dataesr/scientific-paragraphs-categorization huggingface dataset:
Cell death analysis Cultured parasites were incubated for 15 min with 10 mg/ml propidium iodide (Sigma-Aldrich) and diluted in PBS (Gibco). Cells were analyzed with a FACSCalibur flow cytometer (Beckman Coulter) to determine the incorporation of propidium iodide (excitation wave length l ex = 488 nm; emission wave length l em = 617 nm). The percentages of cell death and cell growth were calculated using FlowJo (v7. 6) software (Tree Star, Inc. , San Carlos, CA). Protein extraction and purification 10 9 parasites were washed with ice cold RPMI and lysed in 1 ml lysis buffer containing 150 mM NaCl, 1% Triton X-100, 50 mM Tris HCl pH 8 and inhibitor cocktails for proteases (Complete Mini EDTA-free tablets, Roche Applied Science, IN) and phosphatases (Phosphatase Inhibitor Cocktails I and II, Sigma-Aldrich, MO).
The discovery data were processed with DTASuperCharge (Mortensen, P. DTASuperCharge, an MSQuant application. http://msquant. alwaysdata. net/msq/) and searched against a customized L. mexicana 6-frame translation library as well as a predicted protein list (GeneDB http://www. genedb. org) using an in-house Mascot server (version 2. 2. 06, Matrix Science, London, UK). For SRM analyses, the discovery data were processed in ProteomeDiscoverer, and the MPK10 phosphopeptides identified were imported into Pinpoint, version 1. 0. 0 (Thermo Scientific).
Bioinformatics approaches Leishmania spp and Trypanosoma spp MPK10 gene and protein sequences were retrieved from the web databases GeneDB (http///www. genedb. org) and TriTrypDB (http://tritrypdb. org/ tritrypdb/)  [63]. Homology searches were carried out using BLAST Program with the default BLOSUM-62 substitution matrix  [64] , and pattern recognition analysis using the program PRATT v2. 1  [65]. Multiple sequence alignments were performed using built-in algorithm ClustalXv2. Additional sequence analyses were carried out using the BioEdit Program suite (Tom Hall, North Carolina State University). Statistical analysis and data plotting were performed using Rstudio software (http://www. rstudio. org/) and R language (R Development Core Team (2005). R: A language and environment for statistical computing.
Samples used in (A) were analyzed by western blotting using mouse anti-phospho-tyrosine (a-pTyr) and rabbit anti-MPK10 (a-MPK10) antibodies. (E) SRM analysis. Digested proteins from whole cell lysates of L. mexicana promastigotes (Pro) and axenic amastigotes (Ax. Ama), were subjected to TiO 2 enrichment, eluates were desalted on C8 STAGEtips and vacuum dried. Prior to LC-MS/MS analysis, the eluates were reconstituted in 0. 1% formic acid. The acquired data were imported into the Pinpoint method file for analysis. T-H-pY, peptides represent single phosphorylation of Y192; pT-H-pY, peptides represent dual phosphorylation of residues T190 and Y192. This value of T-H-pY represents the sum of the values obtained with two different peptides (THYVTHR and EDTADANKTHYVTHR). All blots and auto-radiograms are representative of three independent experiments.
This work was supported by 7th  Framework Programme  of the  European Commission  through a grant to the  LEISHDRUG  Project ( 223414 ), the  French Government 's  Investissements d'Avenir program: Laboratoire d'Excellence ''Integrative Biology of Emerging Infectious Diseases' ' (grant no. ANR-10-LABX-62-IBEID ), and  ANR-11-RPIB-0016  TRANSLEISH. MC was supported by a grant from  Region Ile de France. MW and HR were supported by the  Deutsche Forschungsgemeinschaft DFG  ( WI 2044/5-1 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Methods Unfortunately Syria, Lebanon and Libya did not participate to the network. Palestine was not able to comply with the requirement for the study. Israel could not obtain the ethical permission to use data already collected for a similar study. Each referral center from Albania, Algeria, Bosnia Herzegovina, Croatia, Egypt, France, Greece, Italy -Messina and Naples -Malta, Montenegro, Morocco, Slovenia, Spain, Tunisia and Turkey provided a list of 50 unselected consecutive CD cases diagnosed in the center by the best locally available methodologies. Using a standardized form, the clinical and laboratory data leading to the diagnosis were collected for each case. The methods used in each center for the serum assay of tTG were recorded, together with their local normal values. We reviewed the pathology procedure used to evaluate small intestinal biopsy specimens and recorded the methods used to evaluate the HLA haplotype.
Our study therefore also provides a baseline for investigating the susceptibility of this process to disruption, for example as a consequence of exposure to environmental factors. Invitrogen) was used to detect the primary antibody. All slides were mounted in PermaFluor Aqueous Mounting Medium (Thermo Fisher Scientific). Analysis was performed on three to ten fetal testes from three to six different litters for each modification at each time point and representative images captured as specified below. Semiquantification of immunofluorescence was obtained using Image J Software (National Institute of Health). Each complete tubule in the image was analysed, identifying the region of interest as being within the seminiferous tubule, inside the ring of Sertoli cell nuclei. Intensity was expressed as mean pixel intensity for this region, normalised to the mean pixel intensity for somatic cells within the same image.
Acknowledgements CR is supported by the  British Heart Foundation. RMS and SvdD are supported by the  Medical Research Council  (Grant  G1100358 ). Work in RM's lab is supported by the  MRC, IMI-MARCAR  (under grant agreement number [115001]) and the  BBSRC. Work in the AD lab is supported by a  Scottish Senior Clinical Fellowship  ( SCD/09 ) and the  MRC  ( MR/K018310/1 ). We thank  Sheila MacPherson ,  Gael Sugano  and  William Mungall  for expert technical assistance.
The evaluation of more recent data did not support previous studies suggesting that particular products (e. g. recombinant vs. plasma-derived and full length vs. B-domain modified) may be associated with increased risk. In addition, data from three national product switches showed that switching was not associated with increased inhibitor risk, but highlighted the need for regular inhibitor testing and for a centralised, unbiased database of inhibitor incidence. To conclude, current evidence does not suggest that switching products significantly influences inhibitor development.
The Concerted Action on Neutralising Antibodies in severe haemophilia A (CANAL) study was a retrospective, multi-centre cohort study designed to further describe the relationship between treatment and inhibitor development in 366 PUPs with severe haemophilia (residual FVIII activity <2%) born between 1990 and 2000  (9, 16). Data available on product type and inhibitor incidence from 316 PUPs were evaluated. A total of 82 patients (26%) developed clinically relevant inhibitors; of 181 patients first treated with rFVIII product, 53 (29%) developed inhibitors, while inhibitors were reported in 29 of the 135 (21%) patients treated with pd-FVIII, and the relative risk (RR) of inhibitors in pd-FVIII vs. rFVIII products was 0. 8 (95% confidence interval [CI], 0. 5-1. 3) (16). In addition, switching between FVIII products did not appear to increase the risk of inhibitor development (RR, 1.
1; CI, 0. 6-1. 6). Hence, the CANAL study results do not support previous findings suggesting an increased risk of inhibitor development with rFVIII products, nor that switching products may influence inhibitor development  (16). More recently, the potential influence of rFVIII vs. pd-FVIII product type on inhibitor development was also explored in the RODIN (Research Of Determinants of INhibitor development) study, which used data from the PedNet registry that comprised 29 centres in Europe, Canada and Israel. Data were evaluated from 574 PUPs born between 2000 and 2010. Inhibitory antibodies were reported in 177 children (cumulative inhibitor incidence, 32. 4%). Overall, there was no difference in inhibitor risk between pd-FVIII and rFVIII products (adjusted hazard ratio 0. 96; 95% CI, 0.
Recommendations and future directions The implementation of prospective, controlled surveillance programmes on switching and not switching is imperative, as there is insufficient evidence currently available to support the development of clear "Best Practice" guidelines for switching. In addition, such surveillance programmes will provide researchers with the data needed to address the many unanswered questions regarding the patient-related and treatment-related factors that contribute to the risk of inhibitor development. Most importantly, for the full potential of surveillance programmes to be realised, all data on inhibitor development and products received should be submitted to a centralised, unbiased database to establish a baseline on the current inhibitor risk and include all new patients, regardless of which product they receive.
This is the only way to ensure that the field is able to utilise all of the data in the service of our patients. Given the limitations of the existing evidence base, we can make a number of recommendations for the conduct of future studies on product switching. First, inhibitor testing should be performed before and after the switch to determine if any new inhibitors detected may be in association with switching to the new treatment. Similarly, inhibitor testing should also be performed before and after intensive treatment/surgery. Concerning routine patient care, educational materials addressing patients concerns about switching are needed because some of patients' concerns are not supported by the actual evidence about the consequences of switching products. More importantly, physicians are encouraged to discuss directly with patients and parents their therapeutic approach and the other treatment options that are available before a more urgent need arises to consider switching.
Since there are many neurons involved, these population outputs approximate linear functions of the eye position. The essence of our network models is shown in Figure  2  (see also Materials and Methods; a Matlab-based implementation of the models is available in the online supplementary information). In Figure  2A , we plot the population activities of Figure  1F  against each other. Given the staircase shape of the population outputs, the resulting relationship is composed of multiple points on a line, which we here approximate by the red-blue line. This line illustrates the persistent firing states of the system, which range from virtual silence on the right and strong activity on the left side (X R = 0, X L large, red color) to virtual silence on the left and strong activity on the right (X R large, X L = 0, blue color).
However, this effect was small in comparison to eye position changes induced by medium light intensities, so that we are confident to be measuring the integrator performance in our experiments. A custom-written LabVIEW program (National Instruments, Austin, TX) was used to image, record angular eye positions, and to trigger stimulations via a NI USB DAQ box. Images were acquired at 30-45 Hz and particle analysis (NI Vision) was used to detect eye positions and write them to a text file (together with the stimulation time points) for later analysis. Eye positions were measured and plotted in real time and fiber optic stimulations were triggered based on them. In most experiments a single 200 ms stimulation of constant intensity was delivered automatically 1 s after the eyes had made a saccade.
In some experiments four consecutive stimulations were delivered for each saccade (1, 3, 5, and 7 s after the saccade). The stimulation intensities were chosen randomly: we either used five fixed intensities or the computer picked values from an exponential distribution of intensities that biased toward smaller intensities. No stimulation was applied after every third saccade, and these periods served as our control trials. Recordings typically lasted for at least 30 min and up to 12 h. The LabVIEW program can be requested from the authors.
DATA ANALYSIS The files containing eye position trace and stimulation data were analyzed with custom algorithms using MATLAB. We only analyzed the first 3 h of each experiment, since in some recordings (without dish lid) water evaporation affected the camera focus and thereby the correct detection of eye position angles. The induced eye movements were measured as the change in eye position from stimulation start to 1 s after stimulation start. Most induced eye movements consisted of a single monotonic drift that was completed within 400 ms after stimulation. However, a 1 s interval was chosen to account for potential variations of the duration of the post-stimulation drift. The eye position change, averaged across left and right eye, was then plotted against the initial eye position, averaged across eyes.
The results from each fish were fitted by a cubic smoothing spline with boundary second derivatives equal to zero, using the spline fit-package developed for MATLAB by Jonas Lundgren. This fitting procedure was repeated for several stimulation intensity bins. A population plot was generated by averaging the spline fits of all fish, for each intensity bin. We observed some variability of motor ranges across fish, especially in animals expressing ChR2, which tended to have a smaller motor range (average motor range and respective standard deviations in NpHR animals: [-20. 0 • ± 5 • ; 18. 7 • ± 4. 4 • ]; in ChR2 animals  [-13. 7  • ± 3. 9 • ; 13 • ± 3. 5 • ]). Therefore, before averaging across animals, we normalized all motor ranges to generate a smooth population plot. In some fish, there was an undersampling of events at the eccentric eye positions, and therefore we removed the 5% most eccentric events on the right side and on the left side before averaging across animals.
ACKNOWLEDGMENTS Pedro J. Gonçalves  was part of the  PhD Program in Computational Biology of Instituto Gulbenkian de Ciência , supported by  Fundação Calouste Gulbenkian ,  Siemens SA and Fundação para a Ciência e Tecnologia (Portugal)  through grant  SFRH/BD/33210/2007. Aristides B. Arrenberg  was supported by a  Krevans fellowship  and  Aristides B. Arrenberg  and  Bastian Hablitzel  are supported by the  Excellence Initiative of the German Federal and State Governments  ( Centre for Biological Signaling Studies EXC 294-B5-Driever ). Herwig Baier  was funded by  NIH   R01 NS053358 , the  NIH Nanomedicine Development Center "Optical Control of Biological Functions " and the  Max Planck Society. Christian K. Machens  was funded by a  "Chaire d'excellence" of the French Research Agency (ANR) , a  "Chaire d'excellence" of INSERM  and the  Emmy-Noether Program  of the  German Research Foundation.
The images were processed with a home-made program under LabView that generates a ratiometric image by dividing the image of the blue channel by that of the red channel. For each pixel, a pseudocolor scale is used for coding the ratio, while the intensity is defined by the integrated intensity recorded for both channels at the corresponding pixel. 56 he sensitivity of the two detectors was calibrated using solutions of the 7AF dye in DMF and EtOH.
L arge-scale production of biodiesel requires considerable amounts of fatty acids (FAs). The resulting demand for FAs has made oleaginous yeast species a target of choice as an alternative source of oils and fats  (1). The genomic data available for such species have increased over the last few years but still remain scarce. To increase the current knowledge of oleaginous yeast species, we report the sequencing of the basidiomycetous yeast Rhodosporidium toruloides CECT1137. This strain was originally deposed in the Natural Collection of Yeast Cultures (NCYC) (United Kingdom) in 1925 by Antoine Guillermond (strain NCYC162) under the name "Levure de rose. " It was transferred in 1984 to the Spanish Type Culture Collection (CECT) (Spain), where it received the CECT1137 accession number. This strain was originally described as Rhodotorula glutinis var.
glutinis based on physiological characteristics. However, our sequencing data reinstated it as a member of the species R. toruloides. The CECT1137 genome was sequenced by Eurofins Scientific (France), using Roche 454 GS FLX Titanium, on a single-read library and an 8-kb mate-pair library. A complementary run of Illumina HiSeq 2000 was performed on a cDNA library using Illumina TruSeq RNA to improve the predictions of the gene models and their numerous introns. Several assembly runs were performed using a combination of MIRA (2) and Allpaths-LG (3). Smoothing and scaffolding were performed using PILON (version 1. 7; The Broad Institute [http://www. broadinstitute. org/ software/pilon/]) and SSPACE-BASIC-2. 0 (4). Genes were predicted using a combination of tools, including Augustus (5), GeneMark (6), EST2Genome  (7) , BLASTp, and PSItblastn  (8).
The recently published genome of the closely related strain NP11 was integrated in the annotation pipeline as an additional support for prediction  (9). The cDNA reads were mapped on the genome using Tophat2  (10). Exon-exon junctions were extracted from the alignments using a combination of in-house tools developed in BioPerl  (11). Splicing events and structural annotation were manually validated using the Artemis software  (12). The tRNA genes were identified using tRNAscan-SE  (13). The current draft comprises 62 scaffolds, for a total size of 20,445,260 bp and a GϩC content of ca. 61. 9%. Overall, 8,206 putative protein-coding genes have been identified, 212 of which harbor introns alternatively spliced within the coding sequences and/or the untranslated regions (UTR). An additional 145 genes have been annotated as dubious models or pseudogenes, with frameshifts, stops in translation, or dubious starts or stops.
The genome contains 149 tRNAs and 249 miscellaneous RNAs. Whenever possible, a functional annotation was proposed, based on a combination of BLASTp  (8) , EMBOSS Needle  (7) , and Inter-ProScan  (14)  against subsets of genes extracted from UniProt  (15) , with priority given to experimentally validated data from yeasts and fungal species. A total of 8,294 proteins were predicted (including 88 splicing variants), among which 7,080 showed at least 20% sequence similarity on 70% of an alignment with at least one gene from the Swiss-Prot/TrEMBL subsets. Further comparison of the genome of CECT1137 against other yeast species will bring additional insights on the genomic properties of oleaginicity, providing potential targets for future biotechnological applications. Nucleotide sequence accession numbers.
INTRODUCTION Shock metamorphism and impact melting in terrestrial rocks during small-scale meteorite impacts is still not fully known. This is mainly due to the rarity of very small impact craters on Earth (only 17 terrestrial craters of 184 have diameters <300 m; Earth Impact Database), and, more importantly, to the generally low degree of preservation of very small craters. One exception is Kamil crater (southern Egypt). This 45 m diameter crater shows all its original features in an almost pristine state of preservation due to its very young age (most likely <5000 yr), the favorable climatic conditions of the Sahara, and the mechanical strength of the local target rocks. After its discovery in 2008, Kamil has been explored in 2010 by our first Italian-Egyptian geophysical campaign  (Folco et al.
A field emission scanning electron microscope (FE-SEM) Jeol JSM 6500F (upgraded to 7000 series), operating at 10 kV, was used at the Istituto di Geofisica e Vulcanologia (INGV) of Rome. Modal abundances of phyllosilicate minerals and iron-oxide matrix, as well as the porosity of the rock samples from the crater rim and ejecta were determined by digital image analysis of backscattered electron images and X-ray element maps using the JMicroVision software. We determined the crystallographic orientations of planar deformation features (PDFs) in the quartz crystals of sample L23 following procedures described in  Langenhorst (2002)  using a five-axis U-stage mounted on a Zeiss Axioplan optical microscope. For PDF indexing, the automated numerical index executor (ANIE;  Huber et al. 2011 ) was used.
Quantitative chemical microanalyses were carried out with a Jeol JXA 8230 electron microprobe fitted with five wavelength dispersive spectrometers at the Institut des Sciences de la Terre (ISTerre) of Grenoble. Running conditions were 15 kV accelerating voltage, 12 nA beam current, and 1 lm nominal beam spot. The ZAF procedure was employed for raw data reduction. Standards used for instrumental calibration were SiO 2rich glass (USNM 72854), ilmenite (USNM 96189), and hornblende (USNM 143965). Average detection limits are 0. 04 wt% for Na 2 O and ZrO 2 ; 0. 02 wt% for Al 2 O 3 , Cr 2 O 3 , and V 2 O 3 ; and 0. 01 wt% for MgO, CaO, K 2 O, FeO, MnO, TiO 2 , NiO, and P 2 O 5. Typical precisions are better than 1% (relative standard deviation = 1 9 standard deviation/average*100) for oxides concentration >1 wt% and between 1 and 10% for oxide concentrations between 1 and 0.
CONCLUSIONS This is a detailed report of the petrography and some chemical observations of samples from the crater wall and ejecta deposits from Kamil crater (Egypt) collected during the first Italian-Egyptian geophysical expedition in February 2010. Data allow us to draw the following conclusions in terms of shock effects recorded by target rocks, impact scenario, and unique state of preservation of the ejecta rocks: 1. A broad set of shock features is recorded in the target rocks at Kamil (45 m in diameter), ranging from fracturing to whole-rock impact melting. 2. Shock features are classified into two categories (1) pervasive shock features, including fracturing, planar deformation features, and impact melt lapilli and bombs, and (2) localized shock features including high-pressure phases and localized impact melts occurring as intergranular melt, melt veins, and melt films enveloping shatter cones.
Acknowledgments-This work was supported by the  Italian Ministero degli Affari Esteri-Progetti di Grande Rilevanza, Protocollo Esecutivo ITALIA-EGITTO. The 2010 geophysical expedition work was carried out within the framework of the  2009 Italian-Egyptian Year of Science and Technology. We thank  Prof. M. Alsherbiny  (former president of the  Egyptian National Academy for Scientific Research and Technology ) and  Prof. F. Porcelli  ( Scientific Attach e, Italian Embassy, Egypt ) for diplomatic and institutional support; the  Egyptian Army  for logistical support. Agnese Fazio  was supported by the  PhD School Scuola di Dottorato in Scienze di Base Galileo Galilei program on Earth Science of the University of Pisa , and by the  Barringer Family Fund  for Meteorite Impact Research 2014. Luigi Folco  and  Massimo D'Orazio  are also supported by the  University of Pisa Fondi di Ateneo.
Institut des Sciences de la Terre (ISTerre) of Grenoble  is part of  Labex OSUG@2020  ( ANR10 LABX56 ). Astrid Kowitz  and  John G. Spray  are thanked for constructive reviews, and  Uwe Reimold  for editorial handling. The authors are grateful to Valentina Batanova ,  Andrea Cavallo , and  Cristian Biagioni  for their assistance during electron microprobe analysis at ISTerre (Grenoble), field emission scanning electron microscope analysis at  Istituto di Geofisica e Vulcanologia (Rome) , and X-ray powder diffraction analysis at  Pisa University's Dipartimento di Scienze della Terra , respectively. Raman facilities by the  Center "G. Scansetti"  for studies on asbestos and other toxic particulates were funded by the  Compagnia di San Paolo, Torino. PNRA is acknowledged for preliminary Raman microspectroscopy analyses.