dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements Financial support was provided by the  Ontario Ministry of Research and Innovation and by the government of Canada through Genome Canada  and the  Ontario Genomics Institute  in support of the  International Barcode of Life project. Anne McCain Evans and Chris Evans provided support for the BIObus program  (www. biobus. ca),whose students conducted much of the field work. A biotic survey and bioblitz of this magnitude could not be completed without the help of many volunteers; we would like to thank the following for their contributions to this study:  Reza Zahiri ,  Carleigh Pope ,  Cheyanne Richardson ,  Christine Thompson ,  Dan Radoslav ,  Dave Achtymichuk ,  Erika Kastner ,  Kim Robichaud ,  Mike Achtymichuk ,  Tim Skuse ,  Lisandra Gal , and  Suz Bateson. We would also like to thank our reviewers for their helpful suggestions and contributions to this manuscript:  Jeremy Miller ,  Pavel Stoev , and  Torsten Dikow.
rare Charitable Research Reserve. 28 ). Inventory and BioBlitz Records from ,916 records. Online at http://data. canadensys. net/ipt/resource. See Suppl. material 6 for complete list of contributors, institutions and email addresses do?r=rare_ inventory, http://doi. org/10. 5886/hh6td9jn, and http://www. gbif. org/dataset/09e90dfb-5b1b- 4dd9-a796-e2fba53d26f0, released on 2015-08-20, version 1. GBIF key: 09e90dfb-5b1b-4dd9-a796-e2fba53d26f0. *.
Box definitions The selected events are categorized into the different razor boxes according to their event content as shown in Table  1. In the table, the boxes are listed according to the filling order, from the first (at the top of the table) to the last (at the bottom). If an event satisfies the requirements of two or more boxes, the event is assigned to the first listed box to ensure the boxes correspond to disjoint samples. The events in the single-lepton and two-lepton boxes are recorded using the electron and muon razor trigger. The remaining two boxes, generically referred to as "hadronic" boxes, contain events recorded using the hadronic razor trigger. In the two-lepton boxes, the (M R , R 2 ) distribution of events with at least one b-tagged jet is studied. For the other boxes, the data are binned according to the b-tagged jet multiplicity: 1 b-tag, 2 b-tags, and ≥3 b-tags.
A difference is observed between 1 b-tag and ≥2 b-tag samples, due to the observed dependence of the b-tagging efficiency on the jet p T. Consequently, the shape parameters for the 1 b-tag bins are allowed to differ from the corresponding parameters for the ≥2 b-tag bins. The background normalization parameters for each b-tagged jet multiplicity bin are also treated as independent parameters. The background shape parameters are estimated from the events in the two sidebands (Section 5). This shape is then used to derive a background prediction in the signal-sensitive region: 30 000 alternative sets of background shape parameters are generated from the covariance matrix returned by the fit. An ensemble of pseudo-experiment data sets is created, generating random (M R , R 2 ) pairs distributed according to each of these alternative shapes.
Each carried duplications involving a chromosomal region located approximately 600 kb upstream of SOX9  [Benko et al. , 2011; Cox et al. , 2011; Vetro et al. , 2011; Xiao et al. , 2013]. In contrast, 46,XY females with gonadal dysgenesis have been reported to carry overlapping deletions of this region  [Benko et al. 2011; Bhagavath et al. 2014 ]. These individuals presented with no other associated somatic anomalies, suggesting that a regulatory element involved specifically in human sex-determination (termed RevSex) is located in this region  [Benko et al. , 2011]. Here, we describe three novel 46,XX-SRY negative patients, two brothers and an unrelated man with testicular DSD and azoospermia, who carry a microduplication upstream of SOX9. The detailed analyses of these patients and the incorporation of the published datasets have enabled the minimal critical region located ~600 kb upstream of SOX9 to be resolved to an approximately 40kb element that contains putative enhancers elements and DNA-binding sites for known factors to be involved in early testis formation.
Genetic analysis Genetic analyses were performed after obtaining patient's informed consents. Cytogenetic analysis was performed using GTG-banding techniques on metaphase chromosomes obtained by standard procedures from peripheral blood lymphocytes. FISH analysis was carried out using chromosome X specific probe DXZ1 and probes for SRY and SOX9 locus. Genomic DNA was extracted for each patient from peripheral blood samples using FlexiGene DNA Kit (Qiagen, Valencia, CA) according to manufacturer's instructions. For patients 1, 2 and 3, SNP array analysis was performed using the HumanCytoSNP-12 BeadChip from Illumina (San Diego, CA). Data analysis was performed using Illumina's Genome Studio Genotyping Module software allowing the identification of both copy number variations (CNVs) with the Log R ration (LRR) and regions of copy-neutral loss of heterozygosity (LOH) with the B allele frequency.
5 µl of water in a total reaction volume to 50µl. Reaction was cycled under following conditions:94°C for 2 minutes; 94°C for 10 seconds; annealing temperature of 60°C for 30 seconds; 68°C for 10 minutes; cycle 10× from step 2; 94°C for 15 seconds; annealing temperature of 60°C for 30 seconds; 68°C for 10minutes plus 20 seconds per cycle; cycle 30× from step 5; 68°C for 7 minutes; and hold at 4°C. Internal primers were used to sequence the amplicon. Data were analyzed using SeqScape® Software v2. 7 (Applied Biosystems) and Sequencing Analysis Software (Applied Biosystems).
Each individual reaction contained CNV assay (containing two primers and a FAM™ dye labeled MGB probe), RNaseP assay (containing two primers and aVIC® dye-labeled TAMRA™ probe), TaqMan® Genotyping Master Mix (containing AmpliTaq Gold® DNAPolymerase, and dNTPs), 15ng genomic DNA and water to a final reaction volume to 20 μl. Reactions were held at 95 °C for 10 min and then cycled 40 times through 95 °C for 15 s and 60 °C for 1 min. The data was collected using Sequence Detection Software v2. 3 (Applied Biosystems). qPCR data was analysed using a delta delta Ct algorithm with RnaseP as an endogenous control. Calibration with a control sample with two copies of the region was used to calculate delta delta Ct values and assign copy numbers by CopyCaller® software.
The Encyclopedia of DNA Elements (ENCODE) project datasets indicate a weak or poised enhancer at chr17:69,568,380-69,569,850. Chromatin at this position is enriched for experimentally determined CTCF-binding from human mammary epithelial cells (HMEC). The primary role of CTCF is thought to be in regulating the 3D structure of chromatin. CTCF creates boundaries between topologically-associating domains in chromosomes and anchors DNA to cellular structures like the nuclear lamina and thereby facilitates interactions between transcription regulatory sequences  [Murrell, 2011]  This region is also associated with acetylation of histone H3 at lysine 27 (H3K27ac) and enriched in monomethylation of histone H3 at lysine 4 (H3K4me1) from a variety of cell lines (Figure  3 ). Both H3K4 methylation and H3K27 acetylation are epigenetic marks that are generally associated with gene activation  [Eissenberg and Shilatifard, 2010; Smith and Shilatifard, 2014].
The duplicated region itself contains two predicted enhancer motifs. Although interpretation of ENCODE datasets should be taken with caution since the data was generated using cell lines that are not necessarily relevant for DSD, there are potentially interesting observations. The proximal strong enhancer motif  (chr17:69,544,206-69,546,005)  is enriched for H3K4 methylation and H3K27 acetylation that are epigenetic marks characteristic of gene activation  [Eissenberg and Shilatifard 2010; Smith and Shilatifard, 2014]. This enhancer element binds the histone acetyltransferase EP300 that regulates transcription via chromatin remodelling and it is important in the processes of cell proliferation and differentiation  [Ogryzko et al. , 1996]. EP300 is strongly expressed in the somatic and germ cell lineages of the XX and XY gonad during sexdetermination and it can act as a co-activator of both NR5A1 and SOX9  [Ito et al.
Acknowledgements We thank  Joelle Bignon-Topalovic  for technical assistance, Support for this work was provided by the  Agence Nationale de la Recherche-GIS Institut des Maladies Rares  (K. M. ),  March of Dimes Foundation  Research Grant  1-FY07-490  (to K. M. ), EuroDSD in the European Community's  Seventh Framework Programme FP7 /2007-2013 under Grant  201444  (to K. M. and A. B. ). The authors declare no conflict of interest. 11 Regulatory region upstream of  SOX9  and  46 , XX DSD. Hyon  et al.
Optical wavefront analysis For the analysis of single pulse wavefronts, we synchronized the image capture of the Shack-Hartmann sensor to the laser sync and set the AOD acoustic power to zero for all pulses emitted within the integration time of the camera, except for one pulse. The integration time was set to its minimum (500 µs). To meet the dynamic range of the Shack-Hartmann sensor, the pulse power was attenuated by passing the focalized beam through a 45° dielectric mirror with optical grade rear surface (~99% reflectance 750-1100 nm, BB1-E03P, Thorlabs). Optical wavefronts were reconstructed from the measured wavefront slopes using HASO 3. 1 software (Imagine Optic) together with a custom plug-in for processing of large datasets (kindly provided by Imagine Optic) and exported to MATLAB 2013 (Mathworks).
Acknowledgments This work has received support under the program « Investissements d'Avenir » launched by the  French Government  and implemented by the  ANR , with the references:  ANR-10-LABX-54  ( Memolife ),  ANR-11-IDEX-0001-02  ( PSL* Research University ) and  ANR-10-INSB-04-01  ( France-BioImaging infrastructure ). We are grateful to the  IBENS Imaging Facility , which received the support of grants from the  "Région Ile-de-France"  ( NERF N°2009-44  and  NERF N°2011-45 ), the  "Fondation pour la Recherche Médicale " ( N° DGE 20111123023 ) and the  "Fédération pour la Recherche sur le Cerveau -Rotary International France " (2011).
ACKNOWLEDGMENTS Work in Bellaterra was supported by  Spanish MINECO  (Grants No. FIS2012-37549-C05-02  and No. FIS2012-37549-C05-05  with joint financing by  FEDER Funds  from the  European Union , Grants No. CSD2007-00041  and No. CSD2007-00050 ) and  Generalitat de Catalunya  ( 2014SGR301 ). J. A. S. -G. and P. O. acknowledge support of the  Spanish MINECO  through the  Severo Ochoa Centers of Excellence Program  under Grant No. SEV-2013-0295. J. A. S. -G. was supported by an  FPI  Fellowship from  MINECO. The authors gratefully acknowledge the computer resources, technical expertise, and assistance provided by the  Red Española de Supercomputación.
Results are presented from a search for particle dark matter (DM), extra dimensions, and unparticles using events containing a jet and an imbalance in transverse momentum. The data were collected by the CMS detector in proton-proton collisions at the LHC and correspond to an integrated luminosity of 19. 7 fb -1 at a centre-of-mass energy of 8 TeV. The number of observed events is found to be consistent with the standard model prediction. Limits are placed on the DM-nucleon scattering cross section as a function of the DM particle mass for spin-dependent and spin-independent interactions. Limits are also placed on the scale parameter M D in the ADD model of large extra dimensions, and on the unparticle model parameter Λ U. The constraints on ADD models and unparticles are the most stringent limits in this channel and those on the DM-nucleon scattering cross section are an improvement over previous collider results.
Introduction This paper describes a search for new physics using the signature of a hadronic jet and an imbalance in transverse energy resulting from undetected particles. We use the term "monojet" to describe events with this topology. Such events can be produced in new physics scenarios, including particle dark matter (DM) production, large extra dimensions, and unparticles. The data sample corresponds to an integrated luminosity of 19. 7 fb -1 collected by the CMS experiment in proton-proton collisions provided by the CERN LHC at a centre-of-mass energy of 8 TeV. Particle dark matter has been proposed to explain numerous astrophysical measurements, such as the rotation curves of galaxies and gravitational lensing  [1, 2]. Popular models of particle dark matter hypothesize the existence of non-relativistic particles that interact weakly with the standard model (SM) particles.
This acceptance and the selection efficiency are also taken from simulation. Such events will not be rejected by the lepton veto and so contribute to the background in the signal region. In addition, there are similar contributions from W decays to electrons and tau leptons. These contributions are also estimated based on the W(µν)+jets sample. The ratio of W( ν)+jets events to W(µν)+jets events passing the selection steps prior to the lepton veto is taken from simulation, separately for each lepton flavor. The same procedure as that used in the muon case is then applied to obtain the background contribution to the signal region. The detector acceptances for electrons, muons and tau leptons are obtained from simulation. The lepton selection efficiency is also obtained from simulation, but corrected for any difference between the efficiency measured in data and simulation  [53].
(2014)  on threshold effects on wildfire propagation (e. g. threshold on aridity level) by analyzing the influence of wind speed on burnt area. To complete our goal, we need a comprehensive database of recent wildfires that occurred in this region and the accompanying weather. The availability of remote sensing observations since the 1990s allows the analysis of large, consistent data sets on wildfire activity. In this study we use the MODIS-retrieved burnt area with the ERA-Interim meteorology to analyze the dependency of fire size with wind speed and temperature anomaly. In order to better understand the variations seen in the observations we need to use a model of fire spread. In this study we choose to focus on probabilistic cellular automata (PCA). Our study relies on the following data-driven observation: under certain circumstances wildfires tend to decrease in size with moderate wind speed.
A first step of automated classification is used to isolate fire events and a post-processing using human visualization of the burnt scar is performed. A crossanalysis using the active fire MODIS product, fire event news collected in the EFFIS News module as well as land-cover data sets is finally done to ensure a low number of misclassifications (http://forest. jrc. ec. europa. eu/effis/). The system records burnt areas of approximately 40 ha and larger  (Sedano et al. , 2013). Fires under this threshold exist in this data set, with a higher associated uncertainty. Data are provided for the 2006-2012 time period on the Mediterranean Basin. Because the drivers of the wildfires can change over the course of the year, and because the largest wildfires occur in summer, we only consider wildfires detected in July and August.
The processing of the EFFIS data set is simpler. It provides the date coordinates of the shape of each wildfire. We take as location the centroid of this shape. To relate the ERA-Interim meteorological data with the fire products, the ERA-Interim data are extracted at the grid point closest to the wildfire. The ERA-Interim reanal- ysis is the only homogenized gridded data set at the Euro-Mediterranean regional scale available with wind speed information. It is relevant to provide the large-scale environment in the vicinity of the wildfire. Wind speed data at finer resolution would probably add value to refine the relationship between wind speed and wildfire, especially in terms of wind speed range (which is probably underestimated with the ERA-Interim data set).
Data analysis Figure  1  shows the cumulated wildfire burnt areas as retrieved by MODIS over the 10-year period  (2003) (2004) (2005) (2006) (2007) (2008) (2009) (2010) (2011) (2012). If a grid point has burnt entirely during this 10-year period, the cumulated burnt area is 10 000 ha. We see that the most wildfire-prone regions are the Mediterranean Basin and central Eastern Europe. In the following, we differentiate the two regions and the Mediterranean Basin will be referred to as MED, whereas central eastern Europe will be referred to as EAST. In this study large wildfires are considered as extreme fires and are identified when the value of the burnt area exceeds the upper 95th quantile of the local probability density function. These wildfires cause the majority of the destruction (more than 50 % of the burnt area in the EFFIS and MODIS data sets).
Then the extinction probability (1 -p) 8 drops very quickly. When isotropic spreading does not stand anymore, then the probability of extinction transitions to (1 -p) 3 and increases as 3 is a lower exponent than for the isotropic spreading. With increasing wind speed, the probability of extinction decreases again. So instead of enhancing wildfire propagation, moderate winds produce smaller wildfires by cutting off the propagation against the wind. Such analysis explains the two modes observed in the MODIS and EFFIS data over the MED domain. The function of wind f (V , θ ) in the calculation of p is critical in the explanation of the observed behavior (see Eq. 9). The choice of this function by  Alexandridis et al. (2008)  was done empirically to match with the behavior of the rate of spread of real wildfires as a function of the wind 0,max -p crit 0,0 )/p crit 0,0 for different values of the c 1 and c 2 parameters governing the function of local fire propagation probability.
Acknowledgements. This work contributes to the  HyMeX program  (HYdrological cycle in The Mediterranean EXperiment - Drobinski et al. , 2014) through  INSU-MISTRALS  support and the  GEWEX  hydroclimate panel of the  World Climate Research Program  (WCRP). Data were provided by the  European Forest Fire Information System -EFFIS  (http://effis. jrc. ec. europa. eu) of the  European Commission Joint Research Center. Edited by: P. Tarolli Reviewed by: two anonymous referees.
The present work aims to outline how table values of insect OCS can be expressed employing well-known methods from, e. g. , atomic physics. Representative example of an insect detection event observed with the LUMBO lidar, from a distance of one km at 2kHz sample rate and 808 nm wavelength. The parametrized fit with discrete harmonics describes the raw data fairly. Judging from a wing beat frequency of 113 Hz, night time observation, and that the waveform is not spiky as for glossy wings it is presumably a moth. While many local moth species are rather bright the true projected cross section could be roughly twice of the OCS value due a reflectance of ~50%. doi:10. 1371/journal. pone. 0135231. g001.
Acknowledgments The author acknowledges  Majd Salman  and  Elin Malmqvist  for contributing data and graphics on the presented case study and  Anna Runemark ,  Maren Wellenreuther ,  Sune Svanberg , and  Sandra Török  for helpful discussions. The continuous support from  Ernst van Groningen, International Science Program, Uppsala , is greatly appreciated. Hyperspectral imaging was performed with Hyspex push broom cameras, kindly provided by  Norsk Elektro Optikk A/S. This project also received funding from the  Swedish Research Council  through Linnaeus grants to the  Centre for Animal Movement Research and the Lund Laser Centre.
This enabled the post-sequencing identification of each vaccine batch sequence after a single sequencing run. Following emulsion PCR using the GS Junior Titanium Lib-L emPCR Kit, the pyrosequencing was performed using the GS Junior Titanium Sequencing Kit according to the instructions of the manufacturer and the 454 GS Junior sequencer (Roche). Data were analyzed by the Reference Mapper included in the 454 GS Junior software using the SAD Bern genomic sequence as a reference (GenBank accession number EF206708).
3. Illumina whole genome sequencing Total RNA was extracted using the NucleoSpin 1 RNA kit (Macherey-Nagel) followed by purification using the RNEasy mini-column as per the manufacturer's instructions (Qiagen). The RNAs were stored at -70°C. RNA-Seq library construction was performed using a commercial service (Vertis Biotech, Freising, Germany) after ribo-depletion of samples. Following RNA--Seq library construction, 2x100 bp paired-end sequencing was performed on the HiSeq-2000 instrument (Illumina, San Diego, CA). Final sequence analysis was performed using Integrative Genomics Viewer (IGV) software based on variant analysis. The mean percentage of SADB19/ SAG2 mutations for the first half of rabies genome was performed by comparison with the SAD Bern genomic sequence (EF206708) which was used as a reference for all analysis.
This article describes the effectiveness and safety reported for the various hemostatic agents examined in surgical procedures in GT patients, with or without antibodies and/or refractoriness, in the GTR. ©2015 Ferrata Storti Foundation. This is an open-access paper. doi :10. 3324/haematol. 2014. 121384 The online version of this article has a Supplementary Appendix. Manuscript received on November 24, 2014. Manuscript accepted on May 11, 2015. Correspondence: mcpoon@ucalgary. ca Standard treatment for Glanzmann thrombasthenia, a severe inherited bleeding disorder, is platelet transfusion. Recombinant factor VIIa is reported to be effective in Glanzmann thrombasthenia with platelet antibodies and/or refractoriness to platelet transfusions. We aimed to evaluate recombinant factor VIIa effectiveness and safety for the treatment and prevention of surgical bleeding in patients, with or without platelet antibodies and/or refractoriness, using data from the Glanzmann Thrombasthenia Registry, an international, multicenter, observational, postmarketing study of rFVIIa.
*One admission was considered both a surgical procedure and a bleeding episode. † Data used for the primary effectiveness analysis (performed in 2012). ‡ Data used for the secondary data analysis (performed in 2014). All data were included in the safety analysis. 3. Definitions used for treatment effectiveness, past or present refractoriness to platelet transfusions and post-surgical bleeding are summarized in Table  1. 4. Safety assessments included frequency of adverse events (AEs) and serious AEs (SAEs) during and after treatment.
Recruitment into the GTR and effectiveness and safety datasets Data were collected from 1086 admissions (883 for bleeding and 204 for surgery; one admission was considered as both); 218 patients with GT were enrolled from 45 sites in 15 countries from Europe, Africa, Asia and North America (Figure  1 ). All 1086 admissions were included in the safety analysis. However, for the effectiveness evaluations, review of the data showed that four admissions were AEs and not treatments for bleeds and hence were excluded from the evaluations (Figure  1 ). In addition, it was found that on several occasions multiple admissions contained information on the same bleeding episode; in these instances, the admissions were collapsed and one designated as the index event. In total, 64 admissions for bleeds were considered to be linked events and were collapsed into 22 index events.