dataesr/scientific-paragraphs-categorization huggingface dataset:
(XLSX) Database S7 A database of alternative ORFs in Caenorhabditis elegans. For each AltORF, the gene name and accession number of the mRNA in which it is encoded is provided in the first tab. Other information can also be found for both the reference ORF and the alternative ORF, including the reading frame and the coordinates of the start and stop codon (with respect to the first nucleotide of the mRNA). The predicted amino acid sequence of the alternative protein is also indicated. The second tab displays the results of alternative protein conservation analysis against human. The gene name and accession number for nematode and human homolog proteins are provided, as well as standard BLASTP output, and similarity percentage. (XLSX) Database S8 A database of alternative ORFs in Saccharomyces cerevisiae.
For each AltORF, the gene name and accession number of the mRNA in which it is encoded is provided in the first tab. Other information can also be found for both the reference ORF and the alternative ORF, including the reading frame and the coordinates of the start and stop codon (with respect to the first nucleotide of the mRNA). The predicted amino acid sequence of the alternative protein is also indicated. The second tab displays the results of alternative protein conservation analysis against human. The gene name and accession number for yeast and human homolog proteins are provided, as well as standard BLASTP output, and similarity percentage. (XLSX).
67 18. 4/19. 0 Urine b 47 (50) 754 (2,898) 5. 87 24. 9/15. 5 Plasma b 90 (96) 70 (92) 56. 25 34. 7/4. 9 Serum A b 311 (326) 192 (351) 61. 83 23. 4/3. 5 Serum B b 269 (293) 339 (847) 44. 24 28. 4/9. 7 Serum C b 158 (160) 279 (977) 36. 16 43. 1/8. 0 Serum D b 230 (248) 190 (365) 54. 76 N/A Serum total b 928 (1,002) 754 (2,066) 55. 17 N/A TOTAL 1,259 (1,525) 7,341 (85,311) 14. 64 N/A a Total identified proteins = alternative + reference proteins. b PeptideAtlas accession numbers associated with lung, cerebrospinal fluid, urine, plasma and serum samples are indicated in the Methods section. The Serum total line indicates the sum of distinct proteins detected in Serum A, B, C and D. doi:10. 1371/journal. pone. 0070698. t001 7. 6, and proteins alkylated in 50 mM iodoacetamide. Eight hundred mg of sample was migrated in 8 different lanes (100 mg per lane) of a 4212% Bis-Tris polyacrylamide NuPAGE Novex gel (Invitrogen), and stained with SimplyBlue Safestain (Invitrogen).
Two strategies of analysis were applied as shown in Figure  1  to compare the efficiency of Tute's six-colour approach  7  with that of our seven-colour approach. PC subset's clonality was considered for k/l ratios higher than 3 or lower than 0. 66. Account was taken of the presence of residual normal PCs, using the normal k/l ratio observed in the CD19 þ /CD28 À /CD56 À quadrant. Statistical analyses (Kolmogorov-Smirnov and Mann-Whitney) were carried out using Medcalc software (Mariakirke, Belgium). PC subsets were expressed as a percentage of total CD138 þ /CD38 þþ / À PCs. The partition of kand l-chains was assessed as percentages within each subset. Abnormal light-chain-restricted PCs were expressed as the percentage of total nucleated cells, taking into account all patterns of CD19/CD28/CD56 expression.
Data Collection. The standardized procedures of Lohman et al. [16]  were used to measure height with a Siber Hegner anthropometer (GMP instruments) and weight with a Tanita scale (model BC-418 MA); waist circumference was measured at the end of a normal expiration just above the iliac crest, using a nonelastic Holtain tape. Blood samples were collected after an overnight fast of at least 10 to 12 h. Glucose, TC, HDL, and TG were analyzed with an LDX point of care analyzer  [17]. This method has been previously validated against a laboratory reference method  [18] , and daily optical equipment checks were made according to manufacturer instructions. Resting systolic (SBP) and diastolic (DBP) blood pressures were measured with an Omron Model M6 (HEM-7001-E) device according to the International Protocol of the European Society of Hypertension  [19].
Results Table  1  presents the descriptive data for the sample. A total of 1,363 subjects from 515 families were included. The average family size was 2. 6 subjects. Correlations were derived from the following family combinations: 240 spousal, 216 fatheroffspring, 283 mother-offspring, and 208 sibling-sibling pairs. All traits were found to be highly heritable (Table  2 ) with estimates ranging from 0. 12 (GLU) to 0. 60 (WC). This means that there are strong additive genetic effects on the expression of these MetS trait that justifies further specific analysis of their genetic architecture. Table  3  shows the familial correlations and their 95% confidence intervals for each MetS trait. The absence of familial resemblance was rejected for each phenotype (all  < 10 -4 ), and different general family correlations were observed.
Acknowledgments This work was supported by the  FCT-Fundacão para a Ciência e Tecnologia  ( PTDC/DES/67569/2006 ,  FCOMP-01-0124-FEDEB-09608 , and  SFRH/BD/65290/2009 ). PTK is partially supported by the Louisiana Public Facilities Authority Endowed Chair in Nutrition. The authors thank the participants in The Healthy Family Study. The authors state that they have no conflict of interests. The guarantor is Daniel Santos.
The LHCb detector, dataset and analysis strategy The study reported here is based on pp collision data, corresponding to an integrated luminosity of 1. 0 fb -1 , collected at the Large Hadron Collider (LHC) with the LHCb detector  [11]  at a centre-of-mass energy of 7 TeV during 2011. The LHCb detector is a single-arm forward spectrometer covering the pseudorapidity range 2 < η < 5, designed for the study of particles containing b or c quarks. It includes a high precision tracking system consisting of a silicon-strip vertex detector (VELO) surrounding the pp interaction region, a large-area silicon-strip detector located upstream of a dipole magnet with a bending power of about 4 Tm, and three stations of silicon-strip detectors and straw drift tubes placed downstream. The combined tracking system has momentum resolution (∆p/p) that varies from 0.
A multivariate algorithm is used for the identification of secondary vertices consistent with the decay of a b-hadron. The strategy of the analysis is to measure a ratio of branching fractions in which most of the potentially large systematic uncertainties cancel. The decay B 0 → J/ψ (e + e -)K * 0 is used as normalization mode, since it has the same final state as the B 0 → K * 0 e + e - decay and has a well measured branching fraction  [13, 14] , approximately 300 times larger than B(B 0 → K * 0 e + e -) in the e + e -invariant mass range 30 to 1000 MeV/c 2. Selection efficiencies are determined using data whenever possible, otherwise simulation is used, with the events weighted to match the relevant distributions in data. The pp collisions are generated using Pythia 6. 4  [15]  with a specific LHCb configuration  [16].
Fitting procedure Since the signal resolution, type and rate of backgrounds depend on whether the hardware trigger was caused by a signal electron or by other activity in the event, the data sample is divided into two mutually exclusive categories: events triggered by an extra particle (e, γ, h, µ) excluding the four final state particles (called HWTIS, since they are triggered independently of the signal) and events for which one of the electrons from the B 0 decay satisfies the hardware electron trigger (HWElectron). Events satisfying both requirements (20%) are assigned to the HWTIS category. The numbers of reconstructed signal candidates are determined from unbinned maximum likelihood fits to their mass distributions separately for each trigger category. The mass distribution of each category is fitted to a sum of probability density functions (PDFs) modelling the different components.
1. When evaluated in the 30 to 1000 MeV/c 2 e + e -invariant mass interval using B(B 0 → K * 0 γ)  [1] [2] [3] , it predicts a B 0 → K * 0 e + e -branching fraction of 2. 35 × 10 -7. A full calculation has been recently performed  [28]  and the numerical result for the e + e -invariant mass interval of interest is (2. 43 +0. 66 -0. 47 ) × 10 -7. The consistency between the two values reflects the photon pole dominance. The result presented here is in good agreement with both predictions. Using the full LHCb data sample obtained in 2011 -2012 it will be possible to do an angular analysis. The measurement of the A 2 T parameter  [8]  thus obtained, is sensitive to the existence of right handed currents in the virtual loops in diagrams similar to those of Fig. 1. For this purpose, the analysis of the B 0 → K * 0 e + e -decay is complementary to that of the B 0 → K * 0 µ + µ -mode.
Manual Method Ventricular analysis was undertaken on an external workstation (Leonardo, Siemens Medical Solutions, Erlangen, Germany) equipped with a dedicated cardiac post-processing software (Argus, Syngo, Siemens Medical Solutions, Erlangen, Germany) that is routinely used for ventricular volume and function quantification. After manually tracing ventricular contours in a midventricular end-diastolic frame, the contours were propagated throughout the remaining slices imaged at ED. Once checked and corrected, the resulting contours were propagated from ED to ES. Each end-systolic contour was also checked and corrected if required. This segmentation can be considered manual in the sense that the final result was fully under the control of the user. Manual contour tracing of both ventricles was performed for each patient by the radiologist responsible for the study (MS) and, for all patients, segmentation was supervised by a physicist and a computer engineer (LRM and MC) with four years experience in cardiac MRI segmentation, and by a cardiologist (AM) with six years experience in cardiac MRI.
There is also an increasing demand for an accurate method to evaluate right ventricular volumes and function in acquired disorders: for example, the functional capacity of the RV offers important prognostic information in pulmonary hypertension  [16, [25] [26] [27]. Therefore, a quick reproducible and non-invasive method for the anatomical and functional assessment of the RV would be very useful from a clinical viewpoint. To overcome the aforementioned limitations, further improvements will be done in future studies. Particularly, our most immediate aim is now improving right ventricular segmentation. Recent studies suggested that by combining long-and short-axis sections in the dataset, the ventricular apex and the basal parts of the LV and, in particular, the RV, can be delineated with more certainty  [28].
Phylogenetic Analysis of L/F tRNA Transferases Homologous enzyme sequences were retrieved using BlastP  (Altschul et al. 1990 ) from nonredundant public databases. The amino acid sequences were aligned with Muscle  (Edgar 2004 ) and the phylogenetic relationships of selected proteins were reconstructed using MrBayes  (Huelsenbeck and Ronquist 2001). Graphical representations of the phylogenetic trees were obtained with FigTree (http://tree. bio. ed. ac. uk/soft ware/figtree/).
lividans 66 was deposited at DDBJ/EMBL/GenBank (BioProject id PRJNA168962, accession APVM00000000) and was used to perform whole-genome comparative analysis between closely related strains. These analyses lead to the discovery of 241 genes that are absent from S. lividans TK24, of which 136 genes are conserved between S. lividans 66 and S. coelicolor M145. Moreover, 367 genes are specific to S. lividans with respect to S. coelicolor (supplementary table  S2 , Supplementary Material online). Besides these differences, the syntenic regions between the three genomes have an average nucleotide identity of 99%. As discussed further, the vast amount of these genes is held within genomic islands.
Expression of SliGI-1 Metal-Related Genes in Response to Copper To corroborate the possible involvement of sliGI-1 in metal homeostasis the transcriptional response of S. lividans 66 under copper induction was assessed. For this analysis, we used RNAseq data that we have recently reported  (Dwarakanath et al. 2012). The data sets analyzed come from cultures of 66 that were induced after addition of Cu(II) at a concentration of 400 mM for 2 h during early log phase, and control cultures without added copper. After mapping, the available RNA reads against our S. lividans 66 genome sequence, something that could not be done previously due to the lack of a proper reference sequence, differential expression of 137 genes throughout the entire chromosome was confirmed (fold change ! 2, FDR corrected P value < 0.
3 ; see supplementary table  S4 , Supplementary Material online, for a detailed annotation of this biosynthetic gene cluster). Downstream of the NRPS gene, we identified a gene (SLI0883) encoding a leucyl/phenylalanyl tRNA protein transferase (SLI0884), which has 35% aa identity to the enzyme Aat (ECK0876) from Escherichia coli. This enzyme catalyzes the transfer of leucine or phenylalanine, from a charged aminoacyl-tRNA, to an N-terminal basic residue of a protein, usually an arginine, via the N-end rule protein degradation  pathway  (Leibowitz and Soffer 1969; Watanabe et al. 2007). Sequence searches in the database using SLI0884 as a query sequence, followed by phylogenetic reconstructions, showed the presence of two orthologs among streptomycetes. The second ortholog (GI ZP_19189297) was found next to an orthologous NRPS with similar domain organization in the genome of S.
ipomoea (Bioproject PRJNA183480). This suggests a recent recruitment within the context of NPs biosynthesis. The closest homologs outside Streptomyces could be found in Frankia species, although their gene context is not related to NPs biosynthesis, and thus a proteolytic role may be assumed. A similar scenario was encountered outside the Actinobacteria (fig. 4A ). Given that SLI0883 and SLI0884 are potentially transcriptionally coupled, and that a single A domain linked to PCP and R domains seem unlikely to be able to produce a peptide bond, we propose that the L/F tRNA transferase homolog present in SLP3 accounts for the lack of both A and C domains. Indeed, recent mechanistic data for the E. coli enzyme suggest an analogous condensation mechanism as found in ribosomes and C domains  (Fung et al.
Acknowledgments The work in FBG laboratory was supported by  Conacyt ,  Mexico  (No. 82319 ) and Langebio institutional funds. This work was supported by  CONACyT  graduate scholarships to P. C. -M. , F. I. -B. , and L. A. Y. -G. , and the  Dutch Technology Foundation (STW)  grant  10467  to G. G. and G. P. v. W.
5-532. 5 eV attributed to OH species  23. After etching for 10 min of the ZnO films, the OH radicals disappear and only one peak, corresponding to O-Zn bonds located at ,530. 5 eV, was observed  24. Figure  3  shows AFM images for samples with two different thicknesses. The ZnO film with t 5 10. 0 nm (Figure  3a ) shows an island structure, which is likely determined by the glass substrate  25  , whereas the films with thickness t 5 116. 0 nm have a homogeneous surface with a compact structure. The AFM images, Figure  3b  and 3c , reveal that the ZnO films with t 5 116. 0 nm have close packed nanograins with mean grain size of 30. 1 6 1. 3 nm. The grain size was determined using GWYDDION software on Figure  3  and was similar to the grain size determined by XRD, as shown in table 1. The surface roughness of these ZnO films was found to be between 2.
Methods Films preparation and characterization. Zinc oxide thin films of different thickness were synthesized onto glass substrates by DC reactive magnetron technique, using a pure metal target, in the presence of a argon/oxygen gas mixture. The flow rates were controlled with MKS flow-meters and the substrates were placed on a rotating substrate holder parallel to the zinc target with a separation distance of 50 mm. The working pressure was around 0. 3 Pa and the target power was controlled with a MDX Advanced Energy power supply. The sample thickness was measured 25 times using a DEKTAK 150 STYLUS profilometer and, with the data collected, we calculated the standard deviation and average value. A similar procedure was used to calculate the roughness (Root-Mean-Square). After deposition, the samples were annealed in ambient atmosphere at 170uC and 250uC during 1 hour in a MELTA furnace.
The analyzed data correspond to an integrated luminosity of 5. 2 ± 0. 1 fb -1  [39]. The K * 0 is reconstructed through its decay to K + π -and the B 0 is reconstructed by fitting the two identified muon tracks and the two hadron tracks to a common vertex. The values of A FB and F L are measured by fitting the distribution of events as a function of two angular variables: the angle between the positively charged muon and the B 0 in the dimuon rest frame, and the angle between the kaon and the B 0 in the K * 0 rest frame. All measurements are performed in q 2 bins from 1 to 19 GeV 2. The q 2 bins 8. 68 < q 2 < 10. 09 GeV 2 and 12. 90 < q 2 < 14. 18 GeV 2 , corresponding to the B 0 → K * 0 J/ψ and B 0 → K * 0 ψ decays (ψ indicates the ψ(2S) in what follows), respectively, are both used to validate the analysis, and the former is used to normalize the branching fraction measurement.
Reconstruction, event selection, and efficiency The signal (B 0 → K * 0 µ + µ -) and normalization/control samples (B 0 → K * 0 J/ψ and B 0 → K * 0 ψ ) were recorded with the same trigger, requiring two identified muons of opposite charge to form a vertex that is displaced from the pp collision region (beamspot). The beamspot position and size were continuously measured from Gaussian fits to reconstructed vertices as part of the online data quality monitoring. Five dimuon trigger configurations were used during 2011 data taking with increasingly stringent requirements to maintain an acceptable trigger rate as the instantaneous luminosity increased. For all triggers, the separation between the beamspot and the dimuon vertex in the transverse plane was required to be larger than three times the sum in quadrature of the distance uncertainty and the beamspot size.
This bias is less than half of the statistical uncertainty for all measurements. Discrepancies between the functions used in the PDF and the true distribution can also give rise to biases. To evaluate this effect, a MC simulation sample similar in size and composition to the analyzed data set is fit using the PDF of Eq. (  2 ). The differences between the fitted values and the true values are taken as the systematic uncertainties associated with the fit ingredients. Mistagging a B 0 as a B 0 (and vice versa) worsens the measured B 0 mass resolution. A comparison of resolutions for data and MC simulations (varying the mistag rates in the simulation) indicates the mistag rate may be as high as 12%, compared to the value of 8% determined from simulation. The systematic uncertainty in the mistag rate is obtained from the difference in the final measurements when these two values are used.
Acknowledgements We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centres and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWF  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES (Croatia) ;  RPF (Cyprus) ;  MoER ,  SF0690030s09  and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NKTH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  NRF  and  WCU (Republic of Korea) ;  LAS (Lithuania) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  NSC (Taipei) ;  ThEPCenter, IPST, STAR  and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
Other information about the study design and major reasons for hospitalizations of the enrolled controls are provided in detail elsewhere  (Dar et al, 2012). This study was reviewed and approved by the Institutional Ethics Committee of SKIMS. Data collection. Structured questionnaires were administered in face-to-face interviews at hospitals by trained interviewers who were able to speak in participants' primary language. A limited number of staff conducted the interviews and no proxies were used. Detailed information on demographic characteristics, habits, including lifelong history of use of alcohol and several tobacco products, and intake of fresh fruits and vegetables, was collected. Ever use of alcohol and tobacco products was defined as the use of the respective product at least weekly for a period of 6 months or more.
To assess the socioeconomic status (SES), we built a composite score for wealth, based on appliances ownership and other variables by using multiple correspondence analysis  (Islami et al, 2009). This score had shown some association with ESCC risk in this population independent of education level  (Dar et al, 2013). The detailed information about consumption of the various fruits and vegetables was collected using a semi-quantitative food frequency questionnaire. We asked about the usual frequency of use in a day, week, or month and the amount of use in each instance. Using this information, we calculated the intake of each fruit and vegetable in grams per day. In order to cover the intake of seasonal fruits/vegetables, we also collected data on the number of months in which any of these food items had been consumed: the daily intake in these cases was multiplied by the number of months of consumption and divided by 12.
Statistical analysis. In categorizing the continuous variables, we attempted to have equal number of controls in each category of respective variables. Fruit and vegetable intake data (grams per day) were transformed to logarithmic values following addition of 0. 1 to original values. Conditional logistic regression was used to calculate unadjusted and adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs). All statistical analysis was done using Stata software, version 11 (Stata Corp. , College Station, TX, USA). Two-sided Po0. 05 were considered statistically significant.
ACKNOWLEDGEMENTS This study was supported by  Extramural grant of Indian Council of Medical Research (ICMR), New Delhi , under IRIS  ID 5/13/37/ 2007/-NCD-III. NAD was supported by a fellowship ( American Cancer Society  international fellowships for beginning investigators (ACSBI)) from the  Union for International Cancer Control (UICC). This work is published under the standard license to publish agreement. After 12 months the work will become freely available and the license terms will switch to a Creative Commons Attribution-NonCommercial-Share Alike 3. 0 Unported License.