dataesr/scientific-paragraphs-categorization huggingface dataset:
Number of observable layers The size of the dataset that the method uses to solve the inversion problem of finding the parameters for every layer in the turbulence below the LGS is given by the number of uncorrelated pixels contained inside the rectangular box defined in Fig. 6. Nevertheless, this window is symmetric with respect to the baseline between a pair of WFSs, so the number of available pixels in elements used for the fitting is only 4×12 = 48. Furthermore, not all of them have the same quality in terms of statistical independence or signal-to-noise ratio. On the other hand, the number of parameters to be estimated from these elements depends on the number of layers, i. e. if three parameters (L 0 , h and ω) characterize each layer, then the total number of unknowns to be estimated is 3 × N Z.
R E S U LT S F O R L 0 ( h) FROM GeMS T E L E M E T RY A significant amount of on-sky data collected with GeMS during 3 yr of campaigns at Cerro Pachón  (2012) (2013) (2014)  has been reduced to gather some statistics of L 0 (h). The data files are 4×10 3 frames long, taken at different frame rates from 200 to 400 Hz. Based on the error analysis in the previous section, we conclude that the turbulence can be accurately represented by five layers, so we apply the method to GeMS telemetry data using N Z = 5. The results obtained for 1124 samples (out of 529 circular buffers) are presented in Fig. 14 , where the altitude range is divided in slabs of 2 km. Abundant data were obtained for the first division closer to the ground that allowed us to further divide this segment into two 1 km slabs.
AC K N OW L E D G E M E N T S Andrés Guesalaga is grateful to the Chilean Research Council, project Fondecyt-1160236 and to the Institut d' Études Avancées (Aix-Marseille Université, France) for supporting this work. Benoit Neichel acknowledges the financial support from the Agence Nationale de la Recherche, project WASABI. Timothy Butterley is grateful to the Science and Technology Facilities Committee for financial support (grant ST/J001236/1). The research leading to these results also received the support of the A*MIDEX project (grant ANR-11-IDEX-0001-02), managed by the Agence Nationale de la Recherche. All the simulations and analysis have been done with the object oriented MATLAB AO simulator (OOMAO) freely available from https://github. com/cmcorreia/LAM-Public.
(5) Finally, the second harmonic extraction is based on the coefficients h 2 = [h 2 (1),. , h 2 (M )] T. The second harmonic signal y NL can be modelled as: y NL = x T 2 h 2. (6) Note that a Matlab program of a Hammerstein decomposition is available on RunMyCode. org (http://www. runmycode. org/coder/view/2395.
III. SIMULATION MODEL In order to validate the feasibility, we used realistic simulations which have already been proven in medical ultrasound imaging  [4]. The simulation model is composed of different phases: transmission, 2D nonlinear propagation and reception. At the transmitter, a Gaussian pulse x standard (n) at a centre frequency f 0 of 2 MHz and with a bandwidth of 50% is generated digitally with Matlab (The Mathworks, Natick, MA, USA). It is transmitted to an 8-element probe with a pitch of 400 µm and filtered by its transfer function from a realistic transducer, centred at f c = 4 MHz with a fractional bandwidth of 80% at -3 dB. Note that the signal x standard (n) is set in order to guarantee the reception of second harmonics. The pulse wave generated is propagated nonlinearly into an attenuating medium (Fig.
Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome. jgi. doe. gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1. 1 of sPta717 at http://aspendb. uga. edu/index. php/databases/ spta-717-genome) presents only INRA 717-1B4 genomic regions with high similarity to the P. trichocarpa genomic reference sequences. We assembled draft genomic scaffolds by a combination of de novo assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4.
, 2013 ; sequence available at the The Salinity Tolerant Poplar Database: http://lzume. iok. la/stpd. Only few of the Populus species are of high scientific and economic importance, and serve as source material for breeding purposes  (Licht and Isebrands, 2005; Walle et al. , 2007). Important characteristics of some interspecific hybrids are high growth rates and broad applicability ranging from wood and paper to energy production  (Dickmann and Stuart, 1993). Nowadays, breeding of Populus is intensified worldwide due to the application of biotechnological methods  (Fladung et al. , 2012)  and the availability of huge genomic resources  (Stettler et al. , 1996; Stanton et al. , 2010). Superior clones of various Populus species have been developed and are commonly used for biomass production in short rotation plantations.
trichocarpa reference genome" using 20x resequencing NGS (next generation sequencing) data (v1. 1 of sPta717 at http://aspendb. uga. edu/index. php/ databases/spta-717-genome;  Zhou et al. , 2015). This resource has been applied for screening of 717 gRNAs for sequence variants to optimize gRNA design in CRISPR/Cas genome editing experiments  (Zhou et al. , 2015). Unfortunately, the sPta717 sequence represents only genomic regions of INRA 717-1B4 that show a high similarity to the P. trichocarpa reference genome. To provide a basis for the future optimization of genetic transformation experiments also in target regions that are very specific for INRA 717-1B4 and not displayed in the sPta717 sequence, we decided to generate and provide draft genomic scaffolds of INRA 717-1B4 by assembly (de novo and reference-based) of 30x resequencing NGS data.
Read trimming Initial quality control of the NGS reads (MiSeq or Ion Torrent) was performed with FastQC (http://www. bioinformatics. babraham. ac. uk/projects/fastqc/). Based on the FastQC reports all reads were trimmed using the trimming tool of the CLC GWB. All MiSeq short reads containing adapter sequences (i. e. Illumina TrueSeq Universal Adapter, Index adapter I and TruSeq control sequences) were trimmed. Reads containing bases with a quality Phred score less than 20 were trimmed by setting the quality limit of the trimming tool to a value of 0. 01. Ten nucleotides 3' and 5' of every read were removed and finally every read with a length of less than 100 bp was discarded. To reduce the amount of redundant data all overlapping read pairs were merged and duplicate reads were removed from the data set.
De novo-assembly of 717-1B4 1-De novo-assembly of MiSeq and Ion Torrent reads De novo sequence assembly of the MiSeq reads was performed with a preset word size of 29, length fraction of 0. 9, similarity fraction of 0. 95 and without the scaffolding option (Figure  1 ). These assembly parameters provided the least misassemblies according to the quality assessment generated by the software QUAST  (Gurevich et al. , 2013). The minimum and maximum read pair distances were set to 379 bp and 579 bp, respectively (based on the mean fragment size of the 717-1B4 genomic library). All remaining parameters were set to default (with backmapping option per default). De novo sequence assembly of the trimmed Ion Torrent reads was performed with a length fraction of 0. 9 and a similarity fraction of 0. 95.
Results NGS of total DNA of P. tremula x P. alba INRA 717-1B4 resulted in the generation of about 45. 124 million Illumina (MiSeq®) raw reads in pairs (2x250 bp; 20x coverage) and about 61. 797 million Ion Torrent (Ion PGM™) raw reads (10x coverage). In total, 419,969 scaffolds of length larger than 500 bp were generated from INRA 717-1B4 by a combination of de novo assembly and reference-based assembly followed by superassembly (Figure  1 ). The accumulated scaffold length is with about 0. 9 GB larger than the expected size of the haploid nuclear genome of 0. 440 GB for P. tremula and 0. 509 GB for P. alba (estimation based on the C-value of the haploid genomes at the Plant DNA C-values Database; http://data. kew. org/cvalues/). The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp.
Sequence data of the parents of INRA 717-1B4 would therefore be very helpful to fulfil this task and to resolve the two haplotypes; however, unfortunately, the parents of INRA 717-1B4 are not available anymore. New next generation sequencing methods capable of delivering long read lengths with high accuracy are forthcoming and will undoubtedly facilitate resolution of highly heterozygous regions as well as large insertions/deletions, copy number variations etc. The future inclusion of heterozygote SNPs and InDels in the INRA 717-1B4 nuclear genomic sequence would add additional value to this genomic resource. the draft genome within the URGI Blast web page and the URGI to maintaining the infrastructure.
Acknowledgements We acknowledge the support by  CEA-IG/CNG  performing the  DNA QC in its DNA and Cell Bank service (Anne Boland 's team) and providing access to their  Illumina Sequencing Platform. We thank  Isabelle Le Clainche  and  Aurélie Chauveau  for performing DNA extraction and sequencing. We are grateful to  Katrin Groppe ,  Manuela Will , and  Susanne Bein  for technical assistance. We thank  Karine Robineau  for search of publications. We are grateful to  Françoise Alfama-Depauw  to release.
In the past, numerical approaches, including Bayesian techniques, have occasionally been used to find a best fit  (Andreuzzi et al. 2011 , Jørgensen & Lindegren 2005 , Naylor & Jeffries 2006 , Hernandez & Valls-Gabaud 2008 , Janes et al. 2013 , cite altde-Souza:2015). With our Bayesian approach, we can interpolate to high precision using a grid of isochrones and more reliably determine the most likely isochrone fit for a cluster, via the posterior distribution of the unknown cluster parameters  (Jeffery et al. 2016). This enables us to provide principled measures of uncertainty on both the fitted parameters and the fitted isochrones. The Bayesian Analysis for Stellar Evolution software suite (BASE-9; see von  Hippel et al. 2006 , De Gennaro et al. 2009 , van Dyk et al. 2009 , Stein et al. 2013 ), fits a cluster consisting of a single population by deriving the joint posterior distribution of age, distance, absorption, metallicity, and the initial stellar masses, while allowing for field star contamination.
DATA The clusters in our sample were previously observed by the ACS Globular Cluster Treasury Survey (GO Cycle 14 Proposal 10775; PI: Sarajedini). The ACS Globular Cluster Treasury observed 65 clusters in the HST F606W and F814W filters  (Sarajedini et al. 2007 , Anderson et al. 2008; 71 clusters including Dotter et al. 2011). These observations provided a wealth of data and new insights into the Galactic globular cluster population. The new data from HST Cycle 21 Proposal GO 13297 (PI: Piotto) obtained 131 orbits for 47 of the globular clusters in the ACS Treasury survey. The observations extend the wavelength coverage into the ultraviolet with the F275W, F336W, and F438W filters. These passbands disentangle multiple populations in globular clusters due to their sensitivity to C, N, and O abundances.
These posterior distributions can be especially valuable when they are skewed or otherwise non-Gaussian. All of these advantages are particularly important with the added complexity of multiple populations. Our software suite, BASE-9, was developed to determine cluster parameters for a single population of stars using sophisticated Bayesian techniques, given a set of photometry and theoretical models (von  Hippel et al. 2006 , De Gennaro et al. 2009 , van Dyk et al. 2009 , Stein et al. 2013). The software, including the updates developed for this two population study, is available as open source code from GitHub (https://github. com/argiopetech/base/releases) and via executables through Amazon Web Services. Installation and instruction for BASE-9 may be found in the User Manual  (von Hippel et al.
(2) We use Dartmouth Stellar Evolution Database (DSED) models that span an age range (9 to 15 Gyr), metallicity range (-2. 5 to 0. 5 dex), helium fraction range (0. 23 to 0. 40), and different [α/Fe] values (0. 0 and +0. 4). A Markov-chain Monte Carlo (MCMC) algorithm, specifically an adaptive Metropolis (AM) implementation, explores the posterior distribution; see  Stenning et al. (2016)  for details. We run each MCMC chain for 11,000 iterations. After the first 1000 iterations, which we discard as burn-in, the chain automatically adapts to the observed correlations in earlier iterations to make sampling more efficient. For each fitted model, we run three MCMC chains using over dispersed starting values and visually inspect a plot of the chains to assess convergence. We also compute the Gelman-Rubin statistic  (Gelman & Rubin 1992 ) on the 10,000 post burn-in iterations per chain of each parameter in each cluster fit, and all values were below 1.
[α/Fe]=0 enrichment, the clusters NGC 5024, NGC 5272, and NGC 6352 have ∆Y values of 0. 048 to 0. 113. With an enrichment of [α/Fe]=0. 4, we observe a range of ∆Y values of 0. 050 to 0. 079. Additionally, we see the percentage of first population stars in these clusters ranges from approximately 27% to 45%. This material is based upon work supported by the National Aeronautics & Space Administration under Grant NNX11AF34G issued through the Office of Space Science, and through the University of Central Florida's NASA Florida Space Grant Consortium. We thank Giampaolo Piotto as PI of the HST UVIS Treasury and Antonino Milone for the data reduction. Work by DS was supported by NSF grant DMS 1208791. DvD was partially supported by a Wolfson Research Merit Award (WM110023) provided by the British Royal Society and by Marie-Curie Career Integration (FP7-PEOPLE-2012-CIG-321865) and Marie-Skodowska-Curie RISE (H2020-MSCA-RISE-2015-691164) Grants both provided by the European Commission.
Experimental Samples of Portuguese olive oil (two samples from two different batches) were analyzed in triplicate. The samples were heated from 30 °C until 170 °C, increasing it by steps of 10 °C, and a first spectrum being taken at room temperature (25 °C). UV-Vis spectra were acquired in the range from 300 to 540 nm (steps of 2 nm) in a 1 mm quartz cuvette. Data were analyzed using MATLAB version R2007b (The Mathworks Inc. , MA, USA) where curve resolution was performed by Multivariate Curve Resolution with Alternating Least Squares (MCR-ALS). The MCR-ALS algorithm code and Graphical User Interface for MATLAB  [10]  are freely available from the home page of MCR at http://www. mcrals. info/. By this interface, there are two options to estimate the matrix rank: one is based on the percentage of variance captured by singular values decomposition (SVD) analysis and the other is the manual decision of it.
Sometimes it is hard to decide the rank based only on these percentages and the decision can be improved by the graphical visualization of the PCA loadings  [3]. ICA was performed using Joint Approximate Diagonalization of Eigenmatrices (JADE) algorithm  [11] , that involves matrix diagonalization. The MATLAB code of this algorithm can be found on the website <http://perso. telecom-paristech. fr/~cardoso/Algo/ Jade/jadeR. m>.
038, Wilcoxon rank-sum test). We compared the prevalence of mutations in our data sets (n = 78, BC) with their prevalence in The Cancer Genome Atlas (TCGA) invasive breast cancer (n = 507) (Supplementary Figure  S2 ). The prevalence of mutations in BRCA2, CDH1, FGFR2, GATA3, PTEN and TP53 was comparable in all sets. Although the importance of CDH1 inactivation for tumor metastasis has been well demonstrated in several studies  [13, 14] , its mutation frequency was not significantly high and was o10% across all data sets. In contrast, ARID1A (TCGA = 2%, BC = 13%), NOTCH2 (TCGA = 1%, BC = 18%) and USH2A (TCGA = 5%, BC = 26%) mutations were detected at much higher rates in our samples than in those reported by TCGA. Frequent somatic mutations in ARID1A, a tumor suppressor, have been reported in a variety of human cancers  [15] [16] [17].
In our BC cases, p. Q1333_Q1334del mutation was detected in six cases. Based on the report in which the cells expressing the p. Q1134_R1335dupQ mutation exhibited attenuated growth inhibition, it can be carefully suggested that ARID1A p. Q1333_Q1334del mutation can result in loss of ability to suppress cellular proliferation  [18]. Another difference was observed in NOTCH2. The prevalence of mutations in NOTCH2 was significantly higher in our BC data sets (5 cases among 507 TCGA cases, 14 cases among 78 BC cases). And nearly 80% (n = 12) of NOTCH2 mutations in BC data sets was a novel p. R5_P6del frameshift mutation. As NOTCH can have tumor-promoting and -suppressive roles depending on the cellular context, more deeper functional study is required to reveal its role in breast cancer  [19].
With this hypothesis, we have developed a novel approach to identify the pathways that link the above 18 mutations to TFs regulating DEGs. In addition, except for the 18 mutations, we also considered the genes that have mutations occurring only in HRM samples. To identify the TFs regulating DEGs, we assumed that genes with similar expression profiles were regulated by common TF(s). We constructed a co-expression network based on the RNA sequencing data of HRM samples, where a pair of genes were linked if their Pearson's correlation coefficient was 40. 7 with P-value of 0. 01. The ClusterONE  [21]  tool was applied to identify modules from the co-expression network with default parameters. The genes belonging to the same modules were regarded to be regulated by the same TF if its target genes were also enriched in the module (P-valueo0.
01) where the TF-gene regulations were extracted from the UCSC Table browser  [22]. In this way, the TFs regulating DEGs enriched modules (P-valueo0. 01) can be identified (Supplementary Table  S4 ), and these DEG modules were regarded as HRM-specific network signatures hereafter. With the genetic mutations and HRM-specific network signatures, we detected the pathways linking them with our previously developed network flow model  [23, 24]  (for details, refer to Meterials and Methods). After overlaying the genes over a proteinprotein interaction network obtained from HPRD (release 9), 13 pathways were detected with each for one mutant gene. Note that not all mutations can be linked to TFs owing to the incompleteness of current interactome. With the pathways, the 13 mutant genes were further ranked based on the weights accompanying their pathways (see Meterials and Methods).
Exome and RNA sequencing Samples were prepared as an Illumina sequencing library (Illumina, San Diego, CA, USA), and the sequencing libraries were enriched for the desired target using the Illumina Exome Enrichment protocol. The captured libraries were sequenced using Illuminal HiSeq 2000 Sequencer. Raw sequencing data were aligned to UCSC hg19 (http://genome. ucsc. edu/) using BWA (http://genome. ucsc. edu/) and TopHat  [66]. SAMTOOLS (http://samtools. sourceforge. net/) was used to detect the singlenucleotide polymorphisms and Indels  [67]. To prevent miscalls that might be caused by duplicated sequencing errors, possible PCR duplicates were removed using Picard tools (http://picard. sourceforge. net/). The quality of the sequencing data was assessed by evaluating criteria such as on-target coverage, number of on-target genotypes and mean read depth of target regions.
Scratch wound-healing assay To perform scratch wound-healing assay, CellPlayer Migration Assay System (ESSEN BioScience, Ann Arbor, MI, USA) was used. MDA-MB-231 cells were transfected with each of WT and mutant plasmid DNA and 2 × 10 4 cells per well were seeded into collagen-coated 96-well ImageLock plate (ESSEN BioScience). After 95% cell confluency, a scratch was placed in middle of the wells using the WoundMaker (ESSEN BioScience). After washing twice with serum-free RPMI, the cells were incubated in RPMI containing 3% fetal bovine serum and the plate was put into IncuCyte FLR instrument (ESSEN BioScience). The cells were monitored for 48 h in IncuCyte FLR instrument and analyzed using the IncuCyte FLR 2011A software (ESSEN BioScience).
In the framework of the ChArMEx (the Chemistry-Aerosol Mediterranean Experiment; http://charmex. lsce. ipsl. fr/) program, the seasonal variability of the aerosol optical, microphysical and radiative properties derived from AERONET (Aerosol Robotic Network; http://aeronet. gsfc. nasa. gov/) is examined in two regional background insular sites in the western Mediterranean Basin: Ersa (Corsica Island, France) and Palma de Mallorca (Mallorca Island, Spain). A third site, Alborán (Alborán Island, Spain), with only a few months of data is considered for examining possible northeast-southwest (NE-SW) gradients of the aforementioned aerosol properties. The AERONET dataset is exclusively composed of level 2. 0 inversion products available during the 5-year period 2011-2015. AERONET solar radiative fluxes are compared with groundand satellite-based flux measurements.
The dataset is exclusively composed of AERONET (Aerosol Robotic Network; http://aeronet. gsfc. nasa. gov/) level 2. 0 inversion products  (Holben et al. , 2006). Insular sites were selected in order to determine the properties of aerosols representative of the whole basin minimizing local influences. The choice of the western Mediterranean Basin was motivated by the ChArMEx (the Chemistry-Aerosol Mediterranean Experiment, http://charmex. lsce. ipsl. fr/) program which is a collaborative research program federating international activities to investigate, among other questions, Mediterranean regional chemistry-climate interactions. One of the goals of ChArMEx is precisely to improve our knowledge of the potential impacts of aerosols over the Mediterranean Basin  (Dulac et al. , 2014; Mallet et al.
, 2016). In its implementation strategy ChArMEx proposes enhanced observation periods (EOPs) to study the daily to seasonal-scale variability of several parameters measured at several sites and to monitor east-west and north-south gradients over a period of a few years. The AERONET sun photometer from Ersa was deployed in that framework. In order to extend the study of north-south gradients to the southern part of the whole western Mediterranean Basin, a case study is presented by complementing the dataset with 5 months of coincident measurements in 2011 in the remote island of  Alborán (Spain)  between Spain and Morocco. With this seasonal analysis and case study, two goals are pursued: (1) the spatiotemporal quantification of the effect of long-range transport on the aerosol optical, microphysical and radiative properties in the western Mediterranean Basin; and (2) the spatiotemporal variation of aerosol absorption properties during strong aerosol events (aerosol optical depth at 440 nm greater than 0.
Sites The sites selected for this analysis had to fulfill the following criteria: to be located in the western Mediterranean Basin, to be insular sites in order to be representative of aerosol regional background conditions, to be approximately aligned on a north-south axis and to have a recent database with at least 2 years of data. At the same time we wanted to take advantage of the ChArMEx EOP in the framework of which a supersite was installed for 2 years from June 2012 to July 2014 at Ersa on the northern tip of Corsica Island, France  (Lambert et al. , 2011; Dulac et al. , 2014 , Mallet et al. , 2016). As part of that station, situated at 43. 00 • N, 9. 36 • E, 80 m a. s. l. (above sea level), an AERONET sun photometer is in operation since June 2008. According to the AERONET Data Display Interface and applying the abovementioned criteria, the second site that was selected is Palma de Mallorca in the Balearic Islands (Spain) situated at 39.