dataesr/scientific-paragraphs-categorization huggingface dataset:
WNW was funded by a  Medical Research Council   Clinician Scientist Fellowship  ( G0902303 ). WH reports honoraria from  Boehringer Ingelheim ,  Daiichi Sankyo , and  Bayer , receipt of an unrestricted research grant from  Boehringer Ingelheim  to perform the ECASS-4 EXTEND trial, and past chairmanship of the ECASS 1-3 thrombolysis trials. WH is current president of the  World Stroke Organisation. LB, GH, MKo, MGL and PL declare no conflict of interest. Funding The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: The Stroke Thrombolysis Trialists' Collaboration is coordinated by the  MRC Population Health Research Unit , which is part of the  Clinical Trial Service Unit & Epidemiological Studies Unit at the University of Oxford, UK.
Low light levels were obtained using neutral density filters (Lee Filters, Burbank, CA, USA). Bulk fluorescence was measured daily at the same morning time point using a 10-AU fluorometer (Turner Design, Sunnyvale, CA, USA). Cells were acclimated to each light level for !10 generations and average growth rates were calculated over 3 to 5 consecutive transfers after acclimation by following changes in fluorescence. The latter reflect changes in cell abundance, if measured at the same time point each day in synchronized cultures. At the ~350 μmol photons m -2 s -1 light level data from only one transfer was available (therefore the mean and s. d. were computed from the three biological replicates) and data from one biological replicate at 6 μmol photons m -2 s -1 was from a single transfer. Once average growth rates were determined, diel changes in cellular characteristics were studied for cultures grown at three selected irradiances with 2 h interval sampling starting at 6 a.
Flow cytometry Cultures were monitored live on a daily basis using an Epics XL (Beckman Coulter, Brea, CA, USA) with data acquisition triggered by side scatter (SSC). For the light-shift experiments and the higher resolution diel studies, samples were also analyzed using an Influx (BD Biosciences, Franklin Lakes, NJ, USA) equipped with a 488 nm laser (200 mW output), a 70 μm diameter nozzle and run at 25 μl min -1. FALS, SSC and red autofluorescence derived from chlorophyll (692 ± 40 nm band-pass) were recorded for >1 x 10 4 cells per sample. Micromonas and yellow-green 0. 75 μm polystyrene beads (Polysciences Inc. , Warrington, PA, USA; added as normalization standards) were defined based on fluorescence and SSC (Epics XL) or FALS (Influx) characteristics. Fluorescence and scatter properties of cells were normalized to beads (i.
Transcriptome analyses Reads were aligned to the RCC299 nuclear genome using BWA  [39]  and to the plastid genome using Bowtie  [40]. The final mapped read numbers were on average 4. 08 ± 0. 97 million reads per sample, with approximately half of these being aligned to the 73 kb chloroplast genome. For chloroplast genes, reads aligning between start and end coordinates were assigned to that gene. Prior to assignment, chloroplast gene models were improved (primarily by CDS extension) using the transcript data. Extended gene models and those that were unchanged are available at http://www. mbari. org/resources-worden-lab/ and two new protein-encoding genes identified here were deposited in GenBank under accessions KX172140 (ycf2) and KX172139 (ycf1). For nuclear genes, most reads aligned to the 3 0 terminus, within 8 read lengths of the end of existing annotations (see Results and Discussion).
1 and HSP90. 2). To avoid overestimating fold changes due to low nuclear genome read counts, we required that !100 reads map to the respective protein-encoding gene in one or more samples. Thus, a number of nuclear genes were excluded from differential expression analyses due to: i. ) reads assigned, if any, were below this minimum cutoff (LHCSR1, LHCSR2, ELIP1, ELIP2, ELIP4 and ELIP6) or ii. ) they overlapped with other genes in the 3 0 region confounding analyses of non-directional RNA-seq data (LHCP4, ELIP5, and ELIP3/ PSBS-like). Additionally, LHCP2. 1 and LHCP2. 2 are identical in the region where RNA-seq reads mapped and therefore data presented for LHCP2. 2 also represents fold-changes for LHCP2. 1 (using the present dataset). To determine significance of differential expression analyses an ANOVA was performed on expression data meeting the read cutoff criterion using the R programming language  [41].
Quantitative polymerase chain reaction (qPCR) analyses For qPCR, single stranded (ss) cDNA was synthesized using the SuperScript1 III First-Strand Synthesis System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Oligo-dT primers and 6 μL total RNA (12. 5 ng μL -1 ) were used in total reaction volumes of 60 μL. To check for contaminating genomic DNA, negative control reactions (RT-controls) were also prepared by omitting the reverse transcriptase enzyme. TaqMan primer-probe sets were designed for three genes (Table  1 ) using Primer Express software 3. 0 (Applied Biosystems, Brea, CA, USA). The primer-probe sequences were compared to the M. commoda RCC299 genome  [34]  to confirm that only the genes of interest were targeted. Probes were labeled with the fluorescent reporter FAM (6-carboxyfluorescein) and a non-fluorescent quencher at the 5 0 and 3 0 ends, respectively.
The concentration of RNA added to the cDNA reaction fell within the linear part of the curve, equivalent to a 1:1 conversion between RNA and cDNA. The efficiencies of primer-probe sets were determined using a dilution series of 1) qPCR product (purified with the MinElute PCR purification kit, Qiagen, Germantown, MD, USA) and 2) cDNA. C T values were generated for treatment and control experiments and data were analyzed using the 2 -ΔΔC T method  [43]  performed using the 7500 System SDS Software v1. 4 (Applied Biosystems, Foster City, CA, USA) with T 0 as the calibrator. Actin (XP_002503091) was selected as the endogenous control because, using qPCR across the treatments herein, it showed less change in C T than GAPDH (by qPCR; in RNA-seq data from these experiments Actin showed more variability across treatments than GAPDH).
Gene model improvement and RNA-seq analyses RNA-seq was used to assess M. commoda responses to light shifts and UV exposure during the short-term experiments. Prior to comparing gene expression levels in the different treatments we observed reads mapped to unannotated regions of the chloroplast genome. Using this data we extended open reading frames (ORFs) for psbE, psbF, and psbB and for the 23S ribosomal RNA (rrl). We also identified and deposited two previously unrecognized genes, ycf2-like (ftsH, orf1577) and ycf1-like (orf603). The products of these genes are far more diverged from Ostreococcus homologs (ORF1260/YP_717220 and ORF537/YP_717209, respectively) than other proteins encoded by chloroplast genes that are shared by Ostreococcus and Micromonas. For example, the former protein aligned to just 605 of the 1260 amino acids (a.
a. ) comprising Ostreococcus tauri ORF1260/Ycf2/FtsH (with 30% identity) and blastp to NCBI's non-redundant database only otherwise recovered a Bathycoccus prasinos protein (30% a. a. identity). In contrast, the RNA polymerase beta subunits (RpoB) of these two genera share 68% a. a. identity, and the photosystem I P700 chlorophyll a apoproteins A1 (PsaA) are 97% identical. Overall, we identified 60 protein-encoding genes, 26 tRNAs and 6 rRNAs (two copies each of the 16S, 5S and 23S genes) in the chloroplast genome (92 total); these numbers include the 58 protein-encoding, 26 tRNA genes and 3 rRNAs reported previously  [34]. Approximately half the RNA-seq reads generated mapped to the chloroplast genome (Table A in S1 File). Chloroplast gene transcripts are not poly-adenylated and are recovered well by random hexamers (as used here; Table A in S1 File).
Apart from M. commoda, this fusion protein only appears to be present in O. tauri, B. prasinos and M. pusilla based on blastp queries against available plant and algal genomes (GenBank nr database). Although the three-dimensional structure and function of NIRFU is not known, some aspects of the combination of domains have similarities to bacterial nitrite reductase operons. The cytochrome c nitrite reductase (nrfA) operon of several non-photosynthetic bacteria contains not only nrfA (which encodes the catalytic subunit), but also nrfH, encoding a tetraheme cytochrome c  [102]. Together, these form a complex that optimizes the efficiency of electron transfer to nitrite, the terminal acceptor  [102]. We hypothesize that the additional domains in NIRFU enhance the efficiency of electron transfer over classical plant NIR proteins, potentially with both ferredoxin and NAD(P)H dependent nitrite reduction in the chloroplast.
Acknowledgments We thank  C. Bachy ,  C. Berthiaume ,  E. Demir-Hilton ,  A. Engman ,  J. Lake ,  S. McDonald ,  M. P. Simmons ,  R. M. Welsh  and  H. M. Wilcox  for help with experiments, qPCR design, and/or discussion of analysis approaches. We are grateful to  V. Shankey  and  Beckman-Coulter Corporation  for loaning us the  Epics XL instrument, Pierre Setif for discussing NIRFU  and the reviewers of the manuscript for constructive comments. This research was supported by a  Gordon and Betty Moore Foundation   Investigator Award  ( GBMF3788 ),  NSF -IOS0843119  and  DOE-DE-SC0004765  grants to A. Z. W.
The second level, known as the high-level trigger (HLT), consists of a farm of processors running a version of the full event reconstruction software optimized for fast processing, and reduces the event rate to less than 1 kHz before data storage. The particle-flow event algorithm  [19] [20] [21]  reconstructs and identifies each individual particle candidate using an optimized combination of information from the various elements of the CMS detector. The energy of photons is obtained from the ECAL measurement, and corrected for the online suppression of signals close to threshold. The energy of electrons is determined from a combination of the electron momentum at the primary interaction vertex determined by the tracker, the energy of the corresponding ECAL cluster, and the energy sum of all bremsstrahlung photons spatially compatible with originating from the electron track.
Modeling of signal and background All signal events are generated at leading order (LO) using the CompHEP 4. 5. 2 [22]  package and their cross sections are scaled to next-to-leading order (NLO) with an approximate K-factor of 1. 2  [23, 24]. All signal samples are generated with purely right-handed couplings, according to the following model-independent, lowest-order, effective Lagrangian: L = V f i f j 2 √ 2 g W fi γ µ (1 + γ 5 )W µ f j + H. C. , (1) where V f i f j is the element of the Cabibbo-Kobayashi-Maskawa matrix when f is a quark, and V f i f j = δ ij when f is a lepton, and g W is the SM weak coupling constant. Since we consider W R bosons (with right-handed couplings), there is no interference at production with the SM W boson. The simulation for leptonic decays of the W R boson includes decays involving a τ lepton, and no distinction is made in the analysis between an electron or muon directly from the W boson decay and an electron or muon from a subsequent leptonic τ decay.
The relative composition of these components in simulation is known to differ  [36]  from the composition in data, and we apply these correction factors to the predictions. The multijet background in the hadronic analysis is determined from data in independent control regions. The validity of the estimation procedure is then checked using simulated multijet events. More details on the background estimation methods can be found in Section 5. All simulated signal and background events are processed through PYTHIA 8. 2 for parton frag-mentation and hadronization, where the underlying event tune CUETP8M1  [37]  has been used. The simulation of the CMS detector is performed using GEANT4  [38]. Also, all simulated event samples include additional overlapping proton-proton interactions in the same or adjacent bunch crossings (pileup) that are weighted such that the distribution in the number of interactions agrees with that expected in data.
Analysis selections in the hadronic channel Candidate events in the hadronic channel are required to satisfy one of two HLT selections. The first demands at least two AK8 jets with p T > 200 GeV, one of which must have a trimmed  [53]  jet mass greater than 30 GeV, and also requires the leading p T jet to have p T > 280 GeV. In addition, this trigger requires that the event contains at least one b-tagged jet. The second trigger requires that the scalar p T sum of reconstructed jets be at least 800 GeV. The efficiency of the combination of these two triggers is measured with data collected using a trigger with a lower scalar p T sum threshold, and is extracted as a function of the scalar p T sum of the two jets with leading p T (H T ), which provides a way to account for this effect. We require events to have at least two jets with p T > 350 GeV, one of which must be identified as a top jet using the t tagging algorithm, and the other must be tagged as a bottom jet.
Acknowledgments We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centers and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Aus-.
In the thermodynamic limit we thus have e [{(iα,jα,kα,lα)} r α=1 ] , X(λ) = ψ s | 2 α=r L [iα,jα,kα,lα] (λq 1 2 , λq -1 2 ) ∂ µ L [i1,j1,k1,l1] (λq 1 2 , µq -1 2 ) µ=λ |ψ s Λ s (λ) r , (54) X(λ) = N r=2 {kα}∈Z 4r m e [{kα} r α=1 ] , X(λ) N -1 j=0 Ŝj e [{kα} r α=1 ] , (55) where Ŝ is a periodic shift automorphism for two physical sites (due to the staggering of the transfer operator -see (18)), its action being Ŝ(1 ⊗j ⊗ A ⊗ 1 ⊗2N -n-j ) = 1 ⊗j+2 ⊗ A ⊗ 1 ⊗2N -n-j-2 , A ∈ End (H ⊗n ). ( 56 ) An explicit computation of the actions of the Lax components onto the singlet state results in the conclusion that the traceless part of the conserved charge X(λ) contains only terms acting nontrivially on at least four consecutive physical lattice sites, hence the sum over r starts with r = 2. Mathematica code for constructing the matrix product representation of the quasilocal charges X(λ) is available on the web [17].
Acknowledgements LZ thanks  M. Medenjak  for the discussions related to the quasilocality in the isotropic Heisenberg model. We thank  E. Ilievski  and  G. Takacs  for useful comments on the manuscript. The work has been supported by  ERC  grant  OMNES  and  Slovenian Research Agency  grant  N1-0025  and programme  P1-0044.
After a new washing and centrifugation step, RPE-conjugated secondary antibody (10 mL) was added and cells were incubated 15 min longer in the dark at room temperature. A final washing step was necessary, and the resulting pellet was suspended once again in 500 µL of BD FACS Flow (BD Biosciences, San Jose, CA, USA). Cell acquisition was performed on a BD FACS Calibur flow cytometer (BD Biosciences) and data were analyzed using Paint-A-Gate Pro and Cell-Quest Pro software (BD Biosciences). In each experiment, incubation of cells was done according to the above protocol but with the secondary antibody only. This control tube was performed in order to assess the level of unspecific fluorescence signal of the secondary antibody. Selection of primary antibodies' dilutions was as follows: 1. Mouse monoclonal anti progesterone receptor (77201704 AbD Serotec, Kidlington, UK), diluted at 1:10 in PBS; 2.
Acknowledgments: Funding for this work was provided by the  Portuguese Foundation for Science and Technology (FCT)  with co-participation of  European Union Fund (FEDER)  through the research project  UID/CVT/00276/2013. The authors present special thanks to  Sandra Carvalho  and  Rosário Luís  (Histology Dept. , FMV) and  Gloria Nunes  ( Immunology Dept. , FCM ) for technical assistance.
The ring-necked parakeet is considered a major crop pest in its native range and, in areas where it has been introduced, causes damage to agricultural areas  [12]. The exponential demographic growth has raised concerns by urban planners regarding the potential negative impacts of the ring-necked parakeet and a better knowledge of the ecological requirements and the potential future distribution of this species is thus needed. Species occurrences have become increasingly available from online databases covering a range of spatial and temporal scales. These existing databases provide new opportunities to study the relationship between successful introduced species and their environment and are widely used to predict their potential future distribution  [13]. However, the information contained in these databases is often limited to the location and sometimes to the activity of species (e.
g. , nesting, feeding). In the case of the ring-necked parakeet which may compete with native fauna for tree cavities, useful information to acquire is its potential nesting preferences regarding the tree species in which parakeets are nesting. Traditional methods involve field investigation and random sampling of breeding bird populations to record a subset of tree species used, which is time and labor consuming and may not be representative of birds nesting preferences. An alternative method is to use available tree occurrences datasets, which may be incomplete, especially at the local scale and in private areas such as private gardens and residential areas. Remote sensing, especially using Very High Resolution (VHR) satellite imagery, provides a time-effective and cost-efficient way to highlight new information from tree species occurrence databases by allowing one to identify tree species used by birds for nesting.
Pléiades Images The Pléiades constellation of two VHR satellites, Pléiades 1A and Pléiades 1B, was launched in 2011 under the supervision of the Centre National d'Etudes Spatiales (CNES) and Airbus Defence & Space. Cloud-free Pléiades images acquired on 28 July 2015 and 24 March 2016 were used in this study. The acquisition dates of images were selected based on both data availability and the vegetation phenology period in Mediterranean region. The Pléiades images have four multi-spectral bands with a spatial resolution of 2 m and one panchromatic band at 0. 5 m (Table  1 ). Both Pléiades images were acquired pan-sharpened at 0. 5 m spatial resolution. Atmospheric corrections were applied using the Optical Calibration module implemented in the Orfeo ToolBox  [25]. This step allows one to convert pixel values from digital numbers to physically interpretable and comparable spectral reflectance values, and requires one to set several parameters.
Field surveys were conducted from June to August 2016 and June 2017 during the leaf-on period. The study area was divided into a regular grid of 1 km 2 square cells, then ten cells were randomly sampled. Within each of the ten cells, we registered broadleaf species composition by geo-referencing the localization and recording the species of individual trees. Coniferous trees were geo-referencing without details about the species of individuals. The four target tree species were chosen based on their dominance in the broadleaf vegetation community in the study area and their previously documented use by nesting ring-necked parakeets. Table  2  provides details on the final dataset. Figures 2 and 3 illustrate the spectral variability of the reflectance values for the six classes within the delineated reference polygons, respectively, of the spring and summer Pléiades images.
Segmentation Segmentation is an important primary step in object-based classification which consists of dividing an image into homogeneous and non-intersecting regions. In this study, we used the mean shift algorithm, a non-parametric feature space analysis and clustering technique introduced by Fukunaga and Hostetler  [26]  and that has been widely applied for image segmentation  [27, 28]. We applied the Large Scale Mean Shift (LSMS) segmentation algorithm implemented in the open-source software Orfeo ToolBox and which requires assigning three parameters, the spatial radius of the neighborhood, the range radius, and the minimum region size. The optimum segmentation parameters depend on the scale and on the nature of the features to be detected. Segmentation performances were evaluated using Hoover metric (H)  [29] , which compares segmentation outcomes with ground truth regions based on an overlap matrix.
Following the approach of Chen et al. [38] , and Franklin et al. [39] , both Pléiades was classified based on a range of GLCM window sizes. We used the Feature Extraction module implemented in Orfeo ToolBox. Feature measures fall into three categories: contrast based, statistically based, and orderliness based. Given that textural features in the same category may be highly correlated  [40] , multicollinearity was evaluated using the Pearson Correlation Coefficient r, which ranges from +1 to -1. Values of r greater than +0. 7 and lower than -0. 7 indicate, respectively, strong positive and strong negative correlations between considered pairwise features and thus redundancy in information. Pairwise correlations with an r value greater than 0. 7 were considered as correlated and one feature selected.
The Support Vector Machine (SVM) classifier is a supervised nonparametric statistical learning method  [44]  which makes no assumption about the underlying data distribution (for a review, see Mountrakis et al. [41] ). The SVM algorithm separates a given set of labeled training data with a hyperplane which finds the maximum distance. We used a Gaussian Radial Basis Function (RBF) kernel which has shown good performances in object-based image analysis  [45, 46]. Optimal cost and gamma values were determined by the grid search function in the R package e1071. We used the package randomForest  [47]  in the open-source software R 3. 1. 3 to perform RF models, and the SVM was implemented using the package e1071  [48]. A cross-validation technique was used to assess the performances of models. The reference sample is randomly split into k subsets of equal size, k-1 subsets are then used as training data, and the remaining subset is used as validation data.
Ring-Necked Parakeet Breeding Occurrences Breeding site locations of ring-necked parakeets in the study area were compiled from the database of the regional antenna of the French Bird Protection League, a national network which compiles observations made by volunteers (Collectif, in http://www. faune-paca. org, subject to a convention and extracted on December 2016). The dataset was composed by 1830 parakeet breeding occurrences for the period 2009-2016.
In the city of Marseille, Platanus sp. trees have been extensively planted as road/street trees and for ornamental aims. However, it is affected by a fungus, Ceratocystis platani, responsible for the lethal canker stain disease which will require urban planners to cut the dying individuals and replace them with others such as Celtis australis. This species turn-over may have a high impact on biodiversity because of the progressive decrease of cavity availability due to the newly-planted young trees. Cavity availability is a major element of competition and shapes the species composition within the cavity-nesters community inside cities. The presence of old and large trees is critical for the subsistence of animal species such as owls, bats, and other cavity-nesters. Databases of areas with suitable trees are thus crucially needed to study their spatial distribution and may be a useful tool to biodiversity-friendly urban planning.