for ADA', and recommended that any positive or negative results that could be questionable due to assay limitations should be noted in reporting the results and considered in interpretation of the clinical or analytical outcomes. Because of these various known assay limitations, described above and in Table  5 , whenever possible ADA data should be interpreted in combination with pharmacokinetic (or BP concentration), pharmacodynamic and efficacy and safety data to define the immunogenicity profile of the BP and determine the clinical relevance. Prior to use, ADA assays should be validated analytically to assure reliable performance over time and establish which changes in ADA measurements are likely to be meaningful  [20, 22, 47, 49, 50].
Contributions of ABIRISK Data from ABIRISK pertaining to immunogenicity development, prediction and safety will be collected in a single database, requiring standardization of information originating from multiple types of investigational designs (e. g. prospective and retrospective investigations), multiple BPs (including coagulation factor VIII, b-interferons, TNF-a antagonists, natalizumab and rituximab), different diseases (e. g. haemophilia A, multiple sclerosis, rheumatoid arthritis, other autoimmune rheumatic conditions, inflammatory bowel diseases), different cohorts for a given disease and various preclinical, clinical and immune monitoring factors. ABIRISK will collect and publish data in accordance with the recommended terms and definitions and promote their use in the broader communities.
Acknowledgements This work has received support from the  Innovative Medicines Initiative Joint Undertaking (IMI JU)  under grant agreement no. 115303 , the resources of which are composed of financial contributions from the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013 ) and  European Federation of Pharmaceutical Industries and Associations (EFPIA)  companies' in-kind contributions. The following members of ABIRISK are acknowledged for contributions to reviewing this document:  Michael Tovey ,  Cornelia Sabine Viebahn ,  Zoe Waibler  and  Arsalan Zharazmi. We also thank  Sophie Turbot  for her assistance in coordinating the review.
Some studies evaluate the 1-year costs of BC but do not give details about the care services that compose the care pathway  [17]  or assess only hospital-specific cost items, excluding the social and ambulatory care sectors  [17, 18]. A model of the care pathway for new, nonmetastatic BC has been proposed; it describes the temporal sequence of hospital care, but its costs were not assessed  [19]. One published study evaluating BC pathways has been found in the literature. The authors assessed the 1-year care pathway of patients who underwent breast cancer surgery in 2009 in France. They proposed a method for grouping care pathways over a sequence of hospitalizations using claim data  [18]. The pathway studied included only the hospital portion of the BC care at 1 year and did not refer to a specific health territory.
We tested 48 young participants and 55 older participants. Two older participants were excluded from the study for their difficulty performing the UWMT. The study was approved by the Institutional Review Board of the Cognition and Learning Research Center (CeRCA-UMR CNRS 7295) of the University of Tours and the University of Poitiers. Given that no invasive technology was used, and that only adults were involved, and because the data were analyzed strictly anonymously, the authors considered that participants could give their informed consent orally. Consent was recorded in a research logbook alongside each participant's number. This procedure was approved by the authors' Institutional Review Board. Participants performed the Mill-Hill Vocabulary test  [25]. A significant effect of age was found in educational level, younger adults having completed more years of education (M = 14.
Results Three analyses were carried out, using the STATISTICA software, version 12. First, using Student's t test, we examined the effects of age on each executive measure (WSCT, ILFT, EFCI). Second, a General Linear Model (GLM) analysis was carried out to identify main effects of age group, load level, individual executive level, and interactions between these factors. By examining the three-way interaction between these three factors, we specifically tested the main statistical hypothesis of the present article, namely that level of executive functioning determines performance on the Updating Working-Memory Task, but with differences between young and older adults in relation to task demand. Third, to illustrate how the relationship between working memory and executive control varies as a function of age and task demand, we computed correlations between performance at the six load levels in the Updating Working-Memory Task and each measure of executive functioning, in both young and older adults.
Our approach includes the three following features: 1. Optimal registration of a partial surgery: We propose a method to optimally register the on-going surgery (partial surgery) to any complete pre-recorded surgery. Our approach is based on the Dynamic Time Warping similarity measure  [12] , which is consistent with surgical processes  [13]. 2. Voting for high-confidence prediction: Using the optimally registered reference set of surgeries, we use voting to draw a high-confidence prediction about the next action that going to be performed by the surgeon. 3. Detecting when to predict with high-confidence: Using the agreement rate among multiple predictors, we are able to detect when to perform a prediction and when it is not possible to draw an accurate prediction. Our framework is assessed using clinical data of lumbar disc herniation surgeries.
Clinical data Figure  3  presents the dataset. The framework is evaluated using clinical data composed of 24 lumbar disc herniation surgeries recorded at the Neurosurgery Department of the Leipzig University Hospital, Germany. Surgeries contain on average 680 actions. The surgeries involved 10 male and 14 female patients, with a median age of 52 years. These lumbar disc surgeries are divided into three main steps: (1) approach of the disc, (2) discectomy and (3) closure. The herniated disc is approached via a posterior intermyolamar route. The patients were operated on by five junior and five senior surgeons. Senior surgeons have performed at least a hundred removals of lumbar disc herniation. All the junior surgeons have passed more than two years of their residency program but have only performed a few removals of lumbar disc herniation.
The highest number of errors are committed in S 24 with a sequence of four wrong predictions in a row. This corresponds to the green activity in Figure  3 , where the surgeon installs the retractors on the skin without stopping, while all the other surgeries exhibit several pauses. Finally, every prediction is made in less than 200 ms, which is compatible with real-time prediction in the OR. Note that the current system is dependent of the heterogeneity of the sequences inside the reference database. If the reference sequences are highly heterogeneous, the system could have difficulties to perform the partial matching. As the size of the available reference set is limited, we are currently matching all the sequences of the reference database with the target sequence. However, a threshold on DTW score could be used to select only the most similar sequences to perform the prediction.
Another application concerns the training of junior surgeons, where our system could be integrated in a simulation environment in order to provide help and feedback to the junior surgeon  [17]. Our system could, on demand, provide a warning to the surgeon about his or her deviation from the standard practice of his or her colleagues. The agreement rate would then inform about the importance of the deviation. In future work, we want to validate this method on a more important dataset (> 300 surgeries) and use our recent work on Dynamic Time Warping  [18]  to improve the predictions.
A Multi-Angle Absorption Photometer (MAAP, Model 5012, Thermo Electron Group, USA, λ = 670 nm) and a 7wavelength Aethalometer (until January 2015 model AE-31, since then model AE-33) (Magee Scientific Company, Berkeley, CA, USA, λ = 370, 470, 520, 590, 660, 880, and 950 nm) are used for measuring the light absorption by particles. The MAAP and aethalometer have been deployed at ATTO since March 2012. In the MAAP instrument, the optical absorption coefficient of aerosol collected on a filter is determined by radiative transfer calculations, which include multiple scattering effects and absorption enhancement due to reflections from the filter. A mass absorption efficiency (α abs ) of 6. 6 m 2 g -1 was used to convert the MAAP absorption data to equivalent BC (BC e ). For the Aethalometer, an empirical correction method described by  Rizzo et al.
(2011)  was used to correct the data for the scattering artifact. Refractory black carbon (rBC) is measured by a fourchannel Single Particle Soot Photometer (SP2). The instrument is calibrated every 6 months using monodisperse fullerene aerosol particles for rBC calibration, and polystyrene latex (PSL) spheres for scattering calibration. The instrument is sensitive to rBC in the size range between 70 and 280 nm. A recent instrumental upgrade provides a broader rBC dynamic range (70-480 nm). Regular quality checks are performed with all aerosol sizing instruments and CPCs, including flow checks, zero tests, and intercomparisons with ambient aerosol and monodisperse PSL cells. Exemplary plots are already included in the manuscript (Fig. 26 ). The MAAP and aethalometer are subject to frequent intercomparisons with the other optical instruments.
, 2012). A common feature of all these organism groups is their poikilohydric nature, meaning that their moisture status follows the external water conditions. Thus the organisms dry out under dry conditions, being reactivated again upon rain, fog, or condensation. Since September 2014, we have been conducting longterm measurements to monitor the activity patterns of cryptogamic covers at four different canopy heights at 10 min intervals, during which we measure temperature and water content within and light intensities directly on top of biocrusts growing on the trunk of a tree. First analyses of the microclimate data indicate that microorganisms in the upper stem region of the trees are activated by fog or dewfall in the early morning hours, often coinciding with an aerosol particle burst in the accumulation mode.
Evidence from ATTO indicates that it is possible to associate the intermittent events at canopy level with the mean wind shear above the canopy. In Fig. 14 , it is evident that the two intense events at 42 m, around 21:30 and 02:00 LT, are triggered by episodes of intense wind shear between 42 and 80 m. In conditions where the 80 m wind field is dominated by submeso processes, such as in the examples in Figs. 12 and 14, it is this portion of the flow that determines the occurrence of intense wind shear episodes. Furthermore, it is clear from these examples that flow patterns at levels as high as 80 m exert important controls on the exchange of scalars at canopy level. Questions such as the height variation of submeso flow have yet to be answered. Tall tower observations, such as those planned to be carried on at ATTO, are very important to provide the data for this kind of analysis and to deepen the understanding of exchange processes between the canopy and the atmosphere during the calm nights that are common in the Amazon forest.
( 8 ) N is the Brunt-Väisälä frequency, defined as follows: where g is the gravity acceleration and z θ/θ is the dimensionless gradient of the virtual potential temperature. Two kinds of data were used: topographic and meteorological. A digital topographic image of the region surrounding the experimental site (Fig. 15a ) was used to analyze the features of surface undulations and their scales of occurrence, as well as the space-scale analysis by complex Morlet wavelet transforms  (Farge, 1992; Thomas and Foken, 2005). Local geomorphometric variables were derived from the Shuttle Radar Topographic Mission (SRTM) data  (Valeriano, 2008). These data were refined to 1 arcsecond (∼ 30 m) from the original spatial resolution of 3 arcsecond (∼ 90 m) and are available on the site www. dsr. inpe. br/topodata/dados.
php. N = g z θ/θ , (9 Time series of the vertical wind velocity and of the fast response temperature data provided by a sonic anemometer and thermometer were used to detect GW events at a height of 81 m above the ground. The sampling rate of the measured turbulence data was 10 Hz. Wind speed and temperature vertical profiles were provided by cup anemometer and thermometer measurements, respectively, with a sampling rate of 60 Hz for both, making it possible to compute the Brunt-Väisälä frequency, the vertical gradients of wind velocity, and the Scorer parameter for GW classification  (Steeneveld et al. , 2009). Data from five nights were analyzed, consisting of 120 files of 30 min each between Julian days 42 and 46 of the year 2012, representing the first observational data available from the ATTO site.
The analyses were carried out for the time between 18:00 and 06:00 LT for each night with available data (Fig. 15 ). The black points on the arrows in Fig. 15b  represent the GW events that were induced by the topography of the terrain, whereas the gray points represent GW events that were not generated by terrain orography. The results show that a considerable fraction of the analyzed situations represent GWs induced by terrain undulations. This finding is very important for the environmental studies that are being carried out at the ATTO site, as it indicates that some mixing characteristics of the nocturnal boundary layer depend on the characteristics of terrain undulations and therefore change with the wind direction.
, 2013; Zilitinkevich et al. , 2013) , and (v) implications of the existence of CSs for the chemistry of the atmosphere  (Steiner et al. , 2011; Foken et al. , 2012). (45º) (30º) (60º) (75º) (90º) (105º) (120º) (135º) (150º) (165º) (15º) (180º) (0º) (a) [m] Tower W E N S (b) (180º) (165º) (60º) (45º) (75º) (90º) (105º) (120º) (135º) (150º) (0º) (15º) (30º A study on the structure of atmospheric turbulence was performed at the ATTO site under daytime conditions, with the aim of contributing to the detection of CSs and developing a better understanding of their vertical and temporal variability over a very uneven terrain covered by primary forest in central Amazonia. Wind, temperature, and humidity data were obtained using sonic anemometers and gas analyzers, installed at 42 and 81 m above ground, as specified in the methods section.
and the  Brazilian Ministério da Ciência, Tecnologia e Inovação (MCTI/FINEP  contract  01. 11. 01248. 00 )as well as the  Amazon State University (UEA) ,  FAPEAM, LBA/INPA  and  SDS/CEUC/RDS-Uatumã. Leonardo Sá  thanks  CNPq for his Productivity in Research Grant ,  Process 303728/2010-8. Cléo Dias-Júnior  thanks  CAPES  for his Ph. D. grant. Maria Teresa F. Piedade  thanks  CNPq  and  FAPEAM  for research grants ( PELD-Project ,  Process 403792/2012-6 ). The ALS is supported by the Director,  Office of Science, Office of Basic Energy Sciences , of the  US Department of Energy  under Contract  DE-AC02-05CH11231. We thank the  Helmholtz-Zentrum Berlin  for the allocation of synchrotron radiation beamtime at BESSY II. We also thank  M. Weigand ,  M. Bechtel , and  A. L. D. Kilcoyne  for their constant support during the beamtime sessions.
The final 473,558-bp genome sequence exhibited a high AϩT content of 75%. It was predicted to encode 512 open reading frames (ORFs), using GeneMark  (18) , and 12 tRNAs, using tRNAscan-SE  (19). They span over 91% of the genome. Among the 512 predicted ORFs, 274 (53. 5%) exhibited a significant ho-molog in NCBI's nonredundant protein sequence database (BlastP, E value Ͻ 10 Ϫ5 ), of which 163 (59. 5%) were most similar to their PgV homolog and an additional 40 had their closest homologue in other Megaviridae. These best matches in PgV include usual phylogenetic markers such as the DNA polymerase B (CeV_365, 45% identical to PgV's PGCG_248), the major capsid protein (CeV_191, 73% identical to PgV's PGCG_157), as well as two enzymes characteristic of Megaviridae: the mismatch DNA repair enzyme MutS7 (20) (CeV_281 47% identical to PgV's PGCG_223) and an asparagine synthetase (21) (CeV_376, 49% identical to PgV's PGCG_327).
Moreover, CeV and PgV share gene fusion between their DNA polymerase X and NADdependent DNA ligase (CeV_489, 49% identical to PGCG_401) not found in other Megaviridae. Finally, the newly described PgV-MIGE mobile element of which 12 copies were found in the PgV genome  (13)  was also found in 6 copies in the CeV-01B genome. The proposed Megaviridae family, initially composed of Acanthamoeba-infecting giant viruses (now constituting the proposed Mimiviridae subfamily)  (21) , progressively expanded to encompass smaller members infecting other unicellular protists  (12, 13, 21). Its genome sequence clearly classifies CeV-01B in a subclade of "small" Megaviridae  (12)  with PgV as the closest, nevertheless distant relative. Nucleotide sequence accession number. The completely annotated genomic sequence of Haptolina ericina virus CeV-01B is available in Genbank under accession number KT820662.
We compare the performances of several Multi-Layer Perceptrons (MLPs) and Convolutional Neural Networks (ConvNets) for single text image Super-Resolution. We propose an example-based framework for both MLP and ConvNet, where a non-linear mapping between pairs of patches and high-frequency pixel values is learned. We then demonstrate that for equivalent complexity, ConvNets are better than MLPs at predicting missing details in upsampled text images. To evaluate the performances, we make use of a recent database (ULR-textSISR-2013a) along with different quality measures. We show that the proposed methods outperforms sparse coding-based methods for this database.
EXPERIMENTAL RESULTS To compare the performances of our proposed approaches, we use the text image database ULR-textSISR-2013a released by  (Nayef et al. , 2014). The test set contained in this database consists in 30 grayscale images of black text over a white background: 5 different texts, each rendered with 3 different fonts (Arial, Times, Courier) and 2 different sizes (10 and 12 pt, at 150dpi), using anti-aliasing filters during Portable Document Format (PDF) file generation. They contain bold and italic characters.
Framework Global Settings Normalization. We set K in = 256 to normalize the input patch from which we subtract the central value. This way, we ensure that values range from -1 to 1. For output detail pixels, we choose K out = 100 for images of black text over a white background, which is K out ν with ν being the variance of the histogram of target values in the training dataset. Patch Size. In order to provide an equivalent evaluation of the two methods, we try to use an equivalent amount of information at the entrance of both systems. For ConvNets, we use 9×9 LR patches. Taking into account the border effect of convolutions in the first layers, we consider that presenting only 7×7 patches to the MLP is equivalent in terms of information. Experiments show that the MLP does not benefit from larger patches.
Scale. In this study, we only consider ×2 SR since the database  (Nayef et al. , 2014)  was provided for this upsampling factor, although our implementation can handle higher scale factors (the output layers would be 3×3 for ×3 SR, 4×4 for ×4 SR, etc. ) Training Database. For training, we use text images generated with the process employed to build the database  (Nayef et al. , 2014) : Times and Arial fonts (10 and 12pt at 150dpi), bold, italic and normal emphasis; FreeType generation and Matlab downsampling. An interesting aspect of this database is that it includes three different fonts (Arial, Times, Courier) in the test data while only two of them are present in the training data. This allows to evaluate if the SR method generalizes to text of different nature. We extract 120, 000 pairs for training as described in 3.
Results For the selected architectures, we can observe in 1 and 2 the advantage of ConvNets compared with MLP. For an equivalent complexity (e. g. around 20, 000 weights), ConvNets produces a better version of missing high-frequencies, improving both pixel-wise measures (PSNR from 24. 15 to 24. 55 dB) and OCR score (94. 69 to 96. 44%). Some results are shown in figures 7(b) and 7(c). The bicubic image (7(a)) exhibits serious blur artifacts, and the gain of the proposed Neural-based methods is clear. Moreover, we can note a better reconstruction of some sensitive details for the Con-vNets: holes in the "e" letters are more visible, "s" letters are better shaped, and some fine edges such as "n", "k" or "g" curves are more nicely reconstructed. We report in 3 the state of the art results published on this database, and compare them with our best results.
Supplementary Experiments The proposed database is very specific as it only contains text images with black font over a white back-  ground. Thus, for the sake of generalization, we tried our system on natural images. We use the same data as  (Dong et al. , 2014)  or  (Yang et al. , 2010)  for training, and images extracted from BSD100 segmentation database for validation. The test dataset is "Set5". We tried to preserve fairness with the other methods. As  (Dong et al. , 2014)  use 24,800 32×32 subimages for training their system while we use patches (7×7 or 9×9 for this last experiment), we consider that we can randomly extract 2,000 patches from each of the 92 training images without turning into a deeper learning process than they do. In terms of complexity, their system contains W = 8, 032 weights.