dataesr/scientific-paragraphs-categorization huggingface dataset:
affymetrix. com; release from 01/12/2008) to update the Affymetrix gene chips annotations. The probes were then mapped based on their EntrezGeneID. When multiple probes mapped to the same GeneID, we retained the one with the highest variance in a particular dataset. To avoid biases related to IHC analyses across different institutions and thanks to the bimodal distribution of respective mRNA expression levels, ER, progesterone receptor (PR), ERBB2 and Ki67 expression (negative/ positive) was defined at the transcriptional level using gene expression data of ESR1, PGR, ERBB2 and MKI67 respectively, as previously described  [60]. We applied different multigene classifiers in each data set separately. The intrinsic molecular subtypes of tumors were defined using the PAM50 classifier  [61]  as previously described  [62].
To explore the biological pathways linked to PDL1 expression in breast cancer, we applied a supervised analysis to three large data sets including more than 400 samples: the Guedj' s data set  [63]  as learning set, including 100 tumors with and 352 without PDL1 upregulation, and the Ivshina' s data set  [64]  and the TCGA data set  [46]  as two independent validation sets, including respectively 112 tumors with and 336 without PDL1 upregulation, and 123 tumors with and 410 without PDL1 upregulation. In the learning set, we compared the expression profiles of 16,578 genes between tumors with versus without PDL1 upregulation using a moderated t-test with the following significance thresholds: p<5%, q<5% and fold change (FC) superior to |2x|. Ontology analysis of the resulting gene list was based on GO biological processes of the Database for Annotation, Visualization and Integrated Discovery (DAVID; david.
Array-CGH (aCGH) data analysis Genomic imbalances, associated with available mRNA expression data, were available for 3,140 breast cancer samples extracted from 5 sets including ours  [46, [65] [66] [67] [68]  (Supplementary Table  2 ). Data from our set were generated using 244K CGH Microarrays (Hu-244A, Agilent Technologies Inc. Santa Clara, CA, USA) as previously described  [65, 69]. The PDL1 locus at 9p24 was analyzed, and copy number changes were characterized as reported previously  [65]. Five probes (A_16_P02052215, A_16_P02052226, A_16_P18538134, A_14_P120124 and A_16_P02052257) matched the PDL1 gene on our Agilent chips. All our aCGH data can be found in the Array Express database (E-MTAB-1861) and the GEO database (GSE23720). DNA copy number alterations in tumors were defined as a 1.
ACKNOWLEDGEMENTS Our work is supported by the  Institut National du Cancer (INCa)   Translational Research Grant   2007  (FB), Translational Research Grant 2009 (DB) and Biologic Research Grant 2010 « IVOIRES » (FB), the  Ligue Nationale Contre le Cancer  (label DB) and  SIRIC (INCa-DGOS-Inserm 6038  grant).
Thus, by simply computing the correlation between the lip function (Fig. 5B ) or the acoustic envelope (Fig. 5C ) with all the remaining channels, an effective mask can be readily computed to extract the target female speech (and the background male speech too). This example thus illustrates how in general any other co-modulated features of the speech signal (e. g. , location, loudness, timbre, and visual signals such as lip movements can contribute to segregation of complex mixtures). The performance of the model is quantified with a database of 100 mixtures formed from pairs of male-female speech randomly sampled from the TIMIT database (Fig. 6 ) where the spectra of the clean speech are compared to those of the corresponding segregated versions. The signal-to-noise ratio is computed as SNR segregated speechm ax 10 Ã log jS 1 Ã O 1 j 2 jS 1 Ã O 2 j 2 ! ,10 Ã log jS 2 Ã O 1 j 2 jS 2 Ã O 2 j 2 ! ! ð1Þ SNR mixture~10 Ã log DM Ã O 1 D 2 DM Ã O 2 D 2 ð2Þ where S 1 ,S 2 are the cortical representations of the segregated sentences and O 1 ,O 2 are the cortical representations of the original sentences and M is the cortical representation of the mixture.
Average SNR improvement was 6 dB for mixture waveforms mixed at 0 dB. Another way to demonstrate the effectiveness of the segregation is to compare the match between the segregated samples and their corresponding originals. This is evidenced by the minimal overlap in Fig. 6B  (middle panel) across the distributions of the coincidences computed between each segregated sentence and its original version versus the interfering speech. To compare directly these coincidences for each pair of mixed sentences, the difference between coincidences in each mixture are scatter-plotted in the bottom panel. Effective pairwise segregation (e. g. , not extracting only one of the mixed sentences) places the scatter points along the diagonal. Examples of segregated and reconstructed audio files can be found in S1 Dataset.
, 1999; Lacoume et al. , 2009; Yoon et al. , 2009) , life-history traits  (Bressac et al. , 2009; Lebreton et al. , 2009a Lebreton et al. , , 2010;; Chaisaeng et al. , 2010) , behaviour including learning  (Ryoo et al. , 1996; Lebreton et al. , 2009b; Belda & Riudavets, 2010; Ishii & Shimada, 2010)  and physiology  (Zhu et al. , 1999; Howard & Baker, 2003). The ISI Web of Science database (Thomson Reuters) cites more than 100 papers in this respect and many of the older works can be retrieved from the Universal Chalcidoidea Database  (Noyes, 2013). Despite the multitude of studies, little critical attention has been paid to the systematics of Anisopteromalus. As mentioned before, most species have not been re-considered since their description. Furthermore, the taxonomic status of A. calandrae is doubtful.
For this reason, we also employed two graphical tools, the PCA ratio spectrum and allometry ratio spectrum, respectively. Finally, we used the LDA ratio extractor to extract the best ratios for use in the identification key and diagnoses, and calculated the standard distance as well as the measure. The R language and environment for statistical computing was used for data analysis  (R Core Team, 2013; v3. 0. 2). In particular, we employed slightly modified versions of the R-scripts provided by  Baur & Leuenberger (2011, under 'Supplementary material'). Pearson product-moment correlation coefficients were calculated with the function 'cor()' using the default settings. Scatterplots were generated with the package 'ggplot2'  (Wickham, 2009). A few specimens, especially some of the name-bearing types, lacked one body part or another.
Taxonomic sampling We sampled six specimens of Anisopteromalus calandrae and three specimens of A. quinarius belonging to the main strains used in laboratories (Table  S2 ). Specimens were collected alive and stored in 95% ethanol. Adult specimens were identified to species by V. E. Gokhman, A. V. Timokhov and J. -Y. Rasplus. DNA vouchers are deposited at the CBGP collection, Montferrier-sur-Lez, France. Four outgroup taxa belonging to the pteromalid genera Nasonia (three species) and Pachycrepoideus (one species) were included to root phylogenetic trees. Cytochrome b (Cytb) and ITS2 sequences from Nasonia species were downloaded from GenBank (Table  S2 ).
2 ITS2: we used forward primer (5 ′ -TGT GAA CTG CAG GAC ACA TG-3 ′ ) and reverse primer (5 ′ -AAT GCT TAA ATT TAG GGG GTA-3 ′ :  Campbell et al. , 1993). 29 cycles of amplification were performed as follows in 25-μL reaction volumes: denaturation step at 94 ∘ C for 1 min, annealing at 50 ∘ C for 1 min, and extension at 72 ∘ C for 2 min. PCR products were purified with QIAquick PCR purification kit (Qiagen, Venlo, The Netherlands) and directly sequenced on an ABI 377 automated sequencer using TaqFS and dye-labeled terminators (Perkin-Elmer). CP1 and Tser were used as sequencing primers for Cytb. Both strands for each overlapping fragment were assembled using the sequence-editing software Geneious v5. 5. 7  (Drummond et al. , 2012). All sequences were deposited in GenBank (Table  S2 ).
Acknowledgements The present study would have been impossible without assistance from a number of colleagues. We acknowledge receiving samples of a few laboratory stocks of Anisopteromalus spp. from:  James Baker ,  Agricultural Research Service, U. S. Department of Agriculture  ( USDA-ARS ), Manhattan, Kansas,  USA ;  Consuelo Belda ,  IRTA, 08348 Cabrils, Barcelona, Spain ;  Judy Johnson ,  USDA-ARS, Parlier, California, USA ;  Donald Quicke ,  Imperial College, Ascot, Berkshire, UK. For the loan of museum specimens we are grateful to:  Chris Burwell , QMB;  Bernhard Merz , MHNG;  Andreas Müller , ETHZ;  Natalie Dale-Skey.
Methicillin-resistant Staphylococcus aureus (MRSA) infections, in particular due to community-acquired MRSA,  [2]  are extremely prevalent in many countries, including some European ones (European Center for Diseases Control and Prevention. EARSS-Net database. http://www. ecdc. europa. eu),  [3] the USA, South America and Asia. Prevalence of MRSA infections decreased in the last few years in many European countries, and this can be considered as a very positive and promising result. Vancomycin-resistant enterococci (VRE) are also very frequent, with large differences between countries. In the European point prevalence study organized by ECDC,  [4]  VRE prevalence was going from 1% to >50%. The prevalence of Escherichia coli and Klebsiella pneumoniae harboring extended-spectrum beta lactamases is increasing regularly worldwide  [5]  reaching 50-70% for E.
Experimental Section Proteins and DNA Substrates: Native-  [ 43 ]  and biotinylated-AddAB  [ 16 ]  proteins were purifi ed as previously described. DNA molecules for MT experiments were fabricated by polymerase chain reaction (PCR) as stated by Carrasco et al. ;  [ 18 ]  in this work, the 7. 8 kbp substrate called Chi10-Rev-Rev -which is defi cient of regulatory B. subtilis Chi (5'-AGCGG) sites within the fi rst 5 kbp  [ 18 ]  -was used. Stopped-fl ow kinetics were measured using a very similar substrate named pSP73-JY0-TFO, which shares the same parent plasmid as Chi10-Rev-Rev and also lacks Chi sequences within the relevant substrate region. For details of construction of the parent plasmid pSP73-JY0, consult the supplementary data of Reference  [ 16 ]  ; the plasmid pSP73-JY0-TFO additionally contains an engineered triplex binding site at a BstBI site, which is 926 bp away from an XbaI site.
Proportional-Integral-Derivative (PID) Feedback: Temperature data were acquired and processed, and heating foil voltages updated at a frequency of 2 Hz by means of customized software developed in LabVIEW (National Instruments). The application contains two standard PID controllers working in parallel, one for the objective and another for the baseplate heating circuit. We applied the Callendar-Van Dusen equation  [ 44 ]  to the acquired temperatures to correct for nonlinearities in the R ( T )-response of the Pt100 thermometers. The sensitivities S (in V 2 •°C -1 ) for calculating the initial voltage setpoints delivered to the power supplies were determined offl ine by independently raising the voltage of each heater circuit stepwise and annotating the mean equilibrated temperature at least 40 minutes after each step (see Figure  2 A ).
For all MT measurements, the reaction buffer included tris acetate (25 m M , pH 7. 5), magnesium acetate (2 m M ), and dithiothreitol (DTT; 1 m M ); ATP (1 or 4 m M ) was added to start AddAB activity. The assays shown herein were carried out in a constant fl ow of (preheated) buffer at 65 µL•min -1 ≈ 1 µL•s -1 (a compromise ensuring reliable video tracking at suffi ciently short reaction onset times) and with a pulling force between 3 and 14 pN; their corresponding data were treated as explained before. [ 18 ] Briefl y, instantaneous and mean translocation velocities were determined from derivatives of the position-vs. -time signals previously smoothed from 60 to 3 Hzthe latter without taking into account the early ATP gradient and random pauses (if any) of the enzyme along its track. To obtain the histograms of instantaneous rates v * MT shown in Figure  6  , the interval ∼2001-4000 bp from the proximal end of the Chi10-Rev-Rev substrate was chosen because it provided maximum statistics within a region after the initial ATP concentration rise and before any individual Chi sequences (see Figure  4 B ).
The stated temperatures correspond to the values returned from a circulating water bath that controls the fl uorimeter and yields an estimated accuracy of ±0. 1 °C (see supplementary data of Reference [ 13 ] ). All concentrations quoted below are fi nal, after mixing in the stopped-fl ow apparatus. The TAMRA-labelled triplex -located with its far end at 924 bp from the proximal DNA end -was excited at 547 nm with the slits set at 5. 4 nm and the fl uorescence monitored above 570 nm. AddAB (5 n M ) was prebound to substrate DNA (0. 2 n M ) in a buffer containing tris acetate (25 m M , pH 7. 5), magnesium acetate (2 m M ), DTT (1 m M ) and BSA (100 µg•mL -1 ; Sigma). Rapid mixing against a solution of the same buffer containing ATP (1 m M ) initiated translocation, and the fl uorescence changes resulting from TFO dissociation were recorded.
Acknowledgements B. G. and F. M. -H. would like to thank  M. Mahamdeh  and  E. Schäffer  for fruitful discussions about temperature stabilization in optical microscopes. This work was supported by a Starting Grant from the  European Research Council  [ref. 206117, to F. M. -H. ], by a grant from the  Spanish Ministry of Science and Innovation (MICINN)  [ref. FIS2011-24638 , to F. M. -H. ], and by the  Wellcome Trust  [grants  077368  and  100401 , to  M. S. D. ]. Funding  for the open access charge was provided by the  Wellcome Trust  [grant  100401 ]. B. G. thanks the  Spanish Ministry of Education  for an  FPU Ph. D. scholarship. C. C. acknowledges support by the  Juan de la Cierva Program  [ref. JCI-2011-10277, MICINN]. N. S. G. was funded by a  BBSRC  studentship.
Data acquisition For validation we used data from one healthy subject who carried out a visually cued, skilled right hand finger movement task. In each trial finger-thumb opposition was carried out for 16 s followed by 16 s of rest, with each experiment comprising 20 trials. All experiments were approved by the University of Nottingham Medical School Ethics Committee. MEG data were recorded using a third order synthetic gradiometer configuration of a 275-channel CTF whole-head MEG scanner (one channel failed giving 274 useful channels), with a sampling rate of 600 Hz and hardware anti-aliasing filters at 0-150 Hz. Prior to MEG data acquisition, head localisation coils (HLCs) were placed in perspex mounts glued to the scalp at the nasion and pre-auricular points. HLCs were localised inside the scanner continuously during data acquisition with a motion tolerance of 5 mm enforced.
In contrast the noise data are supported equally well by all cortical models indicating that these data are unlikely to derive from the cortical surface. For these data, recorded in a single subject, the functional estimates based upon MNM assumptions follow the anatomy more closely (i. e. they allow us to reject more of the lower order models) than those based on MSP assumptions for both physiological bands. We can now take the model set above the HDH and compute the posterior probability over these surfaces (Eq. (  10 )). In the MSP case (see S1 for MNM case) the posterior distribution (not directly shown here, but the integral over power change in Fig. 2C ) peaks at cortical model L = 31 and this surface is shown in Fig. 2B  with the t statistic map of the 15-30 Hz power change from 1 s before to 1 s after stimulus onset.
Discussion We have shown, for the first time, that it is possible to quantify the accuracy of a non-invasive functional brain image without recourse to the ground truth (which is almost never available). This is of direct relevance to all non-invasive brain imaging methods; but importantly provides an objective function to differentiate between functional assumptions made by different MEG/EEG inverse solutions, for any dataset. In simulation, where data were generated in accordance with MSP assumptions, we saw the power of the technique to differentiate between inversion algorithms. In contrast, for the real data example, the two algorithms had similar performance. Importantly, one could use this objective and non-invasive metric of distortion to refine M/EEG inversion assumptions. These refinements not only include the appropriate prior assumptions to reflect cortical current flow (sparse or distributed in MSP and MNM respectively), as illustrated here, but could also include geometry-defining parameters such as surface vertex spacing and volume conductor models  (Henson et al.
Acknowledgments The  Wellcome Trust   Centre for Neuroimaging  is funded by a strategic award from the  Wellcome Trust. Luzia Troebinger  is funded by the  J Jacob Astor Charitable Trust and Brain Research Trust. Matt Brookes  is supported by a  Leverhulme Trust Early Career Fellowship. Richard Henson  is supported by the  MRC  ( MC_US_A060_0046 ). This work is supported by an  MRC   UK MEG Partnership Grant ,  MR/K005464/1.
Ethics Statement Since 1992, an anonymized database compiles retrospectively and continuously Histoplasma capsulatum var. capsulatum histoplasmosis confirmed incident cases diagnosed in HIV-infected patients according to the case definition of the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/ MSG) Consensus Group  [12]. The revised EORTC/MSG criteria defining a proven case of histoplasmosis are: recovery in culture from a specimen obtained from the affected site or from blood; and/or histopathologic or direct microscopic demonstration of appropriate morphologic forms with a truly distinctive appearance characteristic such as intracellular yeasts forms in a phagocyte in a peripheral blood smear or in tissue macrophages.
Then, they were finally enrolled according to the following inclusion criteria: age. 18 years, admission in one of the three hospitals (the inclusion date corresponding to the date of antifungal treatment initiation), confirmed HIV infection (by Western blot), confirmed incident histoplasmosis infection (EORTC/MSG criteria), and baseline blood screening within 7 days prior to antifungal therapy initiation. Non inclusion criteria were: histoplasmosis relapse or diagnosis of histoplasmosis relying only on Histoplasma Polymerase Chain Reaction (PCR). Data were collected on a standardized form and included sociodemographic, clinical, biologic, radiologic, therapeutic and survival information. These data were then entered in an anonymized database. Ethical approval was obtained for the database and related studies (IRB0000388, FWA00005831).
Methods An observational, retrospective and multicentric study was conducted from 01/01/1992 to 09/30/2011, using the French Guiana HIV-Histoplasmosis database described above. In this study, the primary endpoint was the vital status on day 30 following antifungal therapy initiation. Patients lost to follow up within 30 days following antifungal therapy initiation, or deceased with an unknown date of death, or presenting a relapse of histoplasmosis were excluded from the analysis. This early death criterion appeared as a good compromise to attribute mortality to the histoplasmosis infectious episode under consideration, in a context of severe immunosuppression favouring multiple opportunistic pathogens, ensuring simplicity and reproducibility of the study. The statistical analysis was performed using STATA 10.
In addition, a PCR diagnostic method became available for histoplasmosis in 2006  [15]. Unfortunately, urinary antigen detection for histoplasmosis is still unavailable in French Guiana. The sharp decline of the proportion of early deaths can be attributed to the improvement of the diagnostic capacity along with the improvement of the clinical management of HIV-infected patients following French recommendations  [16]. Thus, French Guiana reached HIV-virological suppression levels comparable to those in Mainland France by 2004. In addition, this trend can also be attributed to the improvement of the clinical management of This study had limitations. Data were collected retrospectively, which might have led to selection biases. Determining retrospectively if death was related to AIDS-associated histoplasmosis incident cases under study is challenging, considering the high percentage of concomitant opportunistic infections.
Target selection Target stars for the spectroscopic observations were selected from the VVV catalogues. The catalogues contain aperture magnitudes for individual stars in the J, H, K s bands derived from the Cambridge Astronomical Survey Unit (CASU) pipeline, and have been complemented with 2MASS data  (Cutri et al. 2003)  for stars brighter than K s =12, where VVV images are saturated. Further details on the photometric catalogues can be found in  Gonzalez et al. (2011c) ;  Saito et al. (2012a). The goal of the programme was to collect spectra for representative samples of bulge field K giants spread over a grid, as regular as possible, across the bulge area covered by the VVV survey. However, starting from a regular position grid at b = -8, -6, -4, -2, +4 and l = -8, -4, 0, +4, +8, the actual center of each field (see Table  1 ) was fine-tuned on the extinction map derived by  Gonzalez et al.
Data Reduction Pipeline In this section we describe our full pipeline, including extraction and calibration of the spectra as well as the adopted procedure to obtain measurements of physical parameters from the reduced spectra. Only the radial velocitites are discussed in detail in this paper, while the analysis of the metallicity and individual elemental abundances will be discussed in forthcoming, dedicated papers  (Vásquez et al 2014 , Gonzalez et al. 2014, in preparation). The spectra were extracted and wavelength calibrated using the GIRAFFE pipeline maintained by ESO, which processes the spectra applying bias, flat-field correction, individual spectral extraction, and wavelength calibration based on daytime calibration frames. Since the pipeline does not perform sky subtraction, the correction was done using IRAF tasks.
Acknowledgements. SV and MZ acknowledge support by  Proyecto Fondecyt Regular 1110393 , by the  BASAL Center for Astrophysics and Associated Technologies   PFB-06 , the  FONDAP Center for Astrophysics 15010003 ,  Proyecto Anillo   ACT-86  and by the  Chilean Ministry for the Economy, Development, and Tourism's Programa Iniciativa Científica Milenio  through grant  P07-021 -F, awarded to The Milky Way Millennium Nucleus.
Aerosol extinction vertical profiles The Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) is an elastic-backscatter lidar on board the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO). CALIOP emits linearly polarized light at 532 and 1064 nm to provide vertically resolved observations of aerosols and clouds on a global scale  (Hunt et al. , 2009; Winker et al. , 2009). Aerosol extinction features at certain heights have being identified using CALIOP level 2 version 3. 01 extinction profiles at 532 nm over Tamanrasset (within a 1. 5 • radius) with a vertical resolution of 60 m (below 20. 2 km height) and a horizontal resolution of 5 km. Data from the period 2007-2008, downloaded from the NASA database (https://eosweb. larc. nasa. gov/cgi-bin/searchTool. cgi?Dataset=CAL_IIR_L1-Prov-V1-10), have been filtered following the methodology of  Tesche et al.