dataesr/scientific-paragraphs-categorization huggingface dataset:
16S rRNA sodA Gene Analyses The nucleic acids of the strain were extracted for gene amplification and cloning of the 16S rRNA gene was accomplished by using a commercial DNA Purification Kit (Wizard Genomic DNA Purification Kit, Promega, Madison, WI, United States) and the 16S rRNA universal primers 27F/1492R (5 -AGAGTTTGATCMTGGCTCAG-3 and 5 -GGYTACCTTGTTACGACTT-3 , respectively). The sequence obtained by sequencing was aligned using Basic Local Alignment Search Tool (BLAST) of NCBI. We collected 16S rRNA gene sequences of all known Streptococcus species from the NCBI database  (Pontigo et al. , 2015). Phylogenetic trees were constructed with two different algorithms, namely neighborjoining  (Saitou and Nei, 1987)  and maximum-likelihood  (Guindon and Gascuel, 2003)  by close-neighbor-interchange (CNI) (search level = 2, random additions = 100) using MEGA version 7.
Analysis of Fatty Acids in Bacteria Fatty acid methyl esters (FAMEs) were analyzed using a gas chromatography/mass spectrometry [see  (Dione et al. , 2016)  and  (Sasser, 1990) ]. FAMEs were prepared from a sample consisting of 40 mg of bacterial biomass, separated using an MS column (Elite 5) and examined with a mass spectrometry (Clarus 500-SQ 8 S, PerkinElmer, France) followed by appropriate searches of spectral databases.
Genome Sequencing Assembly and Annotation After preprocessing, appropriate data were gathered using SOAP (version 2. 04)  (Li et al. , 2008 (Li et al. , , 2010)) , SPAdes  (Bankevich et al. , 2012)  and ABySS  (Simpson et al. , 2009)  assembly software, and finally integrated using CISA software. The preliminary assembly results were optimized and holes filled with GapCloser (version 1. 12) to obtain the final assembly result. Fragments below 500 bp were filtered out. Encoded genes were predicted using GeneMarkS software. The protein-coding sequences produced with BLAST were annotated by comparison with the NR, GO, KEGG, COG, PFAM, TCDB, and Swiss-Prot protein databases.
Genome Properties A draft of the genome of Streptococcus strain E24 revealed that it was comprised of 1,950,659 bp with a 42. 03% G + C content (Figure  3 ). It is comprised of five scaffolds (five contigs). Among the 1,994 genes predicted, 1,942 encoded proteins and 52 RNAs (3 genes were 5S rRNA, 1 gene 16S rRNA, 1 gene 23S rRNA and 47 genes tRNA). Of these, 1,525 genes (78. 52%) were specified with putative functions according to COG or NR BLAST analysis. Twentytwo genes were ORFs (1. 13%) and the remaining genes were responsible for hypothetical proteins. Table  4  shows the COG functional categories of the sorted genes. The sequence of the genome was recorded in the NCBI database (accession no. VFSG00000000).
) isolate gene sequence was aligned with sequences of other Streptococcus species retrieved from GenBank. Strain Streptococcus strain E24 shared 98. 04, 98. 11, and 97. 34 % 16S rRNA gene sequence similarity with S. australis ATCC 700641 T , S. rubneri LMG 27207 T and S. parasanguinis ATCC 15912 T , respectively. The housekeeping gene sodA (Figures 1C,D) of Streptococcus strain E24 shared 94. 94, 92. 74, and 90. 80% similarities with S. australis ATCC 700641 T , S. timonensis Marseille-P2915 T and S. infantis ATCC 700779 T , respectively. Figures 1A,C represent phylogenetic trees constructed with the neighbor-joining and Figures 1B,D phylogenetic trees constructed with the maximumlikelihood method. Taken together, the phylogenetic analyses demonstrated that Streptococcus strain E24 represents a novel species within the genus Streptococcus.
In silico DNA-DNA hybridization showed a closest DNA similarity value of 52% with Streptococcus australis ATCC 700641 T. Streptococcus strain E24 has been deposited in the Korean Agricultural Culture Collection (deposition no. KACC 21425) and Guangdong Microbial Culture Collection Center (deposition no. GDMCC 1. 1634). The genome and 16S rRNA gene sequences are recorded in the NCBI database (accession no. VFSG00000000; accession no. MN592637).
In silico DNA-DNA hybridization showed a closest DNA similarity value of 52% with Streptococcus australis ATCC 700641 T. Streptococcus strain E24 has been deposited in the Korean Agricultural Culture Collection (deposition no. KACC 21425) and Guangdong Microbial Culture Collection Center (deposition no. GDMCC 1. 1634). The genome and 16S rRNA gene sequences are recorded in the NCBI database (accession no. VFSG00000000; accession no. MN592637). temperature being 37 • C. After 48 h of aerobic incubation on 5% sheep's blood-enriched nutrition agar, colonies are Code Value % of total a Description pinpoint, grayish and α-hemolytic, with undulated edges and with a diameter of 0. 5 to 1 mm. Cells are roughly round with a 0. 5 µm diameter. Cells did not hydrolyse arginine, A 0 0 RNA processing and modification aesculin or starch except hippurate and were negative in tests B 0 0 Chromatin structure and dynamics for esterase, leucin arylamidase, valin arylamidase and β-D- C 49 3.
Computational Methods The reaction of perfluoroamines with OH radicals is expected to make a negligible contribution to their atmospheric loss. Here, we used theoretical methods to estimate upper-limits for the reaction rate coefficients, at 298 K, for the reaction of OH radicals with N(C3F7)3. The other amines are expected to have a similar reactivity. Optimized structures, normal mode vibrational frequencies, and thermochemical parameters for N(C3F7)3, OH, and reaction products were calculated using the Gaussian 09 program suite  [10]. The DFT functional B97-1 with the 6-311 ++ G(2df,2p) basis set, with ultrafine grid numerical integration, was used for all calculations. Reaction channels were explored where either OH abstracts an F atom to form FOH + radical, or where the OH radical adds to the amine to form a hydroxylamine and a C3F7 radical (i.
The fit precision uncertainties given in Table  2  are ~5%, or less. The independent experimental N(C3F7)3 reaction measurement results agree to within ~15%. The final rate coefficient for the N(C3F7)3 reaction was obtained from the least-square analysis of all the data. 2. The measured rate coefficient ratios were placed on an absolute basis using the O( 1 D) rate coefficient of CHF3 (channel 8a), (2. 4 ± 0. 12) × 10 -12 cm 3 molecule -1 s -1  [7]. Overall, the O( 1 D) reactive rate coefficients are slow, but consistent with values reported for other highly fluorinated compounds  [7]. The estimated absolute uncertainty in the O( 1 D) reactive rate coefficients was determined from the precision and reproducibility of the experimental data and the uncertainty in the CHF3 reference compound rate coefficient and estimated to be 9% for N(C2F5)3 and 7% for N(C3F7)3 and N(C4F9)3.
Angiosarcoma (AS) is a rare aggressive sarcoma with differentiation toward blood or lymphatic endothelium. There are few epidemiological data available on AS. To address this limitation, we investigated the epidemiological and clinical features of angiosarcoma diagnosed in a French administrative area (the Doubs department) from 1979 to 2016. A retrospective cohort study was conducted using the Doubs cancer registry database. A total of 45 patients with invasive AS were diagnosed between 1979 and 2016 in the Doubs department. Among the 45 AS, 51% were either cutaneous AS (27%), including head and neck and extremities, or breast AS (24%) as compared to visceral AS (42%). Eleven patients had metastasis at diagnosis (26%). Age-standardized incidence rate was 0. 15 per 100,000 persons-years (95%CI, 0.
10-0. 20) for the entire study period (1979-2016) and 0. 26 (95%CI, 0. 15-0. 42) for the last decade (2007-2016). Crude survival at 1, 3, 5 years after diagnosis was 44%, 21%, and 12%, respectively. Our population-based study provides updated data on the incidence and overall survival of AS in a French populationbased cancer registry.
Patients selection A retrospective cohort study was conducted using the database of the Doubs cancer registry, a French populationbased cancer registry which provides continuous and exhaustive recording of all cancer cases diagnosed in patients living in the Doubs Department, a well-defined administrative area located in eastern France (505,557 inhabitants according to the INSEE population census of 2003). Cancer registry population-based studies provide non-biased evidence, since they include all cases of cancer diagnosed in the inhabitants of a given geographical area, regardless of where they receive care. There is therefore no selection bias, as may occur in hospital-based patient series. Moreover, in France, the quality and completeness of registry data are assessed every 5 years by the public health authority's Registry Evaluation Committee.
Cancer registry routinely collected cancer cases from different sources including histopathology laboratories, oncology departments, multidisciplinary meetings, and computerized hospital discharge databases. Inclusion criteria were all primary invasive angiosarcoma (coded M-91203 according to the International Classification of Diseases for Oncology, 3rd edition),  2  diagnosed between 1 January 1979 and 31 December 2016, in patients resident in the Doubs Department. Patients with Kaposi sarcoma were excluded. Data collected from medical records were: demographic characteristics (age, sex), tumor characteristics at diagnosis (date of diagnosis, topography, histology, metastatic status at diagnosis), vital status, date of death, and last available follow-up date.
Discussion The exact overall incidence of sarcomas is unknown and the incidence of the different histological and molecular subtypes has not been determined precisely. The goal of this retrospective study was to describe a population-based cancer registry series of consecutive angiosarcoma (AS) diagnosed between 1979 and 2016 in a define geographic area. AS are one of the most rare subtypes (1%-2%) of adult soft tissue sarcomas. 1, 3 n Europe, AS annual incidence is approximately 0. 31 cases per 100,000 people per year,  4, 5  very close to our rate of 0. 26 per 100,000 for the 2007-2016 period. Angiosarcomas have an overall 5-year survival rate of about 40% 6 decreasing to 15% in metastatic patients. 1 In a recent study 3 from the National Cancer Institute's Surveillance, Epidemiology and End Results database including 4537 US patients diagnosed with primary AS from 1973 to 2014, the median overall survival was 82.
8% (95% CI: 70. 7-78. 9) and 39. 8% (95% CI: 30. 6-43. 2), respectively. 5 he limitations of this study include potential selection bias due to its retrospective nature and the small number of patients. However, this study covers a very large period (38 years) and is derived from a population-based cancer registry. In conclusion, our population-based study provides updated data on the incidence and OS of AS in a French population-based cancer registry.
Compliance measurement The three different groups of VG (P1, P2, P3) were tested under a 60e140 mmHg pulsed pressure range (2 Hz) at 37 C. The testing bench used is represented in Fig. 2. In order to assess the compliance of the samples over cycling, diameter variations were measured using a camera (Stingray, Allied Vision, Exton, USA). Images were analysed with dedicated software (Image J, NIH Image, USA). Moreover, four angular positions were considered over the whole circumference of the samples (0 , 90 , 180 , and 270 ) in order to account for specimen variability. Diameters were measured in six locations along the length of the VG for the same reasons. Average diameter values were then calculated and variation coefficients were assessed (percentage). In order to assess the influence of time on compliance evolution, measurements were made at time 0, and after three, six, and 24 h.
Acknowledgements The  AMICO  project was co-funded by  Copernicus , the  French ministry for the Environment, Energy  and the  Sea, CNRS-INSU and LEFE-GMMC. SEB is currently supported by a postdoctoral grant from the  Centre National d'Études Spatiales (CNES). Numerical simulations were performed on Ifremer HPC facilities DATARMOR of the  Pôle de Calcul Intensif pour la Mer (PCIM)  (http://www. ifremer. fr/pcim). The presented coupled framework is based on a prototype wave-ocean coupled model for monochromatic waves developed by  A. -C. Bennis  from which an idealistic test case can be found in Bennis et al. (2011). The authors would like to thank three anonymous reviewers as well as  N. Suzuki  for their comments that allowed for an improved manuscript.
The specimen was also investigated with Computed Tomography using a ZEISS Xradia 520 Versa, but no additional structures were revealed using this method. Measurements were made on digital photographs using the image processing software ImageJ  (Schneider et al. , 2012). Morphological characters measured include: (1) the total length, measured from the anterior margin of the head shield to the posterior termination of the tailspine; (2) the head, measured from the anterior margin to FIGURE 1. Bushizheia yangi gen. et sp. nov. (YKLP 11421). A, photograph of dorsal view; B, composite line drawing of dorsal view. Both scale bars are 10 mm. Abbreviation: app?ex, exopod of a post-frontal head limb appendage; cw, compression wrinkle; en, endopod; gr, groove; hl, frontal head limbs; hs, head shield; ps; pygidial segment; pyg, pygidium; tg1-8, tergites 1 through 8; ts, tailspine.
ACKNOWLEDGEMENTS We thank  Z. Yang  for discovering and preparing the specimen and donating it to the  Yunnan Key Laboratory for Palaeobiology. We also thank  H. Mai  ( Yunnan Key Laboratory for Palaeobiology ) for performing computed tomography scans. We are indebted to  D. Loydell  and  D. Martill  ( University of Portsmouth ) for suggesting references and  J. Ortega-Hernández  ( Harvard University ) and  C. Haug  ( Ludwig-Maximilians-University ) for discussions. We thank the editor and three anonymous reviewers for their helpful comments. The research of  R. J. O'Flynn  and  D. Audo  is supported by the  China Postdoctoral Science Foundation, Yunnan Province Postdoctoral Science Foundation ,  NSFC  grant ( 41861134032 ),  Natural Science Foundation of Yunnan Province  grants  2015HA021 ,  2018FA025 ,  2018IA073  and  2019DG050.
Materials and Methods e study includes patients diagnosed with EBC at AUBMC and treated between December 2016 and February 2018. e eligibility criteria were the following: women above the age of 18 with EBC (T1-2 N0, including T1pN1mic) that is hormone receptor-positive and HER2-negative. All patients included had undergone a total or partial mastectomy. After assessing pathology, the genomic analysis was carried out on the surgical specimens. We made sure to obtain Institutional Review Board (IRB) approval at our institution before proceeding with patient recruitment. Demographics and clinicopathological data were obtained from a review of charts. Physicians' treatment plans and decisions were recorded as noted before the genomics testing was done and after results were available. e physicians' choice of treatment was divided into three categories: those who planned to give endocrine therapy (ET) only, those who planned to provide endocrine therapy with chemotherapy (ET + CT), and those who were undecided regarding the treatment regimen and wanted to wait for genomic profiling test results.
Rising global temperatures over the last decades have increased heat exposure among populations worldwide. An accurate estimate of the resulting impacts on human health demands temporally explicit and spatially resolved monitoring of near-surface air temperature (T a ). Neither ground-based nor satelliteborne observations can achieve this individually, but the combination of the two provides synergistic opportunities. In this study, we propose a two-stage machine learning-based hybrid model to estimate 1 × 1 km 2 gridded intradaily T a from surface skin temperature (T s ) across the complex terrain of Israel during 2004-2016. We first applied a random forest (RF) regression model to impute missing T s from the Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua and Terra satellites, integrating T s from the geostationary Spinning Enhanced Visible and InfraRed Imager (SEVIRI) satellite and synoptic variables from European Centre for Medium-Range Weather Forecasts' (ECMWF) ERA5 reanalysis data sets.
However, the urbanized meso-scale climate models are computation-intensive and require great expertise to implement. Thus, they have not yet been widely employed in epidemiological studies. In comparison, urban climate models coupled with simplified energy balance schemes constitute a computationally efficient and accurate alternative  (Masson et al. , 2002; Erell and Williamson, 2006; Bueno et al. , 2013; De Ridder et al. , 2015). These models typically require a detailed description of urban morphology and apply forcing at the boundary level or from rural reference stations under the same meso-scale weather  (Kaplan et al. , 2016; Zhou et al. , 2019). This may restrict their application to regions with high-quality geospatial databases and well-maintained weather stations. To overcome limitations existing in previous studies (i.
| Remotely sensed surface skin temperature The daily Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) products (version 6) are collected at about 1 × 1 km 2 resolution from the MODIS sensors on board the Aqua (MYD11A1) and Terra (MOD11A1) satellites. The data used here cover the years 2004 to 2016 for the entire area of Israel corresponding to MODIS tiles h20v05, h20v06, h21v05, and h21v06. The Aqua and Terra satellites overpass the same location on Earth's surface twice per day, but with slightly varying times depending on their (polar) orbits. We retrieved the overpass time (in local solar time) for each MODIS LST value. When the overpass time for a pixel is not produced due to, for example, cloud contamination, the average overpass time in the scene (distinguished between day-and nighttime) is assigned.
SEVIRI provides infra-red images every 15 minutes with a nadir spatial resolution of 3 km, which is geometrically degraded at large off-nadir view angles. In this study, we downloaded the SEVIRI LST data from LSA SAF (https://landsaf. ipma. pt/en/products/ land-surface-temperature/lst, accessed on April 21, 2019) aggregated to hourly means. For Israel, the spatial resolution of the grid cell is about 4 × 4 km 2.
| ERA5 reanalysis data The ERA5 data are the fifth generation of the European Centre for Medium-Range Weather Forecasts' (ECMWF) atmospheric reanalysis of the global climate (Copernicus Climate Change Service [C3S], 2017). ERA5 is produced using data assimilation techniques based on ECMWF's latest Integrated Forecasting System (IFS). The IFS combines model data with all available historical in-situ and spaceborne observations with stringent quality control. ERA5 provides hourly estimates of atmospheric and surface parameters from 1979 onward at 0. 28125 (31 km) worldwide, but can be bilinearly interpolated to any custom grid. Given the aim of this study, we integrated the following ERA5 parameters (summarized in Table  1 ) into the model: (a) skin temperature, (b) 2 m temperature (T a at 2 m height), (c) boundary layer height, (d) 10 m wind speed [horizontal eastward (U) + northward (V) components], (e) soil temperature layer 1 (0-7 cm), and (f) total cloud cover.
These parameters may be used to describe the surface energy balance, and thus are expected to account for the complex land surface-atmosphere interactions  (Jin and Dickinson, 2010). The wind speed used in the model is the root of the sum of the squared U and V wind components. We downloaded the ERA5 data from 2004 to 2016 at 0. 125 (~10 km) for Israel via the Copernicus Climate Change Service (C3S) Climate Data Store (https://cds. climate. copernicus. eu, accessed on April 21, 2019).
| NDVI We used MODIS-derived monthly Normalized Difference Vegetation Index (NDVI) products (version 6) at 1 × 1 km 2 resolution from Aqua (MYD13A3) and Terra (MOD13A3) satellites. The NDVI value for each grid cell is the mean of the two datasets. NDVI is computed as the ratio of the difference in spectral reflectance between near infrared and red wavebands to the sum of the reflectance of the same two bands  (Tucker, 1979). It quantifies the relative abundance and health status of vegetation varying in time and space. NDVI values range from -1 to 1: a higher value indicates dense photosynthetically active vegetation, whereas senesced and dead plants, inorganic materials (e. g. , rocks), and water courses normally have a low or even negative NDVI. For every timestep, each grid cell was assigned the mean NDVI of the month when the observation was taken.
| Distance to large bodies of water Water bodies have a higher specific heat capacity than land, and are expected to modify mesoscale climate conditions, and thus have to be taken into proper account in the model. We calculated the distance of each grid cell to the nearest water body by applying the distance function in R sf package  (Pebesma, 2018)  on the 1:10,000,000 coastline data version 4. 1. 0 from the Natural Earth portal (https://www. naturalearthdata. com/ downloads/10m-physical-vectors/10m-coastline/, accessed on 01/04/2019).
| Elevation and slope aspect The elevation assigned to each MODIS grid cell (1 km resolution) is the mean value calculated from 30 m raster data provided by the Advanced Spaceborne Thermal Emissions and Reflection Radiometer (ASTER) global digital elevation model version 2 (GDEM V2). As the compass direction a slope faces (aspect) can influence the insolation during the daytime, we applied the aspect function in ArcGIS 10. 6 (Esri, 2018) on the elevation data to calculate the slope aspect of each grid cell. Analogously, we aggregated the output to 1 km in line with the MODIS grid.
| Statistical methods We propose a two-stage hybrid model approach based on random forest regression to estimate T a from T s , as shown in Figure  2. Total cloud cover (0-1) tcc First, we imputed T s values for missing T s grid cells (obscured by cloud cover, etc. ). Then we fed the imputed T s data for each grid cell into the Stage 2 model to estimate T a at the same spatial and temporal resolution. We performed the random forest regression using the R ranger package  (Wright and Ziegler, 2017)  wrapped in mlr package  (Bischl et al. , 2016). Like MODIS, SEVIRI data are also limited to clear-sky conditions. However, the hourly SEVIRI data, in contrast with four daily overpasses of the MODIS, may incorporate more information pertaining to the diurnal and seasonal patterns. The additional information could facilitate imputing data gaps in the SEVIRI data.
trees was set to 300. In the Stage 1 model, we only tuned the number of features (mtry). Validation of the model was performed using a fivefold CV resampling scheme, which partitions the dataset into five approximately equal-sized subsets. Each subset is iteratively used for testing model performance, while the remaining 4 subsets comprise the training set. Overall model performance was estimated by calculating the "out-of-sample" Mean Absolute Error (MAE) and Root Mean Square Error (RMSE), maintaining a complete separation between data used to train the model and data used to test its performance.
As CSR JJA is always As shown in Figure  7b , the South of Israel is generally less cloudy and presents less variability in the clear-sky ratio across seasons, whereas the clear-sky ratio in the region of Judaean Mountains (central) and Northern Mountains varies significantly with seasons. This spatio-temporal heterogeneity resulted in varying data abundance/availability of each region, and thus in varying regional representativeness in the model. In the cloudless period of the year, for example, during the summer, each region is equally represented in the training datasets, whereas in the rainy season the data from the South prevail. In comparison, data in the transition period between the rainy and sunniest seasons are well mixed but with a high degree of fragmentation in the central part of the country.