dataesr/scientific-paragraphs-categorization huggingface dataset:
Nonetheless, a major limitation of this analysis was that the inclusion of all the existing eligible participants having different comorbidities could not be guaranteed. The other limitation was the reliance on sputum culture to make the microbiological diagnosis, in spite of the fact that the 17 studies included in this systematic review and meta-analysis were done in tertiary care hospitals in the urban area. Although most reported diagnosis based on clinical signs and symptoms along with microbiological tests (sputum culture and blood culture), 6 of 17 reported diagnoses were based on sputum culture and leukocyte count. In addition, with the criteria established for this analysis, studies on viral pneumonia, or a comparison of viral with bacterial aetiology, were not included. Also, unpublished data such as conference abstracts or papers presented at scientific symposia were not included in the current study.
1999 ) may be useful in certain settings. We, therefore, analyse CMB fluctuations in terms of the purely topological concepts of homology  (Munkres 1984) , as quantified by Betti numbers (Betti 1871) and persistence  (Edelsbrunner et al. 2002; Edelsbrunner & Harer 2010). By the Euler-Poincaré formula, the Euler characteristic is the alternating sum of the Betti numbers, implying that the latter provide a finer description of topology  (Munkres 1984). A broad exposition of these concepts, in a cosmological setting, is given in  (Pranav et al. 2017; Pranav 2015; van de Weygaert et al. 2011) ; also see  (Park et al. 2013; Sousbie 2011; Shivashankar et al. 2016; Adler et al. 2017; Makarenko et al. 2018; Cole & Shiu 2018)  for some applications. Related but slightly different methodologies used for the analysis of cosmological datasets, emanating from concepts in Morse theory maybe found in  (Colombi et al.
Computational Pipeline The computational pipeline is tailored specifically to the Planck data. The preprocessing step involves converting the CMB maps given in absolute units to a dimensionless unit, corrected for mean and scaled by the standard deviation (computed using the non-masked pixels only). We use the HealPix package for the preprocessing step. The output of this operation is the normalized temperature values on 12N 2 pixels, along with their coordinates on the sphere, which is the input to subsequent steps, which we discuss in five subsections: (i) triangulating the surface of the sphere with the pixel centers as vertices, (ii) sorting the vertices, edges, triangles to form an upper-star filteration, (iii) computing the persistence in terms of a reduced boundary matrix, (iv) computing the ranks of the relative homology groups b p , p = 0, 1, 2 and (v) the variationally optimal loops from the reduced matrix.
The software is written in C++ and designed to handle very large data sets. Triangulation. The HealPix format stores the data in twelve square arrays of N 2 pixels each, with N = 2048 at the finest resolution. The centers of these pixels are points on the faces of a rhombic dodecahedron. With central projection, these points are mapped to the 2-sphere and distorted to achieve an approx- imately equal-area decomposition. Taking the convex hull of these points in R 3 , we get a convex polytope whose boundary is homeomorphic to the sphere. Most of the faces will be triangles, and the occasional faces with k ≥ 4 sides can be subdivided into k -2 triangles to get a triangulation of the sphere. This triangulation is the input to all the down-stream computations. Consisting of V = 12N 2 vertices, 3V -6 edges, and 2V -4 triangles, it represents the temperature field, f : S 2 → R, by storing the temperature value at every vertex.
Summary and Conclusions We provide evidence for the deviation of the observed Planck CMB maps from the Gaussian predictions of the standard LCDM model. Specifically, we find an over-abundance of loops in the observed maps, deviating from the simulations at per cent to less than per mil levels. This is in terms of p-values computed using χ 2 statistics, between the resolutions N = 32 and N = 8. The difference in the number of components and loops peaks sporadically at more than 3σ from the predictions between Article number, page 12 of 18 N = 32 and N = 8. Results based on smoothed maps corroborate with those based on degraded maps in terms of approximate scales at which the anomaly is observed. We also compute the absolute homology for the dataset, and confirm that the results are consistent with those from relative homology.
Repetition and Statistical Analysis Each sample of raw millet and fermented meat fish was analyzed in triplicate and the figures were then averaged. Microbial counts and pH data of the different times of incubation (0 h, 24 h and 48 h) for the four fermentation procedures were assessed by analysis of variance (Anova), using The Stata ver. 12. 0 (Stata, Texas, USA) with a probability P ≤ 0. 05.
3. Percentage of the surface of the artery occluded defined as the relative proportion of the occluded area as a percentage of the total area internal to the internal elastic lamina was evaluated. 4. Percentage corresponding to the surface occupied by thrombus / metal / hydrogel in the vessel lumen defined as the relative proportion of the thrombus area, the metal area and the hydrogel area as a percentage of the total area was evaluated. The specific surface of the fibers could not be evaluated separately. Due to the thickness of the section, several fibers overlap making it difficult to focus on the fibers situated in the same plan. To obtain the surface percentage of tissue, the digital images were converted to TIFF images and were analysed using GIMP software. 5. Inflammatory cells in contact with the coil, in the vessel wall and in the surrounding tissue were assessed as follows: At the interface with implants, the thickness of inflammatory cells layers around the fibers or the gel was measured in five different sites.
Material and Methods For brevity we only provide in this section an overview of the methods. For more detailed methodological information on strains and growth conditions, time-lapse imaging, image analysis, determining death and estimating demographic parameters, statistical analyses, the simulations please see the supplemental information. We collected data in two independent sets of experiments. We loaded E. coli K12-derived MG1655 strain cells into a designed microfluidic (PDMS) chip  (Wang et al. 2010 , Gasset-Rosa et al. 2014 , Jouvet et al. 2017 ) from an exponentially growing culture in supplemented minimum media M9. During each experiment, we acquired 77 hours of time lapse phase-contrast imaging (15 frames/hour for each of the 2x44 fields followed) using a temperature-controlled inverted microscope, at 43°C with an accuracy of the temperature control at the chip of ±0.
S2 -8, Table  S1 -3. Analysis on the empirical data were done in program R (R Core Team 2016) using general linear, generalized linear, and non-linear models. Models were selected based on information criteria (AIC)  (Burnham and Anderson 1998)  or based on differential evolution algorithm for global optimization (R package DEoptim). Simulations and extending random deterioration models. For the extended random deterioration model, we first estimated parameters by fitting a fixed frailty model -a Gamma-Gompertz-Makeham (GGM) model -to the observed survival data of the early daughter cells  (Yashin et al. 1994, Missov and Vaupel 2015). We then translated these fitted GGM model parameters to an extended random deterioration process model, an extended LeBras type deterioration model  (Le Bras 1976).
2013). contrast time-lapse images were lowpass-filtered and background flattened (MetaMorph Molecular Devices software) to increase contrast. We further processed the images by a customized ImageJ plugin for cell segmentation to crop each of the growth channels, stabilize the time sequenced images, adjust the brightness and to create a binary image by thresholding and filtering (median filter). Finally, the ImageJ plugin water-sheds the time sliced images. We then applied a final round of segmentation in Matlab by correcting errors in segmentation by checking for minimum (0. 8) and maximum (1. 4) cell elongation rates for each cell (size time-4 min, size time+4min). This way, we recorded for any time points (at 4 minute intervals) the exact location of a cell in the side channel (the pixel coordinate of the center of mass of the cell area), the side channel of the cell, and if a cell divided.
Statistical analysis We did the statistical analysis using the R software (R Core Team 2016). We estimated and plotted hourly rates for division rates, cell elongation, and cell size at division rather than rates on the 4 min intervals because data would be sparse for 4 min intervals at older ages. Already the hourly rates at old ages suffer from sparse estimates and increased uncertainty. We also clustered all data of ages beyond 30 h for the same reason. To guide statistical testing, we used model selection  (Burnham and Anderson 1998)  based on AIC (Akaike Information Criteria) and considered -as common practice -better support between models when the ΔAIC was more than 2. For the parameter estimation of the GGM and extended random deterioration models, we used the DEoptim R package and the optim function within the stats R package.
25% Triton X-100 (Sigma catalog no. T9284; St. Louis, MO) in PBS for 10 min, followed by treatment with 0. 1% Triton X-100 in PBS-fish skin gelatin (FSG) (0. 66%) (Sigma-Aldrich catalog no. G7765) for 20 min. The cells were then stained for chlamydial inclusions with 5 g/ml of mouse anti-human chlamydia LPS (primary Ab) (US Biological catalog no. C4250-51F; Salem, MA) in Triton X-100 -PBS-FSG solution for 90 min. Secondary antibody staining was done by adding 200 g/ml of goat anti-mouse Alexa Fluor 488 (Invitrogen catalog no. A-11029; Carlsbad, CA), in Triton X-100 -PBS-FSG solution and incubated for 60 min in the dark. Image and statistical analyses. For secondary infection assays and primary infection 2D epithelial cell culture models, the number of inclusions, total number of host cells, and number of host cells containing inclusions were determined using the Cell Profiler imaging software (77), from scoring 5 images.
The percentage of infected cells was determined per condition, and the percentage of total number of inclusions was analyzed based on either medium only or pH 7 inclusions used as control. All graphs were created using the GraphPad Prism software (GraphPad Software). 3D images created from compressing confocal slices were opened using the ImageJ program (NIH). Using the cell counter plug-in, the total number of cells (blue) and number of inclusions (green) were manually counted and the percentage of primary-infected host cells was determined and graphed. Using the number of pH 7 inclusions as control, the percentage of total inclusions at the various pHs for each condition was analyzed and then graphed. All graphs were created using GraphPad Prism. Statistical analyses were performed within the GraphPad software with both Student's t test and analysis of variance (ANOVA).
The amount of DNA synthesis was calculated using CellProfiler (version 2. 2. 0 rev 9969f42  [77] ) by counting the number of green nuclei (EdU stained) relative to blue nuclei (DAPI stained) in five fields per duplicate coverslip. A two-tailed t test was applied to test whether differences between means of each scratch assay and EdU experimental conditions were equal to 0, with P Ͻ 0. 05 considered significant (see https://github. com/ravel-lab/smith_thesis_2017/tree/feature/manuscript-2. 0/ AnalysisPipeline/Scripts for script). C. trachomatis infection and inhibition of cell proliferation. A2EN human cervical epithelial cells were seeded at 1 ϫ 10 5 on coverslips, grown overnight, and then exposed to starvation medium (EpiLife medium) for 18 h. Coverslips were exposed to either EpiLife complete medium (control) or CDK4 inhibitor CAS 546102-60-7 at 400 nM (Millipore 219476) or Fascaplysin at 350 nM (Millipore 341251) in complete medium.
Concurrently, C. trachomatis serovar L2 was added at an MOI of 2 to each coverslip and rocked for 2 h at room temperature. A2EN cells were then exposed to complete medium or inhibitors in the presence of EdU (1 nM) as described above for an additional 22 h at 37°C in 5% CO 2. Cells were fixed, stained, and imaged for C. trachomatis, EdU (Alexa Fluor 555; ThermoFisher C10638), or cell viability staining as outlined above. The proportion of infected A2EN cells and new DNA synthesis were determined using manual counting and CellProfiler software. A two-tailed t test was applied to test whether differences between means of each EdU or infection experimental conditions were equal to 0, with P Ͻ 0. 05 considered significant. A linear model was fitted to mean percent cells stained with EdU versus the mean proportion of infected A2EN cells using the R lm package (version 3.
ACKNOWLEDGMENTS We thank  Mary Regan ,  Sebastian Martinez-Greiwe ,  Lisa Bilski ,  Mina Rahimi , and the Sentinel study team for recruiting participants into the Sentinel study;  Bing Yang  for imaging samples for the mucus penetration analysis;  Shaikh Bilal Ali Iqbal  for contributing to sample DNA preparation;  Li Fu ,  Hongqiu Wang , and  Hadassa Guttman  for their help with cell cultures and antibiotic resistance analyses; and  Alison Quayle  ( Louisiana State University ) for providing the cervical A2EN cell line. Research reported in this publication was supported by the  National Institute for Allergy and Infectious Diseases of the National Institutes of Health  under award numbers  U19AI084044  and  UH2AI083264. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Aims. We aim to investigate the impact of the ionized radiation from the M16 H II region on the surrounding molecular cloud and on its hosted star formation. Methods. To present comprehensive multi-wavelength observations towards the M16 H II region, we used new CO data and existing infrared, optical, and submillimeter data. The 12 CO J=1-0, 13 CO J=1-0, and C 18 O J=1-0 data were obtained with the Purple Mountain Observatory (PMO) 13. 7m radio telescope. To trace massive clumps and extract young stellar objects (YSOs) associated with the M16 H II region, we used the ATLASGAL and GLIMPSE I catalogs, respectively. Results. From CO data, we discern a large-scale filament with three velocity components. Because these three components overlap with each other in both velocity and space, the filament may be made of three layers.
The half-power beam width (HPBW) was 53 at 115 GHz and the main beam efficiency was 0. 5. The pointing accuracy of the telescope was better than 5. Mapping observations use the on-the-fly mode with a constant integration time of 14 seconds at each point and with a 0. 5 × 0. 5 grid. The final data were recorded in brightness temperature scale of T mb (K) and were reduced using the GILDAS/CLASS 1 package.
Archival data In order to obtain a complete view of the filament around M16, we completed our observations with Galactic Ring Sur-1 http://www. iram. fr/IRAMFR/GILDAS/ vey (GRS) data of 13 CO J=1-0 emission  (Jackson et al. 2006). The survey covers a longitude range of =18 • -55. 7 • and a latitude range of |b|≤1 • , with an angular resolution of 46. At the velocity resolution of 0. 21 km s -1 , the typical rms sensitivity is 0. 13 K. The GLIMPSE survey observed the Galactic plane (65 • < |l| < 10 • for |b| < 1 • ) with the four IR bands  (3. 6, 4. 5, 5. 8, and 8. 0 µm) of the Infrared Array Camera (IRAC)  (Benjamin et al. 2003)  on the Spitzer Space Telescope. We used these data to identify young stars and H II regions. The spatial resolution in the four IR bands are from 1. 5 to 1. 9. To explore the dust distribution, we used the 250 µm data from the Herschel Infrared Galactic Plane survey (Hi-GAL;  Molinari et al.
2010 ) carried out by the Herschel Space Observatory. The initial survey covered a Galactic longitude region of 300 • < <60 • and |b|<1. 0 •. The angular resolution of the 250 µm band is 18. 2. Additionally, we extracted 870 µm data from the ATLASGAL survey  (Schuller et al. 2009 ). The survey was carried out with the Large APEX Bolometer Camera observing at 870 µm (345 GHz). The APEX telescope has a full width at half-maximum (FWHM) beam size of 19 at this wavelength. To trace the ionized gas of M16, we also used the Digitized Sky Survey (DSS1,  Reid et al. 1991)  and 90 cm radio continuum emission archival data. The 90 cm data is obtained from multiconfiguration Very Large Array survey of the Galactic Plane with a resolution of 42  (Brogan et al. 2006 ).
The NGC6611 cluster and YSO formation We have shown that the M16 H II region interacts with a largescale filament with three layers. M16 is ionized by numerous O and B stars within the open cluster NGC6611. Because the large-scale filament is associated with some IRDCs, as shown in the pink dashed lines in Figure  2 , the NGC6611 cluster may form in a dark IR filament. The age of the YSOs in NGC6611 is estimated to be 0. 25-3 Myr  (Hillenbrand et al. 1993). We also use the Spitzer-IRAC data to identify Class I and Class II YSOs. Class I YSOs have an age of ∼ 10 5 yr, while this is ∼ 10 6 yr for Class II YSOs  (André & Montmerle 1994). The selected YSOs (Class I and Class II) are also concentrated in NGC6611. Furthermore,  Hillenbrand et al. (1993)  found that the stars of 3 M < mass < 8 M have ages ranging from 0.
Conclusions Using the PMO molecular 12 CO J=1-0, 13 CO J=1-0, and C 18 O J=1-0 data combined with IR and radio archival data, we present a comprehensive large-scale picture of the gas and dust towards the M16 H II region. The main findings are summarized as follows. 1. The H II region M16 shows an irregular ionized-gas cavity, which is enclosed by the cool dust traced by the 250 µm emission, and PAH emission traced by the 8 µm emission. From CO data, we observe a large-scale filament with three main velocity components, whose peak velocities are 20. 0, 22. 5, and 25. 0 km s -1. These three components overlap with each other, both in velocity and space, suggesting that the large-scale is made of three layers. Because the large-scale filament is associated with some IRDCs, the NGC6611 cluster may have formed in a dark IR filament.
Acknowledgements. We thank the referee for insightful comments which improved the clarity of this manuscript. We thank the  Key Laboratory for Radio Astronomy, CAS , for partly supporting the telescope operation. This work has made use of data from the  Spitzer Space Telescope , which is operated by the  Jet Propulsion Laboratory, California Institute of Technology  under a contract with  NASA. The  ATLASGAL  project is a collaboration between the  Max-Planck-Gesellschaft , the  European Southern Observatory (ESO)  and the  Universidad de Chile. This includes projects  E-181. C-0885 ,  E-078. F-9040 (A),  M-079. C-9501 (A),  M-081. C-9501 (A) plus Chilean data. This work was supported by the  National Natural Science Foundation of China  (Grant Nos. 11673066 ,  11703040 , and  11847309 ), the  Youth Innovation Promotion Association of CAS , the young researcher grant of national astronomical observatories, Chinese academy of sciences, and also supported by the  Open Project Program of the Key Laboratory of FAST, NAOC, Chinese Academy of Sciences.
Determination of Cytokine Concentrations PBMCs (10 6 cells/mL) (n = 3 volunteers) were incubated with or without phytohemagglutinin (PHA, 5 µg/mL) and BRE (0 or 50 µg/mL) for 24 h. Milliplex ® MAP kits (EMD Millipore™; Merck; Darmstadt, Germany) were used for all assays. All samples were run in triplicate and were assayed for 14 human cytokines (IFNγ, IL-10, IL-12 p70, IL-1β, IL-2, IL-21, IL-4, IL-23, IL-5, IL-6, IL-8, MIP-1α, MIP-1β, and TNFα). Cytokine levels were measured using optimal concentrations of standards and antibodies according to the manufacturer's instructions. After completion of all the steps in the assay, the plates were read in the Luminex Bio-Plex 200 System (Biorad, Marnes-la-Coquette, France) and the data analyzed using BioPlex Manager™ 4. 1 software with a five-parameter logistic regression (5PL) curve fitting.
The traits of the flours were compared with the one-way analysis of variance and Duncan's test at α = 0. 05. In turn, the multi-way analysis of variance and Duncan's test were used to compare the effects of dough development method, fermentation time, and flour type on the quality traits and fructans content of wheat breads, at α = 0. 05. All statistical analyses were performed using Statistica software version 13. 3 (StatSoft Polska Sp. z o. o. , Kraków, Poland).
Funding: This research was funded by  Krajowy Naukowy Osrodek Wiodacy :  2014-2018. Acknowledgments: This work was supported by the  Wroclaw Centre of Biotechnology  under the  Leading National Research Centre Program (KNOW)   2014-2018  and purpose subsidy 2019 (MNiSW) for the  Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences. The authors thank  Sabina Michalik  for contribution to the research.
Generating IUCN Red List assessments must be done on a speciesby-species basis and requires both reliable data and the careful, knowledgeable application of the Red List criteria, a process that takes considerable time. This is reflected by the fact that there are substantial gaps in the Red List (www. iucnredlist. org). While the conservation status of most species in large vertebrate groups has been assessed [e. g. , mammals: 5792 of ca. 6500 species (86%) and birds: 11,133 of ca. 18,000 (61%); www. iucnredlist. org, accessed 20 June 2019], this is not the case for plants, despite their crucial importance for terrestrial ecosystems. Only 28,114 vascular plant species (www. iucnredlist. org, accessed 20 June 2019), representing less than 8% of the estimated 352,000 species worldwide  (6)  have been assessed to date.
PACA can facilitate analyses of the level of conservation concern of a large number of species or of the entire flora of a given area and can help identify species that are likely to be threatened and therefore may require additional attention, including full Red List assessments. To demonstrate the utility and relevance of the PACA approach, we applied it to the flora of tropical Africa based on the recently developed RAINBIO database, which contains more than 600,000 occurrence records of more than 20,000 vascular plant species  (8, 12). Tropical Africa is a highly suitable model for undertaking such a study as it is faced with significant and mounting threats resulting from a wide range of activities, including logging, fuelwood collection, and deforestation for agriculture and mining  (13, 14).
Comparison with published IUCN assessments To evaluate how well the PACA approach agrees with full IUCN Red List assessments, we retrieved all published assessments available on the Red List website for species in our dataset. We found full assessments for 2856 plant species among those in our study set, of which 600 were published before 2001 or were thus performed using outdated IUCN categories (i. e. , LR/NT) (fig. S3 ). Comparisons were therefore restricted to 2009 species (i. e. , 9. 1% of the total number of species assessed in our study). The proportions of species categorized on the Red List as either CR or EN (i. e. , analogous to LT in the PACA system of categories) and VU (analogous to PT) are 26. 1 and 14. 7%, respectively, while the PACA approach based on all species provided 17.