dataesr/scientific-paragraphs-categorization huggingface dataset:
Summary A search has been made for long-lived particles that have stopped in the CMS detector after being produced in 8 TeV pp collisions at the CERN LHC. The subsequent decay of these particles was looked for during gaps between proton bunches in the LHC beams. In a data set with a peak instantaneous luminosity of 7. 5 × 10 33 cm -2 s -1 , an integrated luminosity of 18. 6 fb -1 , and a search interval corresponding to 281 hours of trigger livetime, no excess above background is observed. Limits are presented at 95% CL on gluino and top squark production over 13 orders of magnitude in the mean proper lifetime of the stopped particle. Assuming a cloud model of R-hadron interactions, for E g > 120 GeV, and B( g → g χ 0 ) = 100%, gluinos with lifetimes from 1 µs to 1000 s and m g < 880 GeV are excluded.
Acknowledgments 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 centers 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:  BMWFW  and  FWF (Austria) ;  FNRS  and.
Current refinement programs treat elements of the TLS matrices as independent variables with a constraint on the trace of the matrix S [tr(S); as discussed in x4] and postrefinement enforcement that the resulting U group,n be nonnegative definite  (Winn et al. , 2001). As demonstrated below, enforcing U group,n to be non-negative definite is not sufficient to guarantee that the refined TLS matrices are still consistent with an underlying physical model of concerted motion. Previously,  Zucker et al. (2010)  analyzed all PDB entries containing TLS descriptions and suggested tools to validate the TLS parameters. However, this analysis focused exclusively on the ADP smoothness between neighbouring TLS groups. Failure to enforce all conditions on the individual components of U group,n , i. e. on the TLS matrices, may result in matrices that invalidate the TLS model.
Summary of the presented work In this article, we address the following points. (i) We describe an algorithm (Fig. 1 ) that interprets the TLS matrices in terms of parameters of the corresponding motions. This includes the direction of the principal axes of vibration and libration, the corresponding root-mean-square displace- Number of PDB entries in which at least one of the physical conditions on TLS matrices is broken. The statistics are shown for the matrices in the PDB (25 904 entries with TLS matrices from a total number of 106 761 entries as of March 2015) with the default condition tr(S) = 0 (upper line) and with the optimal choice of the diagonal S elements whenever possible as described in xx3 and 4 (bottom line). The conditions are, from left to right: matrices T and L are positive semidefinite (T ! 0 and L ! 0); an absence of libration around one of the axes requires the corresponding elements of the S matrix to be equal to 0 (s = 0 and w = 0); matrix T is positive semidefinite after the contribution owing to the displacement of libration axes is removed (T C ! 0); elements of the S matrix are limited by the corresponding elements of the T and L matrices according to the Cauchy conditions (S TL); the residual V matrix is positive semidefinite (V ! 0).
We also made two end-user applications available in the PHENIX suite  (Adams et al. , 2010) : phenix. tls_analysis for the analysis and validation of refined TLS matrices and their underlying motions and phenix. tls_as_xyz for generating ensembles of structures consistent with TLS matrices. (v) We applied these programs to all PDB entries containing TLS matrices. We discovered that the majority of these matrices cannot describe motions. In a number of cases a marginal modification of the TLS matrices can correct the errors. (vi) We used phenix. tls_as_xyz to generate a predicted structural ensemble for the calculation of X-ray diffuse scattering from the glycerophosphodiesterase GpdQ  (Van Benschoten et al. , 2015).
Survey of available TLS matrices in the PDB We have analyzed all available TLS matrices in the PDB. From an overall 106 761 entries (as of March 2015), 25 904 use TLS modelling. More than 20 000 of these entries have several TLS groups, resulting in a total of 203 261 sets of TLS matrices (Fig. 2a ), with the largest number of groups per entry being 283 (PDB entry 3u8m;  Rohde et al. , 2012). About a third of these sets have negative eigenvalues for the deposited T or L matrices. Some of these values are only slightly negative (Figs. 2b  and 2c ) and can be considered to be rounding errors, while the worst values are as small as À0. 28 rad 2 for L and À20. 72 A ˚2 for T. For 11 412 T matrices and 138 L matrices all three eigenvalues are negative. Another third of the TLS groups cannot be interpreted by elemental motions owing to other reasons, as described in xx3 and 4 (Table  1 ).
After an initial screen to find the positive definite T and L matrices, we then ran a search for the elemental motions in two modes. Firstly, we tried to decompose the TLS matrices as taken directly from the PDB files. As expected, the average value of tr(S) is 3 Â 10 À5 A ˚(i. e. practically zero) and the corresponding r. m. s. d. is = 10 À2 A ˚. About 120 000 S matrices have |tr(S)| < 10 À4 A ˚. The numbers of matrices with |tr(S)| larger than 1, 3, 10 and 20 are only 3772, 486, 31 and three, respectively. We then applied the aforementioned algorithm with the optimal choice of the value t S to be subtracted from the diagonal S elements in each case. Table  1  shows the results of both runs and illustrates that it is possible to fix the problems found in 6500 of the TLS sets (corresponding to about 500 PDB entries) by a correction of the diagonal elements of the S matrix as described above.
Synaptotagmin The crystals of synaptotagmin III (PDB entry 1dqv;  Sutton et al. , 1999)  contain two copies of the molecule in the asymmetric unit. The structure after re-refinement by phenix. refine without TLS modelling has an R work of 0. 200 and an R free of 0. 231 at a resolution of 2. 5 A ˚. Performing TLS refinement with each molecule taken as a single TLS group reduced the R factors to R work = 0. 177 and R free = 0. 211, indicating that this additional modelling significantly improves the agreement with the experimental data. Table  2  shows the two sets of matrices and Table  3  contains the corresponding motion parameters extracted using our approach. For the two groups both vibrations and librations are practically isotropic and are of the same order of magnitude. Fig. 3 (a) shows the principal axes of these motions.
Calmodulin The structure of calmodulin (PDB entry 1exr;  Wilson & Brunger, 2000)  has been determined previously at a resolution of 1. 0 A ˚. This example illustrates possible problems that can be solved by a minimal correction of the TLS values. For re-refinement with phenix. refine the model was automatically split into four TLS groups. For the first group, one of the eigenvalues of the matrix L was equal to À2 Â 10 À5 rad 2. If we consider this value to be zero (in this case the zero value must be also assigned to off-diagonal elements of the first row of the matrix S), the composite motions contain only two libration axes and their parameters can be extracted. Corresponding modifications of the resulting matrices U group,n (2) can be compensated for by respective adjustment of the individual contributions U local,n.
Initiation translation factor 2 (IF2) The structure of IF2 (PDB entry 4b3x) has recently been solved in one of our laboratories  (Simonetti et al. , 2013)  with an R work of 0. 180 and an R free of 0. 219 at a resolution of 1. 95 A ˚. A posteriori TLS refinement was performed with two groups: the first group included the N-terminus and the following long helix, and the second included the rest of structure. Rerefining the model produced better statistics, with R work = 0. 176 and R free = 0. 203. In this example, the TLS matrices from the first group were not directly interpretable because the residual matrix V [L] was not positive semidefinite (the minimal eigenvalue was À0. 05). Similarly to the last TLS group in calmodulin, we artificially added 0. 06 A ˚2 to all diagonal elements of the matrix T, corresponding to roughly 5 A ˚2 (the same amount has been removed from the residual atomic B values, thus leaving the R factors unchanged).
Finally, this strategy will reduce the chance of overfitting data with atomic models that represent implausible concerted motions. The survey of PDB entries refined with TLS revealed that roughly 85% of these deposited models contain matrices that are not consistent with the underlying physical model of the concerted motions. Therefore, these matrices cannot be interpreted in terms of rigid-body rotations and translations, and in turn cannot represent these motions (Table  1 ). This highlights two urgent needs. Firstly, existing refinement programs should be updated so that they apply appropriate restraints or constraints on refinable parameters of the TLS model. This should be followed by the implementation and use of comprehensive validation of TLS refinement results. The utility of our presented algorithm is twofold: it validates TLS matrices to confirm that they can represent concerted structural motions and interprets TLS matrices in terms of the elemental motions that they describe.
Acknowledgements PVA and PDA thank the  NIH  (grant  GM063210 ) and the  PHENIX Industrial Consortium  for support of the  PHENIX  project. JSF is a  Searle Scholar  and a  Pew Scholar , and a  Packard Fellow , and is supported by  NIH   OD009180 ,  GM110580  and  NSF   STC-1231306. This work was supported in part by the  US Department of Energy  under Contract No. DE-AC02-05CH11231. AU thanks the  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INSB-05-01  and Instruct, which is part of the  European Strategy Forum on Research Infrastructures (ESFRI)  and is supported by national member subscriptions.
If this again did not retrieve an ortholog for the species of interest, we extended our BLASTn search to Genbank (default settings). Additionally, we used the sequences of the Nile tilapia as query in a BLASTn search against the available East African cichlid genomes/ transcriptomes of Neolamprologus brichardi, Astatotilapia/Haplochromis burtoni, Pundamilia nyererei, and Maylandia zebra in Genbank at http://blast. ncbi. nlm. nih. gov/Blast. cgi. If orthologous blast hits were found outside annotated genomic regions, coding sequences were annotated manually; in this case chromosome or scaffold information is given (Table  S1 ). In addition to identification of homologous genes using BLASTn, we confirmed gene localization and copy number using syntenic analysis over the Genomicus genome browser [http://www.
Codon alignments For each gene, the longest available coding sequence was exported and loaded into SeaView 4. 5. 4 to be manually verified  (Gouy et al. 2010). Subsequently, in-frame alignments from start to stop codon were performed using a codon empirical model with PRANK v. 140110  (Löytynoja and Goldman 2005, 2008) , which has been shown to outperform other alignment software for alignments of codon blocks and, in particular, generates less false-positive cases in selection analysis  (Fletcher and Yang 2010).
2. 4)  (Pond et al. 2005; Smith et al. 2015) , which allows for different Ka/Ks ratios among sites and among branches. Resulting trees with selection values were visualized using the http://veg. github. io/hyphy-vision/absrel/ web interface, following the developer's instructions (Figure  S3 ). We finally ran gene-wide Ka/Ks estimates using KaKs_calculator_2. 0 (Version 1. 2) under the MA method  (Zhang et al. 2006 ) on the following alignments: all cichlids [East African Lake (EAL) cichlids + Nile tilapia] compared with medaka and EAL cichlids compared with Nile tilapia. Ka/Ks comparisons were performed over the entire sequence length.
Gene expression in cichlid fishes To examine gene expression profiles, we retrieved RNA-sequencing information for the gene members of the AR-signaling pathway for four species from Lake Tanganyika (A. burtoni, Eretmodus cyanostictus, Julidochromis ornatus, and Ophthalmotilapia ventralis) from  Böhne et al. (2014). The sequenced tissues of this study are brain and gonad from adult males and females. Note that genomic information is currently only available for A. burtoni  (Brawand et al. 2014). Cleaned reads for each individual sample for each species as described in  Böhne et al. (2014)  were mapped against our A. burtoni dataset of gene coding sequences. Mapping was done using Novoalign (Novocraft) with the following settings: -r All, -t 60, -l 30, and -s 5. Alignments were reported in SAM format and sorted, indexed, and transformed into count tables (number of mapped reads per transcript per sample) with the use of SAMtools  (Li et al.
2009). In total, the data set comprised read counts for four male brain, four female brain, four ovary, and four testis samples per species except for A. burtoni, where three biological replicates per tissue type were available. Differential expression analyses on raw read counts were performed with the Bioconductor edgeR package (Version 3. 1)  (Robinson et al. 2010 ) by use of the "classical" model as described in  Böhne et al. (2014). Count numbers were subsequently transformed into fragments per kilobase of transcript per million mapped reads (FPKM) to estimate relative transcript abundance within edgeR. FPKM values of paralogs were compared with a two-sided Welch t-test. Analyses using PRANK, PhyML, Novoalign, and SAMtools were run on sciCORE (center for scientific computing, University of Basel, http://scicore.
ACKNOWLEDGMENTS Fish pictures in Figure 2 are courtesy of  Hugo Gante  (N. brichardi),  Dario Moser  (G. aculeatus),  Manfred Schartl  (P. formosa), and  Anya Theis  (A. burtoni). Pictures of L. oculatus, A. mexicanus, D. rerio, O. latipes, and T. nigroviridis were taken from Braasch et al. (2015). We thank the support team of sciCORE (center for scientific computing,  University of Basel , http://scicore. unibas. ch/)for providing access to computational resources and advice. This work was supported by the  European Research Council  ( ERC Consolidator Grant "CICHLID~X" ) and the  Swiss National Science Foundation  to WS. A. B. and W. S. designed the study; T. L. and A. B. performed data analyses; and A. B. , T. L. , and W. S. wrote the manuscript.
SANS measurements Beamline D22 at the Institute Laue-Langevin (ILL), Grenoble, France, was used for small-angle neutron scattering. The measurement position was equipped with a hot plate for in situ ageing at 453 K. To cover a wide scattering vector magnitude (q) range, two sample-to-detector distances were chosen, 1. 4 and 5. 6 m. The neutron wavelength selected was = 0. 5 nm with Á/ = 0. 1, and the detector was 102. 4 Â 98 cm in size. The q range covered was therefore about 0. 15-4. 1 nm À1. Background subtractions, data reduction and absolute normalization were performed using the software GRAS ans P  (Dewhurst, 2008) , which is based on MATLAB (The MathWorks Inc. , Natick, MA, USA). The subsequent two-dimensional model fitting was performed through inhouse written MATLAB scripts. As the (111) Bragg edge in face-centred cubic aluminium lies at = ½2ð3 1=2 Þ=3Â 0.
405 nm = 0. 468 nm, only marginal anisotropic scattering is expected. Two full measurements of precipitation kinetics were carried out. The sample was first solutionized at 813 K for 60 min and then quenched in ice water and aged for one week at room temperature, i. e. at approximately 293 K (before the measurement campaign). After this, the first in situ ageing experiment with simultaneous SANS measurement was carried out. The time needed for the sample to reach 453 K was estimated to be less than 1 min. For the first 30 min of the experiment, images were acquired every minute at the shortest detector distance (1. 4 m). Then, 5 min acquisitions were obtained continuously, alternating between 1. 4 m and 5. 6 m for the remaining experiment (about 18 h). Counting the time needed to change the detector distance, this leads to a total time for acquiring a complete composite data set of $12 min.
The number density of 00 precipitates formed during AA has also been measured by TEM. Alloys high in Si and Mg have been found to show a lower number density in the aged condition if NA has taken place before for alloy 6111  (Wang et al. , 2003) , alloy 6082  (Cuniberti et al. , 2010; Marioara et al. , 2003) , alloy AlMg0. 6Si0. 8 (Liang, 2009) , alloy 6061  (Pogatscher et al. , 2013)  and alloy AlMg0. 8Si0. 9 (Torsaeter, 2011). Alloys low in Mg or Si show a slightly higher or the same number density for AlMg0. 4Si0. 4 (Liang, 2009; Torsaeter, 2011) , as well as for AlMg0. 4Si0. 8 (Wenner et al. , 2012) and AlMg0. 9Si0. 4 (Wenner et al. , 2012). Our SANS data indicate that the number density of precipitates after AA is higher if NA has been performed prior to AA. In this respect, our alloy again represents a situation closer to the alloys low in Mg or Si.
TEM images taken at selected ageing times could then be used to check whether there are any anomalies in the size distribution that could affect the SANS analysis. Atom probe measurements could provide the actual (possibly time-dependent) concentration of the precipitates, which could be used to calculate a time-dependent scattering length density and to correct the volume fractions now calculated assuming a constant composition. Precipitate volume fraction (a) and number density (b) for experiment AA calculated from SANS data using different precipitate compositions. Filled symbols: compositions of pre-stages of 00 precipitates supposed to be occurring sequentially during ageing  (Chen et al. , 2006). Open symbols: compositions suggested for fully evolved 00 precipitates  (Hasting et al. , 2009; Zandbergen et al.
MATERIALS AND METHODS Aus-ALL was a national, population-based, multi-center case-control study conducted in Australia between 2003 and 2007. The study design and data collection methods have been described elsewhere  (41, 42). Briefly, incident ALL cases were identified through all 10 Australian pediatric oncology centers, where the large majority of cases are treated. Inclusion criteria were: initial remission achieved, biological mother available and able to complete questionnaires in English, and Australian residence. Controls were prospectively recruited in the same time period by national random digit dialing (RDD), and frequency matched to cases by age (within 1 year), sex and state of residence. For the genetic component of Aus-ALL, controls were frequency matched to cases on age, sex and state of residence in a ratio of approximately 1.
Statistical analysis Mendelian inconsistencies were identified in family data using the PedCheck software (46); 31 case and 88 control families were excluded. Hardy-Weinberg Equilibrium (HWE) analysis was performed in STATA v10 using unaffected, unrelated individuals. No polymorphisms were found to significantly deviate from HWE (data not shown). The results of the quality assurance analyses were excellent with genotyping call rate 99%, within-laboratory concordance 99. 7% and between-laboratory concordance 98%. However, quality assurance analysis of genotypes derived from WGA'd buccal DNA samples showed discrepancies of 2. 3-7. 4% with those derived from lymphocyte DNA. Therefore, we applied a statistical adjustment method (using discordance estimates empirically derived from qualitycontrol data in cases) in all our analyses.
Acknowledgements This study was supported by the  Australian National Health and Medical Research Council  (Grant  ID 254539 );  National Health and Medical Research Council Career Development Award and Cancer Council Western Australia Research Fellowship  (to EM);  National Health and Medical Research Council PhD Scholarship  (to HB);  National Health and Medical Research Council Fellowship and Program Grant  (to CB). We would like to acknowledge the valuable contribution made by our laboratory technical staff:  Lan Nguyen ,  Stewart Smith ,  Jayne Murray  and  Raewyn Billings. Consortium Statement The Aus-ALL consortium conducted the study and the  Telethon Kids Institute ,  University of Western Australia , and was the coordinating centre. Bruce Armstrong  ( Sydney School of Public Health ),  Elizabeth Milne  ( Telethon Kids Institute), Frank van Bockxmeer (Royal Perth Hospital ),  Michelle Haber  ( Children's Cancer Institute Australia), Rodney Scott (University of Newcastle ),  John Attia  ( University of Newcastle ),  Murray Norris (Children's Cancer Institute Australia) ,  Carol Bower  ( Telethon Kids Institute ),  Nicholas de Klerk  ( Telethon Kids Institute ),  Lin Fritschi  ( WA Institute for Medical Research ),  Ursula Kees  ( Telethon Kids Institute ),  Margaret Miller  ( Edith Cowan University ),  Judith Thompson  (WA Cancer Registry) were the research investigators and  Helen Bailey  ( Telethon Kids Institute ) was the project coordinator.
The increase is significantly greater than the overall rate of growth of publications found in the database (dashed line in Figure  1 ). As shown in Figure  2 , an examination of the publications on portfolios reveals that there are three categories of articles and reviews according to a clustering algorithm  (Waltman et al. 2009 ) that finds topics focused on biomedical research (top right), on science policy in general (bottom right) and on industrial research (left), which is the focus of this section. The size of the circles represents the number of occurrences (with the smallest circles representing 10 occurrences, for clarity), while the closeness between two given terms is a two-dimensional representation of the frequency of co-occurrences (i. e. , the "relatedness") of the terms. These categorizations, in particular the distinction between health and science policy-oriented scholarship on the one hand, and innovation policy on the other hand, are supported out by a co-citation analysis of sources (not shown here) using the same software and data from the Web of Knowledge.
Separate high-density areas (i. e. , high-occurrence of the term, in dark/red colour in the figures) are found around common terms such as "university" or "report", indicative of distinct contexts for research portfolios. As is found from the scholarly literature (see Figure  2 , above), the health sector remains most prevalent among web results, which are associated primarily with universities, government institutes and private companies. However, the most important conclusion to draw from this exploratory exercise is that although the term is broadly used in public and private science policy contexts, it is so far used without semantic specificity. extract the context of each "research portfolio" result using the Outwit software package. Finally, we perform a manual cleaning, removing spurious and duplicate results, which leaves us with 1186 distinct search contexts.
Acknowledgements We thank  Tommaso Ciarli ,  Jochen Gläser ,  Jordi Molas-Gallart ,  Richard Wooley , and two anonymous referees for their insightful comments and suggestions. We acknowledge support from the  UK Economic and Social Research Council  (grant  RES-360-25-0076 , Mapping the  Development of Emergent Technologies ) and the  FP7 EU Marie Curie Integration Grant  to IR (MapRePort). Mowery, David C. 2012. Defense-related  R&D as a model "Grand Challenges " technology policies. Research Policy 41. Elsevier B. V. :  1703-1715. doi:10. 1016/j. respol. 2012. 03. 027. National Research Council. 2005. A prospective evaluation of applied energy research and development at  DOE (Phase One ). Washington. National Research Council. 2012. A Review of  NASA Human Research Program 's Scientific Merit Processes: Letter Report.