dataesr/scientific-paragraphs-categorization huggingface dataset:
A general strategy was implemented to handle positional ambiguity for indels of any size. Transcript reconstruction. Transcript assembly was conducted with Cufflinks version 2. 0. 2. The option library-type was set to fr-firststrand for the K562 data, which are strand specific, and to fr-unstranded for the simulated data, which are not. Default values were used for other parameters. Cufflinks requires spliced alignments to have a SAM format tag (XS) indicating the genomic strand (plus or minus) on which the transcript represented by the read is likely to be encoded. Alignment programs such as TopHat can set the XS tag by using information about the library construction protocol (for strandspecific libraries) or by inspecting sequence at exon-intron boundaries. Five of the methods evaluated here (BAGET, GEM, ReadsMap, SMALT and STAR) did not provide XS tags; we therefore post-processed the alignment output from these methods to add them.
For the strand-specific K562 data, XS tags were set on the basis of alignment orientation and read number (first or second in pair), as done by TopHat. For alignments of simulated reads, we set XS tags according to the initial and terminal dinucleotides of the inferred introns, which are expected to be GT/AG, GC/AG or AT/AC for plus-strand transcripts and CT/AC, CT/GC or GT/AT for minus-strand transcripts  24. For the XS tag to be added to an alignment, at least one exon junction was required to have these signals, and conflicting signals among junctions were not allowed. We noted that the annotation-based TopHat2 protocol uses the annotation provided to set the XS tag for unspliced alignments that overlap annotated exons. As this is a unique feature of TopHat2 that might confer an advantage in the evaluation of transcript reconstruction, we investigated the effect of removing the XS tag from unspliced alignments in the TopHat2 output before running Cufflinks.
This modification had a negligible effect on the Cufflinks accuracy metrics presented here (data not shown), demonstrating that provision of XS tags for unspliced alignments cannot explain why the annotation-based TopHat2 protocol resulted in better Cufflinks performance than other protocols. For K562 data, exon precision was defined as the fraction of predicted exons matching GENCODE annotation, and exon recall as the fraction of annotated exons that were predicted. Only exons from protein-coding genes were considered when computing recall, as some noncoding RNA classes are likely to be underrepresented in the RNA-seq libraries. Results on simulated data were benchmarked against simulated gene models, using analogous definitions of precision and recall, such that exon precision measures the proportion of predicted exons matching an exon in the simulated transcriptome, and transcript precision is the fraction of predicted spliced transcripts matching a simulated spliced transcript.
To stratify recall by expression, we divided simulated transcripts into three groups of equal size according to expression level (Fig. 6b ). Internal exons were required to be recovered with exact boundaries, first and terminal exons were required to have correctly predicted internal borders only, and exons constituting unspliced transcripts were scored as correct if covered to at least 60% by a predicted unspliced transcript. For the simulated data, only exons of spliced transcripts were required to be placed on the correct strand, as the orientation of single-exon transcripts cannot be reliably predicted unless RNA-seq libraries are strand specific. Spliced transcripts were considered to be correctly assembled if the strand and all exon junctions matched. Program availability. Source code for the evaluations performed in this study can be obtained from https://github.
ACknoWledgments This work was supported by the  European Molecular Biology Laboratory, US National Institutes of Health/NHGRI  grants  U54HG004555  and  U54HG004557 ,  Wellcome Trust  grant  WT09805 , and grants  BIO2011-26205  and  CSD2007-00050  from the  Ministerio de Educación y Ciencia. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3. 0 Unported License. To view a copy of this license, visit http://creativecommons. org/licenses/by-nc-sa/3. 0/.
There are few native annual grasses in these systems  [57]. The phylogenetic groupings were as follows (annual/perennial): Brome (Bromus hordeaceus/Bromus carinatus), Oat (Avena fatua/Koeleria macrantha), and Rye (Taeniatherum caput-medusae/Elymus glaucus). Note that K. macrantha is referred to by its synonym K. cristata by Borer et al. [40]  in their related analysis of data from this experiment. Seeds of each species were collected at each site or from as nearby as possible. Hosts were pre-germinated in 25625 mm soil plugs in greenhouses at Oregon State University, Corvallis, Oregon and transplanted to each site in January 2008, prior to the first aphid flight. One individual of each species was planted within a series of 20-30 quadrats (20650 cm) arrayed along transects within each experimental plot.
This conservative approach did not affect the overall prevalence estimates but may have somewhat reduced our estimate of coinfection by serologically related viruses. Note that we were only able to assay about half of the hosts for BYDV-SGV (2,320 hosts) due to a lack of antibody. We conducted analyses on both subsets of the data (5,095 hosts with 4 viruses and 2,320 hosts with 5 viruses). As results are qualitatively similar, we present the results with the full suite of viruses but fewer individual hosts. We collected data on plant biomass and community composition at two locations along transects in each of the 40640 m plots. We estimated total plant biomass in each plot by clipping all aboveground plant material in two 0. 161 m strips, sorting it into categories (previous year's dead material and current year's grass, forb, legume, woody, bryophyte growth), drying it to constant mass at 60uC, and weighing it to the nearest 0.
01 g. We estimated areal cover of all species in an adjacent 0. 561 m quadrat. Cover of each species was estimated independently, so that total summed cover exceeds 100% in quadrats with multilayer canopies. Laboratory aphid experiments. We use aphid fecundity and preference data from two experiments published by Borer et al. [58]  to explain prevalence differences among host species: Preferential herbivory and Greenhouse multivector fecundity (Experiments III and IV in  Borer et al. 2009a ). In the Preferential-herbivory experiment 30 aphids (R. padi) were placed in the center of 3. 78 l L pots in which one individual of 10 different host species (including our six focal species) were planted around the pot perimeter. Aphids were counted on all plants after 24 hours and, because plants of the same age differed in size, counts were calculated on a per gram of host tissue basis.
Acknowledgments The work presented here would not have been possible without the support of many people and organizations. Marty Dekkers ,  Burl Martin ,  Emily Orling , and  Jasmine Peters  were responsible for much of the data collection. Vincent Adams performed the aphid feeding preference trials. We also acknowledge the generous support of the staff of the  University of California Reserve System (McLaughlin Natural Reserve), University of California Research and Extension Centers (Hopland REC  and  Sierra Foothill REC) , and the  U. S. Fish and Wildlife Service (Baskett Slough and William L. Finley National Wildlife Refuges ).
Samples were viewed and analysed using a Zeiss Axioplan 2 microscope equipped with an AxioCam C camera and Axiovision software or using a Zeiss LSM 510 confocal microscope equipped with LSM 510 imaging software (v4. 2). Images were formatted, resized, enhanced by brightness and contrast, and arranged using Axiovision or Imaris software (v7. 4, Bitplane Scientific Software AG, Zu ¨rich, Switzerland) and Adobe Photoshop CS4.
Cell Counts Cell counts were based on 4 different animals if otherwise is not stated. Minimum 4 sections from each animal were counted. All eyes were oriented based on the pecten and sectioned identically. For all stage-specific cell counting, only the central part of the retina was analysed to avoid bias imposed by the temporal and centroperipherial aspects of retinal development. When counting ventricular (apical) and vitreal (basal) cells the retina was divided in 3 areas and the inner third was considered as basal. The mean (+/2 SD) for each combination of labelling and stage was calculated and the data were analysed and presented in GraphPad Prism (v3. 02, GraphPad software Inc. ). Statistical analysis; Analysis of variance (one-way ANOVA) followed by Tukey's multiple comparison post-hoc test and p-values,0.
Measurement of Lim1+ Nuclei Volumes The nucleus volume of st42 Lim1+ HCs was determined using immunohistochemistry, confocal microscopy and 3D analysis. Z-stacks projections were used to generate 3D models of the HC layer. Lim1 staining was used to generate an iso surface by use of the Imaris software, Vantage module and the volume of the Lim1+ nuclei was calculated using default value settings.
Determination of the Sex of the Embryos The sex of the embryos was determined by analysing the expression of W-linked protein kinase C inhibitor-8 (WPKCI-8) mRNA by using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) as described in  [26, 27]. Briefly, complementary DNA was made from total RNA and two-step qPCR were performed using the iQ SYBR Green supermix (Bio-Rad Laboratories, Inc. , CA, USA) and MyiQ Single-Colour Real-Time PCR Detection System (Bio-Rad Laboratories, Inc. ). Primers were designed with Primer Express 1. 5 (Applied Biosystems, Carlsbad, CA, USA) software; WPKCI-8 mRNA identifier AB026677. 1; forward primer AGATTGTGGCG-CACCTCTTC, reverse primer CACTTCTCGCCAACAAT-CATCA. Male tissue does not express the gene.
4A , grey arrow heads, more than 200 cells inspected, n = 4). The same analysis was performed at st27 with similar results. The results were consistent with the hypothesis that a proportion of the Lim1+ cells are post-mitotic. Next we analysed the expression of p27Kip1. The Lim1 and p27Kip1 antibodies are both made in mouse and we had to use a rabbit Prox1-antibody as a marker for HCs. The transcription factor Prox1 is expressed in differentiating Lim1+ HCs  [31, 39]. We analysed st24 retinas 3 h after EdU injection and triple-stained for Prox1, EdU and p27Kip1. The result showed that most of the p27Kip1+ cells were located on the basal side of the retina and those cells were Prox1, EdU double-negative post-mitotic retinal ganglion cells (data supported by ganglion cell specific markers and not shown).
For the initial Rab6B Q72L screen, the coding sequence of Rab6B Q72L was cloned into pLex9 as a C-terminal fusion to LexA. The construct was used as bait to screen at saturation a highly complex, random-primed human placenta cDNA library constructed into the plasmid pP6. pLex9 and pP6 derive from the original pBTM116  [44]  and pGADGH  [45]  plasmids, respectively. More than 130 million clones (13-fold the complexity of the library) were screened, using a mating with the Y187 (MATa) and L40DGal4 (MATa) yeast strains as previously described  [46]. Positive colonies were selected on a medium lacking tryptophan, leucine and histidine supplemented with 5 mM 3-aminotriazole. The prey fragments of the positive clones were amplified by PCR and sequenced at their 59 and 39 junctions. The resulting sequences were used to identify the corresponding interacting proteins in the GenBank database (NCBI) using a fully automated procedure.
The cells were permeabilized for 10 minutes at room temperature in 0,1% NP40 in PBS and blocked for 1 hour in 5% goat serum in PBS. The primary antibody GM130 (cis-Golgi marker, BD-Bioscience) was added 1:200 overnight in 1% goat serum in PBS at 4uC. The following day, the secondary antibody Alexa-Flour 647 (Molecular Probes, Invitrogen, Karlsruhe, Germany) was added 1:500 in PBS and 1% goat serum for one hour at room temperature and cells were embedded in Mowiol. GFP Mint1 826 was visualized via reflector 488 and APP-RFP via reflector 568. Z-stack imaging was performed with the fluorescence microscope Axio observer Z. 1 from Zeiss with the software Axiovision 4. 8. 1 and analysis followed via ImageJ. Co-localization studies between Mint1 826, APP and GM130 have been performed in primary mouse neurons, additionally.
Mint1 826 is Expressed Endogenously on mRNA and Protein Level Due to the lack of an antibody able to discriminate between Mint1 826 and Mint1, finding evidence for Mint1 826 via standard Western blot analyses was not possible. We therefore set out to show that Mint1 826 is a transcribed gene by detection of the specific mRNA sequence. During a search of the EST database we identified an EST clone (BE937843. 1) that corre-  After co-transformation, Y190 strains were cultivated in synthetic media lacking leucine, tryptophan and histidine, supplemented with 30 mM 3 AT (his3). bgalactosidase reporter gene activity was determined on replica filters using Xgal as substrate (b-gal). Mint1 (NM_001163. 3) was tested against the constitutively active or inactive variant of either Rab6A or Rab6B. -no growth on selection media or staining in b-galactosidase filter assay.
The cDNA was tested using the Mint1 826 specific primer. A distinct signal was detected in murine and human brain as well as in human testis samples. Together these data indicate that the endogenous human and murine Mint1 826 is predominantly transcribed in brain and testis (Figure  4 ). Additionally, we tested the mentioned libraries and tissue samples for the existence of the conventional Mint1. Surprisingly, it was found in all samples that also contained Mint1 826, although it has been described as being transcribed and expressed neuron-specific  [33]  (Figure  4B ). The fact that the conventional Mint1 was found in all samples that also contained Mint1 826, strengthens the fact that Mint1 826 is not a product of accidental exon-skipping processes, neither in tissues nor in cell cultures.
Acknowledgments The authors would like to thank  Lutz Haalck ,  Luminartes, Muenster, Germany  for conjugating the Rab6A antibody with OY 594,  Simone Back ,  University Kaiserslautern, Germany  for her assistance for preparation and imaging of primary mouse neurons,  Dieter Gallwitz ,  Max Planck Institute for Biophysical Chemistry, Goettingen, Germany  for providing us with the YTH control plasmids and  Jean Paul Borg ,  Marseille University, France  for the pACT Mint1 plasmid. We thank  Mechthild Rosing  for technical assistance,  Joachim Kremerskothen  for total RNA isolation,  Sabine Kliesch ,  University Hospital Muenster, Germany  for providing us with the testis samples,  Sascha Gromnitza  for initial experiments on the Mint1/ Mint1 826 localization,  Carsten Schmidt ,  ZMNH, Hamburg, Germany  for providing us with the APP695 cDNA,  Toshiaki Koda ,  Hokkaido University, Sapporo, Japan  for providing us with the pAS Rab33 plasmids and  Ulrike Mu ¨ller ,  University Heidelberg, Germany  for sending us the MEF dKO APP695 cells.
036 ± 0. 002 rad  [5]. The LHCb collaboration recently measured the weak phase in this decay to be 0. 068 ± 0. 091(stat) ± 0. 011(syst) rad  [6] , which is consistent with the SM and places stringent constraints on CP violation in B 0 s -B 0 s oscillations  [7]. In the SM, the phase in the B 0 s → φφ decay, φ s , is expected to be close to zero due to a cancellation of the phases arising from B 0 s -B 0 s oscillations and decay  [8]. Calculations using QCD factorization provide an upper limit of 0. 02 rad for |φ s |  [1] [2] [3]. In this Letter, we present the first measurement of the CP -violating phase in B 0 s → φφ decays. Charge conjugate states are implied. The result is based on pp collision data corresponding to an integrated luminosity of 1. 0 fb -1 and collected by the LHCb experiment in 2011 at a centre-of-mass energy of 7 TeV.
In the software trigger, B 0 s → φφ candidates are selected either by identifying events containing a pair of oppositely charged kaons with an invariant mass close to that of the φ meson or by using a topological b-hadron trigger. In the simulation, pp collisions are generated using Pythia 6. 4  [12] , with a specific LHCb configuration  [13]. Decays of hadronic particles are described by EvtGen  [14]  and the detector response is implemented using the Geant4 toolkit  [15]  as described in Ref. [16]. The B 0 s → φφ decays are reconstructed by combining two φ meson candidates that decay into the K + K -final state. Kaon candidates are required to have p T > 0. 5 GeV/c, and an impact parameter (IP) χ 2 larger than 16 with respect to the primary vertex (PV), where the IP χ 2 is defined as the difference between the χ 2 of the PV reconstructed with and without the considered track.
Data variables Data variables were collected between July and August 2012 in relation to the three objectives of the study into a structured proforma by the primary investigator (TJ) assisted by fi ve staff members from the Ministry of Health. Three teams, comprising two members each, were trained over one day and travelled to the three assigned regions for data collection (this included 30 of the 32 TB Registration Units, because two were not yet fully functional in 2010). Data variables were collected as follows: 1) the number of TB and EPTB patients registered between 2001 and 2010 was obtained from annual health bulletins held in the Health Management and Information System (HMIS) and TB reports from the NTCP; and 2) data on EPTB patients were collected from the TB patient registers and TB treatment cards at each of the TB Registration Units.
Data entry, analysis and statistics The data in the structured proforma were extracted and double-entered into the electronic database EpiData, version 3. 1 (EpiData Association, Odense, Denmark), and validated for data verifi cation. The analysis was performed using the statistical package STATA version 11. 1 (Stata Corporation, College Station, TX, USA). Categorical variables were analysed using the χ 2 test, with differences at 5% accepted as statistically significant. Odds ratios (OR), their 95% confi dence intervals (CI) and P values were calculated as appropriate.
After 1 h in the dark at 4uC, the slides were immersed in freshly prepared alkaline electrophoresis buffer (300 mM NaOH, 200 mM Na 2 -EDTA, pH 13) for unwinding (25 min) and then electrophorezed (25 V/300 mA, 25 min). All the steps were carried out under minimal illumination. Once electrophoresis was completed, slides were neutralized (365 min, 0. 4 M Tris, pH 7. 5). The dried microscope slides were stained with 20 mg. l 21 ethidium bromide (50 ml per slide) and covered with a cover-glass. Tail DNA was assessed under fluorescence microscopy using the Comet Analysis Software 4. 0 (Kinetic Imaging Ltd. , Liverpool, UK). Fifty randomly selected cells per slide were analyzed for each triplicate condition.
8-s relaxation delay and the 100-ms mixing time of the sequence. The spectral width was 12 ppm with 16K complex data points and 32 transients. This resulted in 2:50 min acquisition duration. After Fourier transformation, low order phase correction and baseline spline correction were applied in a standardized way. Signal attribution in spectra was done as previously described  [27, 28]. Quantification of one-dimensional (1D) NMR spectra was performed using the Topspin 2. 0 software (Bruker Biospin, Karlsruhe, Germany). A two-dimensional (2D) NMR spectrum was recorded immediately after the 1D NMR spectrum, using a Total Correlation Spectroscopy (TOCSY) sequence involving water signal suppression at low power, 6-ppm spectral bandwidth along both frequency axes, 256 samples along the first axis, and 2K samples along the second axis, 75-ms mixing time during which was applied the spin-lock pulse train (DIPSI-2), 1-s relaxation delay, and 16 repetitions.
l 21 , respectively). The variable importance in the projection (VIP) was calculated for each metabolite. Criteria of quality of modeling were R2X, the cumulative modeled variation in metabolite data, R2Y, the cumulative modeled variation in class values, and Q2, the cumulative predicted variation in metabolite data according to cross-validation. These parameters range between 0 and 1, where 1 indicates a perfect fit. The highest values of VIP identified metabolites that complied best with the tested model. Multivariate statistical analyses were performed using the XLSTAT 7. 5 software (Addinsoft, Paris, France).
33 mg grape extract/PCB per capsule) were to be taken daily: three during breakfast and three at dinner. Evaluation of compliance ($80% of the capsules taken) was done before starting the tests by counting the number of returned capsules after 4, 8, and 9 weeks from baseline. Volunteers were instructed to avoid polyphenol-rich foods and to follow a balanced, isoenergetic diet, which was controlled by a food diary during the 3-day period preceding each test and assessed with GENI software (Micro 6, Villers-les-Nancy, France). Intake of dietary polyphenols was further evaluated using phenol explorer (version 1. 5. 7; INRA, Clermont-Ferrand). Subjects were advised to avoid vigorous physical activity during the 6 days preceding each test.
AcknowledgmentsdThis study was funded by the  French National Research Agency Agence Nationale de la Recherche  (Poly-OxResist-2007- A01375-48 ). No potential conflicts of interest relevant to this article were reported. The authors thank the two major distilleries of the  Languedoc-Roussillon area, Société Française de Distilleries  and  GRAP'SUD , for provision of the grape extracts. M. H. , E. B. , H. V. , K. L. , M. L. , and A. A. researched data, contributed to discussion, and reviewed, edited, and wrote the manuscript. E. M. researched data. C. F. -C. and C. C. contributed to discussion and reviewed and edited the manuscript. S. P. , C. L. , S. L. -P. , V. S. , C. F. , J. -F. B. , and J. R. researched data. C. B. , A. S. , J. M. , J. G. , A. -M. D. , and J. -P. C. contributed to discussion and reviewed and edited the manuscript.
Methods The KABP 2010 survey, approved by the National Data Protection Authority, was carried out anonymously over the telephone after oral consent for participation in the study  [18]. Selection of the individual to be interviewed was carried out by random sampling in two phases: after a random generation of two samples of telephone numbersone landline, the other mobile -one individual was randomly drawn from all the eligible people in that household (landline) or from all the eligible principal users of that phone number, if there was more than one user (mobile). All persons who could speak French, were aged between 18 and 69 and resident in metropolitan France were eligible. In order to take into account the probability of being selected and to keep the structure similar to that of the national population, the sample was first weighted for numbers of eligible adults in households and for the distribution of listed and unlisted landline and mobile phones.
It was then adjusted for sociodemographic data gathered in the 2006 national census. The data collected for hepatitis B, just as those collected for HIV/AIDS, focused on the interviewed person's knowledge of transmission modes, perceptions and fears regarding these infections, knowledge of someone in his/her circle of family or friends being infected by HBV or HIV, and whether he/she had been screened for HBV or HIV or vaccinated against HBV. These indicators reflecting knowledge, perceptions and practices regarding HBV were compared with those for HIV. Furthermore the following indicators were examined in multivariate analysis using logistic regression: "having a good level of knowledge on the transmission modes of HBV", "considering oneself to be at a higher risk of HBV contamination with respect to the average person", "selfreported screening for HBV during one's lifetime", and "self-reported vaccination against HBV during one's lifetime".