dataesr/scientific-paragraphs-categorization huggingface dataset:
3 (TBE) for 10 min. Electrophoresis was carried out at the rate of 1. 0 V/cm for 20 min. The slides were then washed in deionized water for 5 min. MACA on post-mitotic neurons was performed as described. 34 After electrophoresis, Comet slides were fixed with pre-chilled methanol, air dried overnight, stained with ethidium bromide (0. 1 mg/ml) for 10 min, and images acquired with an Eclipse E1000 Nikon fluorescence microscope equipped with a DMX1200F CCD camera. Comet images were processed with Comet Score software (v1. 5; TriTek Corporation, Sumerduck, VA, USA). Rapid approach to DNA adduct recovery. Post-mitotic neurons (D30) were incubated with or without 30 mM CPT for 1 h. Following treatment, part of the cells was immediately lysed, while the remaining washed with PBS and incubated in fresh medium for 3 h before lysis.
Acknowledgements. This work was financially supported by  Comitato Telethon Fondazione Onlus  (grant #  GGP10066  to DD) and by the  Italian Association for Cancer Research (AIRC)  (grant #  IG-10248  to DD). Dr. Carlessi Luigi  is recipient of a post-doctoral fellowships award from  Fondazione Umberto Veronesi. We wish to thank  Dr. Sherif El-Kamisy ,  Department of Molecular Biology and Biotechnology, Sheffield University, UK , for kindly providing the detailed MACA protocol, and  Dr. Christian Unger ,  Centre for Stem Cell Biology, Sheffield University, UK , for providing training (to DL) and expertise in the field of iPSCs, as well as reagents.
g. see  Bruderer et al. (2012) ,  Fedele et al. (2013b)  and  Podio et al. (2013). The broad instantaneous bandwidth of the Herschel SPIRE spectrometer, covering 10 consecutive CO lines of J up = 4-13, allows the first comprehensive study of the mid-J CO rotational ladder, providing important information about the gas excitation conditions between radii of typically several tens au and several hundreds au. This paper is organized as follows. Section 2 describes the SPIRE FTS observations and the data processing. Section 3 presents all spectral line detections and upper limits. The detected CO rotational ladders are analysed and compared with existing, detailed physical-chemical protoplanetary disc models in Section 4. Section 5 describes tentative trends in the data set and discusses detections and upper limits of species other than CO.
HERSCHEL S P I R E S P E C T RO S C O P I C O B S E RVAT I O N S A N D DATA P RO C E S S I N G A sample of 18 protoplanetary discs was observed with the SPIRE spectrometer  (Griffin et al. 2010 ) on board the Herschel Space Observatory  (Pilbratt et al. 2010)  in the context of two Guaranteed Time (GT) projects and one Open Time project. Table  2  outlines the observational details: 12 targets under GT1_golofs01_4, two in GT2_jbouwman_3 and four in OT1_kponto01_1. The execution time (and on-source integration time) for the targets studied in this paper from each of the three respective programmes was 12. 9 (12. 0) h, 1. 6 (1. 5) h and 9. 9 (9. 5) h. The observations span the spectral range between 450 GHz and 1540 , simultaneously observed in the two bands of the SPIRE Fourier Transform Spectrometer (FTS).
Lines originating from cold gas in individual circumstellar discs will be spectrally unresolved, given the instrumental resolution of 1. 2 GHz (ν/ ν ≈ 400-1300). The processed spectra of the two GT projects have been made available in electronic form through the 'user provided data products' section of the Herschel Science Archive. 1  The steps taken in the data processing are described in the remainder of this section. The raw data were processed with the SPIRE FTS 'point source' pipeline  (Fulton et al. 2010)  in version 11 of HIPE, the Herschel Interactive Processing Environment  (Ott 2010). A non-standard version of the pipeline was used for five specific observations   1 ), based on the mid-infrared dust SED shape  (Meeus et al. 2001)  (see Table  2 ), which included an empirical correction 2  of the SLW continuum shape for effects of an anomalously low cryocooler evaporator temperature (Hopwood, private communication; see also  Hopwood et al.
2013). The resulting data products contain the source spectra, observed with the central detectors of the two arrays, and spectra of the surrounding background emission observed with the remaining unvignetted detectors (16 for SSW and 6 for SLW). For the majority of our source sample, a contribution from diffuse, extended background emission is evident and results in an offset in flux density between spectra from the central detectors of SLW and SSW at frequencies where the two bands overlap (960-985 GHz). If the source spectrum is contaminated by emission from spatially extended components, the considerably larger and more complex SLW beam  (Makiwa et al. 2013 ) will pick up more power than the corresponding SSW detector in the same spectral range. To establish a representative spectrum for the background emission component, measurements from the off-centre detectors (first ring for SLW, second ring for SSW, both centred at ∼50 arcsec from the central position) are used.
Comparison with protoplanetary disc models In this paper, we do not aim to provide an exhaustive explanation of the observations using complex protoplanetary disc models. Instead, we present in this section a comparison of the new SPIRE data of three sources for which detailed chemical-physical models have been published in the literature. These models of the discs around HD 100546, HD 163296 and TW Hya are generated by the thermochemical protoplanetary disc model code PRODIMO  (Woitke, Kamp & Thi 2009; Kamp et al. 2010)  and are based on a large set of multiwavelength observational constraints. The spectral line energy distributions (SLED) for the first two of these targets are shown in Fig. 5. In any targets where the CO 23-22 is reported in PACS studies  (Meeus et al. 2013) , we regard this value as an upper limit (see Section 4.
Observed CO SLEDs of the two targets with at least three CO lines detected in the SPIRE bands, for which a PRODIMO model is also available (black crosses). In addition, for HD 100546 we also show in green plus symbols the model provided by Bruderer (private communication), calculated directly from the model as published in  Fedele et al. (2013b). Observed line detections are shown as (blue) squares, and 3σ upper limits are shown as triangles for lines that are either not detected or detected at ≤3 σ. Error bars represent the combination of line intensity errors (see Table  3  for SPIRE) and the absolute calibration uncertainty, 6 per cent for SPIRE, 30 per cent for PACS (see PACS Observers' Manual 2013, section 4. 10. 2). Data points with open markers are either ground-based (Appendix A), i.
From the collected data and models, we find the following. (i) The 12 CO SLED of the disc around Herbig Ae/Be star HD 100546 is optically thick across the SPIRE frequency range and is well matched, within a factor 3, by two completely independent model codes. (ii) The 13 CO line detections in our SPIRE spectrum of HD 100546 exceed the values predicted by the PRODIMO model by factors >10. It is not straightforward to adjust the model to scale to the 13 CO observations without compromising the match to the 12 CO counterpart. Isotope selective (photo)chemical processes may play a role, and should be investigated in more detail in numerical models. (iii) In the sample, composed of 12 Herbig Ae/Be objects and 6 T Tauri objects, the brightest mid-J CO emission is typically observed in discs around Herbig objects, specifically those with flaring disc geometries.
In contrast, there are also Herbig objects with little to no detectable line signal in our SPIRE observations. In addition, two of the six T Tauri discs do show significant CO line emission, although these detections are aided by the deeper integrations towards these targets. (iv) There may be a correlation between the cooling power through the [O I] 63 μm line and that of the CO rotational lines, but our collection of overlapping data points is too sparse to be definitive. (v) Besides the 12 CO and 13 CO lines, we tabulate for all 18 targets upper limits at the frequencies of CH + (J = 1-0) and of eight low-energy H 2 O transitions, to be used as constraints for future physical-chemical modelling. (vi) The SPIRE observation of HD 100546 reveals a detection of [C I] 3 P 2 -3 P 1 at 809 GHz (370 μm) that is inconsistent with a previous ground-based measurement with the APEX observatory  (Panić et al.
AC K N OW L E D G E M E N T S MHDvdW and DAN are supported by the Canadian Space Agency (CSA) and the Natural Sciences and Engineering Research Council of Canada (NSERC). IK, WFT and PW acknowledge funding from the European Union Seventh Framework Programme FP7-2011 under grant agreement no. 284405. SPIRE has been developed by a consortium of institutes led by Cardiff University (UK) and including Univ. Lethbridge (Canada); NAOC (China); CEA, LAM (France); IFSI, Univ. Padua (Italy); IAC (Spain); Stockholm Observatory (Sweden); Imperial College London, RAL, UCL-MSSL, UKATC, Univ. Sussex (UK); and Caltech, JPL, NHSC, Univ. Colorado (USA). This development has been supported by national funding agencies: CSA (Canada); NAOC (China); CEA, CNES, CNRS (France); ASI (Italy); MCINN (Spain); SNSB (Sweden); STFC, UKSA (UK); and NASA (USA).
We acknowledge Gibion Makiwa and Hugh Ramp for early data processing efforts and initial exploration of the GT1 data set, and Rosalind Hopwood for running the adjusted pipeline to process the five observations with low CEV temperatures. We thank Simon Bruderer for providing his model predictions for HD 100546 and for discussions on gas physics in discs, and Giambattista Aresu for discussions on UV and X-ray induced chemistry in discs. We warmly acknowledge the thoughtful review provided by the anonymous referee. This research has made use of NASA's Astrophysics Data System Bibliographic Services. This research made use of ASTROPY, a community-developed core PYTHON package for Astronomy (Astropy Collaboration 2013), and the matplotlib plotting library  (Hunter 2007).
app f ( app f x ) ) ) Reasoning about such representations requires a logic that can support arbitrarily nested implications and universal quantification, such as the logic of higher-order hereditary Harrop formulas (HOHH) [10, sec. 5. 2. 2] that forms the basis of λProlog and the Abella interactive theorem prover  [19, 5]. Such logics are generally presented in terms of sequents (or hypothetical judgments) of the form Γ ⊢ C where C is a formula and Γ is a context of formulas. As an illustration, suppose we wish to represent the following type-checking judgment that relates a λ-term to its type. In λProlog we write it using a relation of 1 with these program clauses. of ( app M N ) B ⇐ of M ( arr A B ) , of N A. of ( abs A R ) ( arr A B ) ⇐ p i λx. ( of x A ⇒ of ( R x ) B ). 1 Note: all relations have target type o, the type of λProlog formulas.
e. , two terms that may be rewritten to each other by αβη and a systematic permutation of their nominal constants are equated; 3  and • the nabla (∇) quantifier  [11]  and nominal abstraction  [7]  for reasoning about nominal constants. One particular inductive definition for a focused sequent calculus for HOHH is treated specially, with a notation using { } and tactics designed to leverage certain meta-theoretic properties of this definition  [19]. This inner specification logic is a fragment of the λProlog language, so Abella can be used to reason about λProlog specifications of object logics. Thus, Abella is an instance of the two-level logic approach to specification and reasoning  [8]. As a concrete illustration of the use of Abella, let us take the typing example from the previous section.
The type and kind declarations are placed in a signature (here, stlc. sig), and the clauses for the declared relations are placed in a corresponding module (here stlc. mod). The pair of. sig and. mod files can be directly executed in λProlog, such as using the tjcc compiler and tjsim interactive toplevel of the Teyjus implementation  [17]. Reasoning about a given specification (a signature/module pair) is done either interactively at the Abella toplevel or in a batch form using a. thm file (here, type_unique. thm). Figure  1  lists the contents of the signature, the module, and an initial portion of the reasoning file for a theorem stating that the types of λ-terms are uniquely determined by the of predicate. The theorem unique is proved by induction on the structure of the first HOHH derivation, viz.
where the <text> is arbitrary text that must not contain the token '!'. Abella will scan its list of known plugins for a plugin named Plug, which will then be asked to elaborate the <text> into either toplevel commands or core tactics, depending on where it was encountered. Plugins can be stateful: they can store and recall all the text that they have encountered in a single run of Abella. However, they are not allowed to modify any associated specification or reasoning files, nor the internal data structures of Abella's core. 4 ore precisely, every plugin is an OCaml module that ascribes to the following module type:.
Flow cytometry Surface staining for CD4 + T-cells was performed for 30 minutes at room temperature with antibodies to CD4 and HLA. A2 from BD Biosciences (San Jose, CA). All cells were fixed with 1% paraformaldehyde and at least 50,000 events acquired on an LSRII (BD Bioscience, San Jose, CA). Data analysis was performed with FlowJo 9. 4 software (Tree Star Inc. , Ashland, OR). THP-1 staining was performed with antibodies to CD14, CD83, HLA-DR from Biolegend (San Diego, CA) and CD80/ CD86 and CCR7 from BD Bioscience (San Jose, CA).
This work was supported by a  European Marie Curie fellowship  ( PIOF-GA-2011-300753 ) to BF and grants from the  European Research Council  ( ERC StG 240132 ) and  Agence Nationale de la Recherche  ( ANR-11-0001-02 PSL*  and  ANR-10-LABX-0087 ) to RB and from the  National Institute of Health  ( DC007690 ) to JLP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
In the full analysis set 452 out of 18,624 patients were unblinded for any reason prior to database lock (DBL). There was no imbalance between treatment arms. 238 (2. 6%) patients randomized to ticagrelor were unblinded by any reason prior to DBL, as compared to 214 (2. 3%) of the patients randomized to clopidogrel. In many of these cases unblinding did occur after patients had completed the randomized study period event free or after experiencing an event comprised by the primary endpoint. 155 (1. 7%) of the patients randomized to ticagrelor were unblinded while still contributing to the primary analysis, as compared to 118 (1. 3%) of those randomized to clopidogrel. The number of patients being unblinded prior to experiencing an event included in the primary endpoint was also similar between treatment arm, 13 on ticagrelor and 15 on clopidogrel.
Marciniak seems suspicious, neither he nor DSI found evidence of sponsor misbehaviour. Considering the effort Dr. Marciniak expended on review of individual cases, he found relatively few problems of any kind. As far as I can tell, data quality issues are not of great concern. " The IJC paper also accuses the PLATO trial for unfair reporting and analyses of myocardial infarction and present some tables on this issue based on data accumulated from a diversity of documents  [23]. These results are not in agreement with our recently presented analyses of myocardial infarction using the raw data sets from all individual PLATO patients (Mahaffey K et al, ACC Scientific Sessions, March 2013). The following is a summary of these results. "In the PLATO trial a central clinical events committee (CEC) prospectively defined and adjudicated all suspected MI events.
Treatment comparisons used CEC-adjudicated data and, per protocol, excluded silent MI. Overall, 1300 (611 ticagrelor, 689 clopidogrel) MIs reported by the CEC occurred during the trial. Of these, 1097 (504 ticagrelor, 593 clopidogrel) contributed to the primary composite endpoint. Site investigators reported 1198 (580 ticagrelor, 618 clopidogrel) MIs. Ticagrelor reduced overall 12-month Kaplan-Meier MI rates (5. 8% ticagrelor, 6. 9% clopidogrel; hazard ratio [HR]: 0. 84; 95% confidence interval [CI]: 0. 75-0. 95). Analyses of overall MI using site investigator reported data showed similar results HR: 0. 88; 95% CI: 0. 78-1. 00. " Thus, in contrast to what is stated in the IJC manuscript, ticagrelor significantly reduced the incidence of MI compared with clopidogrel, with consistent results both based on CEC evaluation and site reporting.
Given the severity of the accusations made, we would have expected the IJC editors to provide the PLATO authors an opportunity to review and respond to this manuscript before committing to its publication. As members of the cardiovascular scientific community, we support the notions of open access to analyses of data as one more way to assure validity of clinical trial information. The complete PLATO database is available at two independent academic institutions, which continuously perform and publish new analyses in peerreviewed major scientific journals based on requests from and collaboration between the PLATO investigators and involving also other investigators. Unfortunately the paper in IJC is an example of the dangers of open access to data when the peer review and editorial processes fail to do due diligence.
The twelve spectra were imported into the MALDI BioTyper software (version 2. 0, Brüker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 4,706 bacteria, including 1 spec-trum from N. lacusekhoensis, the only validly named Nesterenkonia species for which a spectrum was available in the BioTyper database. A score enabled the presumptive identification and discrimination of the tested species from those in a database: a score > 2 with a validated species enabled the identification at the species level; and a score < 1. 7 did not enable any identification. For strain NP1 T , no significant score was obtained, suggesting that our isolate was not a member of any known species (Figures  4  and 5 ).
Genome project history The organism was selected for sequencing on the basis of its phylogenetic position, 16S rDNA similarity and phenotypic differences with other members of the genus Nesterenkonia, and is part of a "culturomics" study aiming at isolating individually all bacterial species within the human gut flora  [1]. It was the third genome of a Nesterenkonia species and the first genome of N. massiliensis sp. nov. A summary of the project information is shown in Table  3. The Genbank accession number is CBLL000000000 and consists of 141 contigs. Table  3  shows the project information and its association with MIGS version 2. 0 compliance  [42].
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [54]  with default parameters but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database  [55]  and the Clusters of Orthol-ogous Groups (COG) databases using BLASTP. The tRNAScanSE tool  [56]  was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer  [57]  and BLASTn against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP  [58]  and TMHMM  [59]  respectively. ORFans were identified if their BLASTP E-value was lower than 1e -3 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an Evalue of 1e -5.
Such parameter thresholds have already been used in previous works to define ORFans. Artemis  [60]  and DNA Plotter  [61]  were used for data management and visualization of genomic features, respectively. The Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignment  [62]. To estimate the mean level of nucleotide sequence similarity at the genome level, we used the Average Genomic Identity Of gene Sequences (AGIOS) home-made software  [34]. Briefly, this software combines the Proteinortho software  [63]  for detecting orthologous proteins in pairwise comparisons of genomes, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm. As only one genome was available for the genus Nesterenkonia, we used genomes from closely related genera for the calculation of AGIOS values.
nov. that contains the strain NP1 T. The strain has been isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. Several other bacterial species were also cultivated from different fecal samples through diversification of culture conditions , thus suggesting that the human fecal flora of humans remains only partially known. The G+C content of the genome is 62. 47%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX424770 and CBLL00000000, respectively. The habitat of the microorganism is the human digestive tract. The type strain NP1 T (= CSUR P244 = DSM 26221) was isolated from the fecal flora of a 32-year-old French female suffering from AIDS.
Plant material and phenotypic trait data The plant material consisted of 73 wild (39 females and 34 males) and 39 hermaphrodite domesticated grapevines (Additional file 1). These grapevines were chosen among 139 wild genotypes and 2. 323 domesticated genotypes  [24]  to maximise both genetic diversity and geographic representation. Three genotypes from other species were also considered to represent genetic variation in the subgenus Vitis: V. balansaeana, V. coignetiae and V. monticola  [25]. The grapevines were sampled either in natural populations or from the French National Grapevine Germplasm Collection (INRA, Domaine de Vassal, France; http://www1. montpellier. inra. fr/vassal/). The genotypes considered varied according to the genetic analyses (Additional file 1). Sex phenotypes (male, female or hermaphrodite) were evaluated by observations of flower morphology repeated over several years, and coded according to the International Organization of Vine and Wine descriptors (code number OIV-151  [26] ).
Fisher tests were calculated with the fisher. test function of the R statistical software  [32]. We only considered sequence polymorphisms with less than 20% missing data and with a minimum allele frequency in the sample higher than 5%. A test was considered significant when the probability of deviation from the null hypothesis was inferior to a 0. 05 Pvalue threshold adjusted by a Bonferroni correction for multiple hypotheses testing (0. 05/n with n corresponding to the total number of studied polymorphisms).
Linkage disequilibrium in the sex region To explore linkage disequilibrium between and within amplicons covering the sex region, we used the Measure. R2VS() function in the R package LDcorSV  [33]. r 2 VS is the square of each pairwise correlation corrected by both the relatedness and genetic structure of the sample  [33]. The sample considered here was composed of 18 male and 18 female individuals (Additional file 1). These 36 specimens were chosen among those with the least missing data, eliminating the most closely related individuals and equilibrating their geographic representation. The genetic structure matrix was calculated from a dataset of 20 SSRs  [24]  of all the wild genotypes in this study, using STRUCTURE software  [34]. We used the model with uncorrelated allele frequencies, admixture, and no prior population information, previously showed to be pertinent in grapevine  [35].
Ten STRUCTURE runs (each with 5 × 10 5 iterations and 5 × 10 5 replicates) for each K-level were obtained and compared to estimate group assignation stability. The most probable number of sub-populations was inferred based on both the similarity pattern among the 10 STRUCTURE replicates and Evanno's Δks statistics  [36]. The kinship matrix was obtained using ML-Relate software  [37]  with the same SSR markers and genotypes as above.