dataesr/scientific-paragraphs-categorization huggingface dataset:
One full lane of the library was sequenced on a HiSeq 2500 instrument on High-Output V4 paired-reads (2 Â 125 bp) mode  (Fasteris, Switzerland). A total of 72,998,800 paired reads were filtered to remove adaptors and quality trimmed (Quality Phred score cutoff: 20) with TrimGalore v0. 4. 0  (Krueger, 2015). The resulting reads were de novo assembled using Trinity v2. 1. 1  (Haas et al. , 2013) , giving a total of 38,158 transcripts (37,059 predicted trinity genes), a GC content of 42. 4%, an N50 of 312 bp. The genome-guided assembly rendered a total of 4612 transcripts (4280 predicted Trinity genes), a GC content of 48. 2%, a N50 of 819 bp and a coverage of 1127x, calculated with bedtools (genomecov) v2. 17. 0  (Quinlan, 2014). The Maker pipeline  (Cantarel et al. , 2008)  was used for de novo gene annotation with the default settings except that keep_preds = 1, to insure maximum retention of protein models.
The Trinity RNA assembly was used as EST data, and all proteins in the SwissProt reviewed database (accessed May 20, 2016)  (Boeckmann et al. , 2003)  plus protein models from early diverging Fungi were used as protein evidence data (Supplementary file 3). The Augustus training species was Rhizopus oryzae  (Stanke and Morgenstern, 2005) , and a custom repeat library was created using RepeatScout v 1. 0. 3  (Price et al. , 2005)  and the model organism for RepeatMasker v 4. 0. 6 was set to 'Fungi'  (Smit et al. , 2014). Whole nuclear and mitochondrial genome sequences and protein annotations have been deposited in GenBank under the accession MTSL00000000. MFAnnot was used to annotate genes and proteins for the mitochondrial genome  (Beck and Lang, 2010). Manual annotation of the mitochondrial ribosomal large subunit gene (rnL) and NADH dehydrogenase subunit 6 (nad6) was conducted via homology searches for conserved regions using blastn procedures against nr and a selected list of LSU sequences from Fungi, and blastp with 'No Adjustments' setting for compositional adjustments against Genbank nr database for nad6.
Allelic frequency plots were plotted using the free software environment for statistical computing and graphics, R v3. 1. 3 (R Core Development Team, 2013). Meiosis-related genes and homeodomain proteins were identified along the genome of P. saccamoebae using reciprocal blastx and tblastx procedures using a list of fungal meiosis-related genes available in  Halary et al. (2011). The genomic organization of P. saccamoebae HDs was manually compared against those of R. allomycis and available Microsporidia available in GenBank. To identify flagellum-related proteins, a blast database was created using the set of genes identified in Naegleria fowleri. Blastp was used to identify P. saccamoebae and M. daphniae proteins with hits at e-values <1*e-20 (Supplementary file 2), and results were compared with those found in  James et al.
(2013). For annotation of KEGGs in analyzed taxa, all protein models were uploaded to the KAAS server  (Moriya et al. , 2007) , and the 'for Eukaryotes' representative set was chosen and amended with the following taxa: Neurospora crassa, Botrytis cinerea, Aspergillus fumigatus, Parastagonospora nodorum, Tuber melanosporum, Ustilago maydis, Nosema ceranae, and Monosiga brevicollis. Finally, other functional annotation was performed using BLAST+ v 2. 2. 29 against the Uniprot TrEMBL database downloaded May 20, 2016  (Boeckmann et al. , 2003).
Phylogenomic analyses To cluster orthologous proteins, the Fastortho implementation  (Wattam et al. , 2014)  of orthoMCL  (Li et al. , 2003)  was run using default settings and inflation parameter of three with select outgroups and target taxa (Supplementary file 3). Ancestral character estimation of orthogroups present or absent in the internal nodes of the tree were estimated using the 'ace' command as a part of the APE package in R  (Paradis et al. , 2004). Data were recoded into a presence/absence binary matrix of each orthogroup, and ancestral states estimated using a symmetrical model (SYM). A 50% inclusion cutoff was used, meaning the orthogroup was reconstructed as being present in the ancestral node if it received greater than 50% marginal likelihood. For phylogenomic analysis, HMMs were built for each of the 53 protein alignments used in Capella-Gutierrez et al.
saccamoebae-specific contigs. (C) Contigs with blastn hits to the de novo Trinity assembly are in yellow, and found in many parts of the map including concentrations in the P. saccamoebae area, whereas those contigs with no hit to the assembly (in white) are not found in P. saccamoebae area. (D) Phylogenetic classes mapped onto the topology (based on best blastn to GenBank 'nr' database). P. saccamoebae region contains contigs with hits to mostly Fungi, animals, NO HIT, plants, Nuclearia, Microsporidia, and the P. saccamoebae rDNA. There are a few hits to bacteria that map within the genome, which were further tested to insure they belong on contigs which have multiple fungal proteins on them as well. DOI: https://doi. org/10. 7554/eLife. 29594. 002.
WIMPs become gravitationally bound to the Earth if their velocity is smaller than the escape velocity from Earth, which ranges from 11. 1 km/s to 14. 8 km/s (at the surface and at the centre respectively). The velocity of WIMPs follows a Maxwell-Boltzmann distribution, the canonical value for the velocity dispersion is 270 km/s (this value is subject to considerable uncertainty  [4] ). Under these conditions, only a small fraction of WIMPs would lose enough energy to become captured if there is a large difference between the mass of the WIMP and the mass of the nucleus the particle is scattering on. Capture of WIMPs in the Earth is expected to be dominated by spin-independent elastic scattering on the most abundant heavy nuclei, mainly iron and nickel. In this paper, an indirect search for DM towards the centre of the Earth using data collected in 2007 -2012 by the ANTARES neutrino telescope is presented.
Event selection and reconstruction For this paper, data collected with the ANTARES neutrino telescope from 2007 to 2012, with a livetime of 1191 days have been analyzed. As shown in Figure  2 , the flux from dark matter annihilations is restricted to certain (narrow) cones from the centre of the Earth and to a certain energy range. As the background increases quadratically with the search cone, the size of the cone which maximizes the signal-to-background ratio is determined for different WIMP mass intervals. Furthermore, the energy range in which neutrino candidates are searched for is determined as a function of the WIMP mass and annihilation channel. The event selection criteria are therefore chosen in a way that they restrict the minimal zenith angle and maximal energy of the events. The former is done by selecting events which are reconstructed by either Qfit or Λfit with a high zenith angle θ Q and θ Λ , respectively.
Conclusion In this paper, the results of a search for neutrinos from dark matter annihilation in the centre of the Earth using data taken with the ANTARES neutrino telescope from 2007 to 2012 (corresponding to a lifetime of 1191 days) have been presented. The number of neutrinos observed from the direction of the centre of the Earth is compatible with the background expectation from atmospheric events. Assuming natural scale for σ A v , the 90% C. L. upper limits on the WIMP self-annihilation rates have been set as a function of the WIMP mass. WIMP pair annihilation into either τ + τ -, W + W -, bb or (non-SUSY) ν µ νµ channels have been considered. These are translated into limits on the spin independent scattering cross-section of WIMPs off protons. A scenario where the annihilation cross-section for dark matter in the Earth is enhanced compared to the value during the freeze out of WIMPs has also been considered.
(C) Direct observation of liposome samples with a continuous size distribution from 50 nm to 5 µm. Rhodamine fluorescence was used for 4% PI(4,5)P 2 , 1% PI(3)P, 65% PC, and 30% PS liposomes (all percentages by molecular fraction, purple) and NBD for 4% PI(4,5)P 2 , 1% PI(3,4)P 2 , 65% PC, and 30% PS (cyan) using spinning-disk confocal microscopy. (D) Maximal activation of actin polymerization by liposomes containing 4% PI(4,5)P 2 , 1% PI(3)P, 48% PC, and 47% PS assayed by pyrene actin assay with HSS compared with 4% PI(4,5)P 2 alone or 4% PI(4,5)P 2 + 1% PI(3,4)P 2. Data show mean of four traces from two independent experiments. AU, arbitrary units. (E) As in C, except 10% PI(3,4)P 2 (cyan). (F) 10% PI(3,4)P 2 liposomes (cyan), extracts + SNX9. In all experiments, we exclusively observed the formation of comet tail at the surface of PI(4,5)P 2 /PI(3)P liposomes.
(A) Mutations in the various proposed lipid-binding sites within the PX and BAR domains of Xenopus SNX9. K511E/K517E, which are residues that make up a positively charged patch within the SNX9 BAR domain, and Y276A/K302A, which is the phosphoinositide lipid-binding pocket within the PX domain. The structure shown is 2RAI, downloaded from the Protein Data Bank and visualized in the CCP4mg molecular graphics package with the Xenopus numbering inferred from a sequence alignment performed in Lasergene software. (B) The liposome compositions used were 5% PI(4,5)P 2 , 5% PI(3)P, or 4% PI(4,5)P 2 /1% PI(3)P with 65% PC and 30% PS. Mutagenesis shows that binding of SNX9 to 100-nm PI(4,5)P 2 liposomes is driven by positively charged patches on the BAR domain binding to PI(4,5)P 2. The pocket on the PX domain is important for binding PI(4,5)P 2 and PI(3)P.
To measure the effects of INPP4A knockdown on the rate of CCP maturation, we quantified the dynamic, diffraction-limited CCPs using previously described software  (Aguet et al. , 2013). As expected for HeLa cells as well as the larger clathrin plaques, numerous clathrin spots within the cells remain for a duration longer than the length of the video. The numbers of these persistent CCPs were unaffected by INPP4A siRNA (Fig. 6 F ). However, the mean lifetime of the bona fide CCPs was increased (Fig. 6  G) from a mean of 24. 3 s in control to 56. 4 s for INPP4A siRNA1, 35. 9 s for siRNA2, and 47. 9 s for siRNA3. These lifetime data are consistent with the inhibition of CME we detected by transferrin uptake. Thus, inhibiting the conversion of PI(3,4)P 2 to PI(3)P inhibits the recruitment of BAR domain protein SNX9 to CCPs and decreases the efficiency of CME.
Nile red localizations in the image were determined using the Peak Fit plugin for ImageJ (National Institutes of Health). Individual liposome diameters in the superresolution image were determined by calculating the full width half maximum (FWHM) from the standard deviation of a two-dimensional Gaussian fit. With the FWHM value, we calculated the surface area (A) of individual liposomes using the equation A = 4 πr 2 ≈ 4π ( FWHM ______ 2 ) 2. Liposome size determination by dynamic light scattering Liposome samples were measured by dynamic light scattering using a molecular size analyzer (Zetasizer Nano ZS; Malvern Instruments), with liposomes at a 150-mM final concentration in XB buffer. The size distribution output in intensity was converted into number distribution using the Zetasizer software transformation method, with the following parameters: shell refractive index at 1.
25-µl reaction mixes were prepared in XB containing (final assay concentration) 0. 2 mM ATP, 2 mM DTT, 8 µM unlabeled actin, 0. 3 µM Alexa Fluor 647labeled actin, 50 nM X. laevis Arp2/3 complex, 100 nM SNX9, and 100 nM N-WASP-WIP and were added to the sample, and several representative regions were imaged after 10 min of incubation. Images were analyzed using MetaMorph software.
Analysis of CME in HeLa cells The representative microscopic images viewed in the figures were drift corrected using ImageJ and prepared (cropped, rotated and linearly adjusted for intensity) using Photoshop CS5. Spots of GFP-SNX9 or clathrin-Lca-mCherry after siRNA transfection were evaluated by analyzing TIRF live-cell acquisitions (800 ms between frames, over 193 s) using the Imaris software V7. 5 (Bitplane), tracking mode. A region of interest sized 100 × 100 pixels (256 µm 2 ) was segmented for spots using an estimated diameter of 0. 4 µm, background subtraction, a filter using a quality threshold >102, Brownian motion, maximum distance of 0. 7 µm, maximum gap size of 1, no fill gap, and a track duration minimum of 32 s. Graphs were made in Excel and Prism (GraphPad). Analysis of persistent CCPs and endocytic lifetimes was performed in MatLab (MathWorks) using custom-written software  (Aguet et al.
, 2013). The latest software is available for download from M. Mettlen. In brief, the analysis focuses on diffraction-limited objects, and the detection of all clathrin-labeled structures is based on the assumption that all relevant fluorescent signals can be described by a Gaussian point spread function. Signals were selected as valid detections if their amplitude was higher than a 95th percentile confidence threshold in the local background noise distribution. Fluorescent trajectories were automatically calculated from the detections obtained in individual frames, and bona fide CCPs that undergo stabilization and maturation were distinguished from transient subthreshold clathrin-labeled structures based on quantitative analysis of the progression of their fluorescence intensity during early stages of growth, as previously described  (Aguet et al.
5 mM CaCl 2 , pH 8. 7) and incubated two times for 20 min with freshly prepared 100 mM Mesna (Sigma-Aldrich) in stripping buffer. Cells were then incubated with 1:25,000 DAPI in PBS for 15 min and mounted for microscopy. Z stacks of the samples were imaged with a spinning-disk confocal live-cell imaging system (Cell Observer; Zeiss), controlled by ZEN interface with an inverted microscope (Observer. Z1; Axio) and equipped with a spinning-disk unit (CSU-X1A 5000) and an EMC CD camera (iXon Ultra; AND OR). Endosomes were segmented as spots using IMA RIS. Total intensity of detected endosomes in the Z stacks was divided by the amount of cells in the image (DAPI). Data were prepared, analyzed, and presented in Excel and Prism.
4 µm (determined by manually tracking a selection of control comets from several reference cells), with no gap closing. Detected tracks were categorized as comets when they persisted for 8 s or longer (five consecutive frames), with the number detected for each region recorded. The duration, track displacement, and mean track speed for all the comets in the image were also recorded. For data analysis, each cell region represents the number of comets detected in an individual image. These normally come from a single cell, but can include more than one cell when neighboring cells are also expressing F-tractin and therefore included after the thresholding step, with the data expressed as the number of tracks detected/thresholded area (micrometers squared)/total time (minutes). Graphs and statistical analysis were prepared using Prism software.
(D) Maximal activation of actin polymerization by liposomes containing 4% PI(4,5)P 2 , 1% PI(3)P, 48% PC, and 47% PS assayed by pyrene actin assay with HSS compared with 4% PI(4,5)P 2 alone or 4% PI(4,5)P 2 + 1% PI(3,4)P 2. Data show mean of four traces from two independent experiments. AU, arbitrary units. (E) As in C, except 10% PI(3,4)P 2 (cyan). (F) 10% PI(3,4)P 2 liposomes (cyan), extracts + SNX9. In all experiments, we exclusively observed the formation of comet tail at the surface of PI(4,5)P 2 /PI(3)P liposomes. (G) 10% PI(3,4)P 2 liposomes (cyan) preincubated with INPP4A. Actin polymerization occurred from the cyan liposomes. Bars, 3 µm.
Acknowledgments We would like to thank the  Biochemical Imaging Centre Umeå  and  Maria Teresa Vidal-Quadras  for help with the imaging processing and presentation, the  Protein Expertise Platform at Chemical Biological Centre, Umeå University , for help with cloning INPP4A,  Matylda Sczaniecka-Clift  from the  Gurdon Institute  for assistance with OCRL CRI SPR/ Cas9 implementation,  Andy Riddell  at the flow cytometry core facility of the  Stem Cell Institute , and  Richard Butler  from the  Gurdon Institute core imaging facility  for help with actin comet tracking. We also thank  Sandra Schmid ,  Brigid Hogan , and  Daniel St Johnston  for critical reading of the manuscript. The EM was conducted at the  Cambridge Advanced Imaging Centre. J. L. Gallop is supported by a  Wellcome Trust   Research Career Development Fellowship (grant   WT095829AIA ).
F. Daste ,  A. Walrant ,  J. R. Gadsby , and  J. Mason  are supported by an  H2020 European Research Council   Starting Grant  ( 281971 ) awarded to J. L. Gallop. Gurdon Institute funding is provided by the  Wellcome Trust  (grant  092096 ) and  Cancer Research UK  (grant  C6946/A14492 ). The  Swedish Medical Research Council  and the  Swedish Foundation for Strategic Research  supported the work of  M. R. Holst  and  R. Lundmark. S. F. Lee  is funded by a  Royal Society University Research Fellowship  (grant  UF120277 ). M. Mettlen is funded by grant  MH73125  to  Sandra L. Schmid  ( University of Texas Southwestern Medical Center ). The authors declare no competing financial interests. Author contributions:  F. Daste  and A. Walrant performed the in vitro liposome and actin experiments assisted by  J.
This is particularly true when searching for self-luminous companions embedded in an optically thick circumstellar disk, and is especially complicated when using adaptive optics (AO) imaging with the Angular Differential Imaging technique (ADI,  Marois et al. 2006). During an ADI sequence, the field of view rotates with respect to the detector while the optics of the telescope and the instrument remain stable. Any rotating astrophysical source can then be separated from the fixed point spread function (PSF) and from quasi-static speckles. This observing mode, and the associated data reduction process, induces flux loss of the astrophysical signal and produces morphological hence measurement biases. For extended and inclined structures like disks, PSF subtraction techniques may also create asymmetries and blobs  (Milli et al.
2015). However, beyond the extent of the resolved emission, the rest of the field of view is clear of any disk emission, and HD 100546 b lies in an weakly polarized region of the disk  (Quanz et al. 2013a; Avenhaus et al. 2014) , favoring a protoplanet scenario compared to a disk hot spot. Recently, with shorter wavelength (λ c = 1. 64 µm), a detection of HD 100546 b was reported with the Gemini Planet Imager (GPI,  Macintosh et al. 2014 ) along a very bright disk arc extending from the protoplanet location to the coronagraph edge  (Currie et al. 2015). To follow-up this peculiar system, we obtain considerably longer dataset with large field rotation as previously reported. HD100546 was observed with the GPI Instrument at Gemini South as part of the Gemini Planet Imager Survey (GPIES) and with the Visible AO (VisAO) camera at the Magellan Clay Telescope at Las Campanas Observatory.
OBSERVING STRATEGY AND IMAGE PROCESSING 2. 1. Gemini Planet Imager HD 100546 was observed on UT 2016-02-27 (program ID: GS-2015A-Q-501). These data are fundamentally new observations that gave us the capacity to present the first spectrum in H band. A total of 120 × 60 second IFU images were taken in H band (1. 49 -1. 79 µm, λ/∆λ ≈ 45) in coronographic mode using ADI. A total of 51. 6 deg of field rotation (FoV) was obtained over the sequence. Observing conditions were stable and good with an average DIMM seeing of 0. 8 and coherence time of 4 ms. The observing parameters are reported in Table  1. Observations of an argon arc-lamp were acquired at the target elevation immediately prior to the sequence and were combined with reference arcs taken at zenith to calculate flexure compensation  (Wolff et al.
2014). The θ 1 Ori field was observed to calibrate the platescale (14. 166 ± 0. 007 mas. pixel -1 ) and the correction to the detector position angle of ADI observations between the North and the vertical axis (0. 1 ± 0. 13 deg,  Konopacky et al. 2014). Another set of observations of HD 100546 was obtained on UT 2014-12-17 (GS-2014B-Q-500) but with only 12. 9 deg of FoV rotation. Therefore, this dataset was not used in the present paper. The raw 2-D images were initially processed with the GPI Data Reduction Pipeline v1. 3. 0 (DRP,  Perrin et al. 2014 ) which performs dark subtraction, bad pixel identification and removal, instrument flexure correction, extraction of spectra to create 3-D (x, y, λ) data cubes  (Maire et al. 2014) , interpolation over a common wavelength axis, and distortion correction as measured with a pinhole mask  (Konopacky et al.
2014). The positions of the four satellite spots -attenuated replicas of the central occulted star -at each wavelength in each data cube were also measured with the DRP  (Wang et al. 2014). The barycenter of each set of spots was then used to align all the images to the location of the star. The reduced data cubes were then processed to subtract the stellar point spread function (PSF). Large-scale structures (e. g. , temporal variation of the residual turbulence affecting the stellar halo and background) slowly varying from one frame to another are not fully subtracted by ADI algorithms and must be removed before the PSF subtraction. The data were therefore high-pass filtered. An apodized Fourier filter was used to attenuate, following a Hanning profile, spatial frequencies lower than a parametrized cutoff.
First, the data were processed with pyKLIP  (Wang et al. 2015) , a python implementation of the KLIP algorithm, to produce a RDI PSF subtracted broad-band image. Second, since the RDI pyKLIP pipeline does not handle spectral datacubes, the data were processed with TLOCI to produce 37 RDI PSF subtracted spectral images. For the first reduction, a library of reference images was created from all the 6265 individual spectroscopic H band observations obtained with GPI as part of GPIES,at the time were the data were reduced, but rejected targets with known disks and/or companions to ensure star subtraction only  (Draper et al. 2016, Millar-Blanchaer et al. in prep). Each observation was reduced with the GPI DRP as described previously and collapsed over the wavelengths to populate a homogeneous library of broadband images.
HD 100546 data cubes were processed through pyK-LIP, using the 1000 most correlated reference images in a 10-70 pixel annulus to avoid the mask edges and the satellite spots. This process produces a broad-band image subtracted from the star PSF that can be compared to the ADI reduced images. For the second reduction, the TLOCI quicklook pipeline was used. The library and the HD 100546 datacubes were spatially scaled to align speckles based on the satellite spot locations in each wavelength channel and flux normalized with the spots. Each reference library datacube was median-combined to create 426 achromatic reference images. For each frame of HD 100546, the 20 most correlated images of the library were median-combined and subtracted to remove the star PSF. No high-pass filter was applied to preserve large scale disk structures.
MagAO Magellan Adaptive Optics observations of HD100546 were taken on UT 2014-04-12 in better than median conditions (average seeing 0. 58). Total integration time for the image set was 187 minutes, and individual exposures were limited to 2. 3 seconds to minimize saturation effects. The data were taken in Angular Differential Imaging mode, and a total of 72 • of rotation were achieved (see Table  1 ). We utilized the Simultaneous Differential Imaging (SDI) mode of MagAO's visible light camera VisAO to image the disk simultaneously in Hα and in the neighboring continuum as part of the Giant Accreting Protoplanet Survey (GAPlanetS,  Follette et al. , in prep). Under this mode, the continuum channel serves as a sensitive and The airmass and the DIMM seeing averaged over the observing sequence when available.