dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis Data were analyzed by using Epi Info software version 7. 0. 8. 0 (Centers for Disease Control and Prevention, Atlanta, GA, USA). Mantel-Haenszel χ 2 and Fisher exact tests were used to compare the prevalence between groups (i. e. , febrile and afebrile children), seasons, and geographic areas and by the participants' sex and age. A 2-tailed p value <0. 05 was considered statistically significant.
Recruitment A total of 465 febrile children were recruited from Franceville (n = 80), Koulamoutou (n = 167), Lastourville (n = 155), and Fougamou (n = 63) (Table  2 ). However, 55 of these children were excluded from the statistical analysis because their sex and age data were unavailable; 3 of the excluded children were from Franceville, 26 from Koulamoutou, 21 from Lastourville, and 2 from Fougamou. Of the 410 children included in the statistical analysis, 52. 7% (216/410) were recruited during a rainy season, and 47. 3% (194/410) were recruited during a dry season. A total of 60 afebrile children were recruited and enrolled in parallel from Franceville (n = 24), Fougamou (n = 20), and Lastourville (n = 16); no afebrile children were enrolled from Koulamoutou. The 410 febrile patients included in the statistical analysis consisted of 212 boys and 198 girls (sex ratio 1.
ACKNOWLEDGEMENTS We would like to thank the  ISOLDE technical group  for their support and assistance. This work was supported by the  Belgian Research Initiative on Exotic Nuclei  (IAP-project  P7/12 ), the  FWO-Vlaanderen , GOA grant  10/010  and  10/015  from  KU Leuven, NSF  Grant No. PHY-1068217 ,  BMBF  ( 05 P12 RDCIC ), the  Max-Planck Society , the  Science and Technology Facilities Council , and  EU   FP7 via ENSAR  (No. 262010 ).
Methods Monocenter study on patients with severe sepsis and septic shock. Data recorded: demographic, clinical severity, blood cell count, mHLA-DR, lymphocyte phenotype (flow cytometry, CD3+, CD3+CD4+, CD3+CD8+, CD19 +, CD16+CD56+). Samples taken as part of routine care without additional blood collection and did not required patient´s consent. Patients data compared with a historical group of healthy volunteers from the laboratory. Statistics: results expressed as median (25 th -75 th percentile), Mann-Whitney test, Pearson correlation.
First experimental results First measurements were conducted at the University of Reading Meteorological Station, where data was available from a sonic anemometer mounted at 10 m. Fig. 8  shows an example of spectra obtained from a 20 m range gate centered on 80 m height using a pulse duration of 0. 1 s. The characteristic sinusoidal variation of the spectral peak with microphone position is evident. Fig. 9  shows the corresponding spectral peak frequencies. The estimated wind direction is 194 °based on (2. 2). The estimated direction for the following 10 minute period is 177 °. The standard deviation of the estimate of the phase angle for the sinusoid fit was 18 °for this data set. However, the 10 m mast data 5-minute averages were 4. 8 m s -1 , 181 °and 4. 6 m s -1 , 212 °for the first 10 minute period, and 5.
The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences.
Phylogenetic Analyses Sequences used in this study were obtained from various databases [NCBI-protein, NCBI-Assembly, Phytozome, Ancestral Angiosperm Genome Project (AAGP), Comparative Genomics (CoGe)] using either tBLASTn or BLASTp (as of 3. 2015) with an A. thaliana IDL or HSL query. Outgroup taxa for both monocot and eudicot receptors were closely related A. thaliana representations within the subclass XI LRR-RLKs. IDA was inferred without an outgroup. An aa alignment (∼59 aa) of angiosperm IDA without the N-terminal secretion signal and LRR-RLK group (full length 1926 aa) was constructed using MAFFTv6 E-INS-I model under default settings  (Katoh and Toh, 2008). The resulting alignments were checked with Gblocks v0. 91b  (Castresana, 2000) , under the least stringent parameters (small final block, gap positions in final block and less strict flanking), to exclude poorly aligned positions and divergent regions from subsequent phylogenetic inferences.
Primers are specified in Supplementary Table  S1. Expression was normalized to PtACTIN1 expression. mRNA was isolated from AZs of unripe and ripe of oil palm (Elaeis guineensis) fruit, and AZs of fruit treated with ethylene as described previously  (Roongsattham et al. , 2012). Primers were designed to fit the various EgIDA genes, EgHSL2, and EgHSL1 (Supplementary Table  S1 ). qPCR was performed as previously described  (Roongsattham et al. , 2012). All expression was normalized to the EgEfα1 (accession number: AY550990) expression. No change of EgEfα1 transcript accumulation was found in the fruit tissues treated or not treated with ethylene. Controls were conducted to validate the absence of DNA in each sample.
IDA lacks phylogenetic information and is also present in a high number of copies in many species; any possible pattern was unclear, with no clear clades, branching patterns, and a general lack of stability. Despite this we attempted an inference based on multiple datasets (PIP, EPIP, and EPIP-C, Figure  3A ), considering species that have undergone fewer genome duplications  (Vanneste et al. , 2014) , however, without success. As an alternative approach to understand the evolution of IDA/IDL peptides, we grouped the different PIP motifs of the BLAST-identified proteins based on their amino acid composition. In all eudicots, peptides could be classified either as IDA/IDL1 ([P,L][V,I]PPS[A,G]PSKRHN) or like IDL2-5 (PIP[A,T,H,P]S[A,G]PSRKHN), named PIP R and PIP K respectively based on the residue in position 10 (Figures  3B, C ).
Both motifs were found in every eudicot species tested. In the monocot dataset PIP R was found in the orders Arecales and Zingiberales. Additionally, we identified a version in all monocots with close resemblance to PIP R , but containing a glutamine (Gln, Q) in position 10 (PIP Q , Figure  3D ). The IDL Gene Family has Expanded in Many Taxa of Core Eudicots About 65 million years (Myr) ago after the split of the core eudicots into Rosids and Asterids, whole genome duplication (WGD) took place in a number of eudicot lineages and expanded both the number of species and the gene number of each species (Van de  Peer et al. , 2009). In line with this, detailed inspection suggests independent evolution especially of the IDL2-5 genes in these two clades. Soybean (Glycine max), common bean (Phaseolus vulgaris) and A.
HSL1/HAE duplication is found on syntenic genome regions in the other eudicots, but not rice, supporting that HAE was generated by a WGD event  (Tang et al. , 2008). Specific genomic locations of AtIDA and HSL2 and their neighboring genes in A. thaliana are preserved in Populus and Vitis, respectively  (Woodhouse et al. , 2011). The IDL4 is positioned in synteny with other eudicots, but the other IDL genes may rather be a result of duplications known to have taken place after the divergence of Brassicaceae and Caricaceae families  (Tang et al. , 2008). Duplications provide the opportunity for the new copy to evolve, like giving rise to the PIP K or PIP Q motif varieties. Transition from Arg to Lys or Gln may only require one nucleotide change. Based on available sequence data we hypothesize that IDL4 with PIP K evolved before the split of Proteales, however this variant may have a more basal history within angiosperm evolution.
ACKNOWLEDGMENTS We thank  Nora M. Tandstad  for the images of 35S:IDL1 plants, and  Even Sannes Riiser  for the pHAE:GUS and pHSL2:GUS reporter lines. We thank  Anek Limsrivilai  at  GoldenTenera Oil Palm Plantation in Thailand  and  Roberto Poveda  at the  PDA/Murrin Company in Quinindé, Ecuador  for the oil palm material. We appreciate the technical support from  Julien Serret  for the oil palm qPCR analysis.
All crystals were grown using the hanging drop vapor diffusion method at 13 °C. The nanopipetting was performed using the Mosquito nanoliter liquid handling system (TTP LabTech). The native HetR-DNA crystals were obtained against the reservoir solution of 0. 3 M calcium acetate and 0. 1 M Bicine, pH 9. 0, while the SeMet HetR-DNA crystals were grown against 0. 2 M magnesium acetate for two days. The native PatS6-HetR Hood crystals were obtained from 25% PEG 4000, 0. 1 M sodium citrate, pH 5. 6 and 0. 2 M ammonium acetate. All the crystals were transferred to the cryoprotectant (reservoir solution supplemented with 30% glycerol) and flash-cooled in liquid nitrogen before data collection. Data collection and processing. X-ray diffraction data were collected at 100 K in a liquid nitrogen stream, using beamline BL17U with a Q315r CCD (ADSC, MARresearch, Germany) at the Shanghai Synchrotron Radiation Facility (SSRF).
All diffraction data were integrated and scaled with the program HKL2000  35. Structure determination and refinement. The selenium sites from the data of SeMet HetR-DNA complex were determined using the program SHELXD  36. The initial phases were calculated with the program OASIS  37  , then improved with the programs RESOLVE and Buccaneer  [38] [39] [40]. Autobuild in PHENIX  41  was used to perform automatic model building. The initial model was refined by REFMAC5  42. The corresponding modules of SeMet HetR-DNA complex were used as the search model against the native data of HetR-DNA and PatS6-HetR Hood by molecular replacement using Molrep program as part of CCP4i  43  program suite. The models were refined by REFMAC5 and rebuilt interactively with the programs PHENIX (or REFMAC5) and COOT  44  until the free R-factor converged.
Molecular dynamics simulation with enhanced sampling method. To study the conformational changes of HetR, a previously developed enhanced sampling method  28  was performed in molecular dynamics simulation, which can efficiently accelerate large-scale conformational changes of a multi-domain protein in a relatively short-time simulation. The simulation was set up using the modified GROMACS-4. 5. 5 package  47  and the CHARMM27 force field  48. The HetR-DNA complex (or the modeled PatS6-HetR-DNA complex) was first placed in a rhombic dodecahedron box, with the minimum distance between the solute and the box boundary of 1. 2 nm. TIP3P water molecules  49  were then filled the box. The energy of the system (DNA, protein and waters) was minimized by the steepest descent method, until the maximum force was smaller than 1500 kJ mol -1 nm -1.
Acknowledgements This work was supported by the  National Natural Science Foundation of China  (Grants No. 31370757  and  31270760 ), the  Ministry of Science and Technology of China  (Grants No. 2012CB911000  and  2014CB910100 ), the  Innovation Center for Cell Signaling Network , the  Hefei Science Center of CAS  (Grants No. 2015SRG-HSC045  and  2015SRG-HSC046 ), and the  Program for Changjiang Scholars and Innovative Research Team in University. We thank the assistance of the staff at the  Shanghai Synchrotron Radiation Facility (SSRF)  and the  Core Facility Center for Life Sciences in University of Science and Technology of China. We are grateful to all the developers of CCP4 Suit, ESPript, MolProbity and PyMOL.
86 74. 39 Nucleic acid 65. 14 Ligand/ion 103. 54 65. 07 Water 73. 20 44. 19 R. m. s. deviations Bond lengths (Å) 0. 007 0. 012 Bond angles (°) 1. 256 1. 378 PDB entry 4YRV 4YNL. Values in parentheses are for highest-resolution shell.
The clinical application of MSCs in specific cases seems to be approaching, with two phase-2/3 and four phase-3 clinical trials been recently completed (www. clinicaltrials. gov; NIH; same key words as before). Nevertheless, several fundamental aspects of MSCs biology remain unknown and it is expected that broadening of this knowledge will improve their beneficial uses. For instance, the possibility of selecting MSCs types according to their phenotype (i. e. , in vivo cell source or their cell membrane expression profile) and functional (i. e. , anti-fibrotic) properties, and of pretreating them with compounds/factors or genetically modifying them to express antifibrotic proteins, would likely improve their therapeutic outcome. In this review we aim to discuss most recent evidence, highlighting some unsolved questions and bringing suggestions to foster MSCs research.
Acknowledgments The authors are supported in part by grants from the  Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT)  ( PICT PRH 2007 N°51 ;  PICT 2008 00123 ;  PICTO 2008 00122 ). EJF and JBA are also supported by grants from the  Universidad Austral. Disclosures The authors indicate no potential conflicts of interest.
Patient disposition and baseline characteristics Ninety patients received treatment and 89 were included in the ITT population; 26 patients (29 %) withdrew before week 48 and 64 patients (71 %) completed the trial. The most common reason for withdrawal was insufficient IGF-1 response as per protocol at week 12 (n = 18), followed by consent withdrawn (n = 4), adverse events (n = 3), and other reasons (n = 1). One patient in the ITT population did not have data available on biochemical control; for this reason, there were 88 patients in the overall population in the current analyses. Of these, all completed the PASQ at baseline and 83 completed the AcroQoL questionnaire. Baseline demography and clinical characteristics are summarized in Table  1  for the overall population and for those with and without biochemical control, and in Supplementary Table  S1  for the 18 patients who withdrew because of insufficient IGF-1 response.
Data and simulated samples The data used in this search were recorded with the ATLAS detector in proton-proton collisions at a centre-of-mass energy of 8 TeV. The ATLAS detector is described in detail elsewhere  [15]. The integrated luminosity of the data sample, selecting only periods where all relevant detector subsystems were operational, is 20. 3 ± 0. 6 fb -1  [16]. The data used in the τ τ and bb final states were collected using a combination of single-electron, single-muon, dielectron (ee) and dimuon (µµ) triggers. Depending on the trigger choice, the p T 2  thresholds vary from 24 to 60 GeV for the single-electron and singlemuon triggers, and from 12 to 13 GeV for the ee and µµ triggers. The data used in the ννbb final state were collected with a missing transverse momentum (E miss T ) trigger with a threshold of E miss T > 80 GeV.
The transverse momentum of the lepton and E miss T system (p W T ) is required to be above 120 GeV to approximately match the phase space of the signal region. The sample is split into events with zero, one or two b-tagged jets and into events with 2 and 3 jets. A correction depending on ∆φ jj is applied to W + ll and W + cl events, following studies similar to those performed for the Z+jets background  [43]. A correction is made to the p T distribution of t t production in the simulation to account for an observed discrepancy with the data  [44]. The normalization of top-quark pair production in the bb channel is measured by defining a sample of events with exactly one electron and one muon, one of which has p T > 25 GeV, and two b-tagged jets with 50 < m bb < 180 GeV.
Conclusions Data recorded in 2012 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 20. 3 fb -1 of proton-proton collisions at a centre-of-mass energy 8 TeV, are used to search for a CP-odd Higgs boson, A, decaying to Zh, where h denotes a light CP-even Higgs boson with a 125 GeV mass. No deviations from the SM background predictions are observed in the three final states considered: Zh → τ τ , Zh → bb, and Zh → ννbb. Upper limits are set at the 95% confidence level for σ(gg → A)×BR(A → Zh)×BR(h → f f ) of 0. 098-0. 013 pb for f = τ and 0. 57-0. 014 pb for f = b in the range of m A = 220-1000 GeV. This Zh resonance search improves significantly the previously published constraints on CP-odd Higgs boson production in the low tan β region of the 2HDM.
Stable short hairpin interfering RNA constructs A previous study was used to guide the generation of short 19-bp hairpins for RNA interference: p53 (nucleotides 611-629 Genbank NM000546)  [30]. The oligonucleotides were annealed and ligated into a self-inactivating lentiviral vector under the control of the H1 promoter  [31]. The vector used was also designed to carry the GFP reporter gene under control of the human ubiquitin-C promoter in order to monitor infection efficiency. A scrambled shRNA construct was also utilized as a control  [30]. Lentiviral shRNA virus-containing supernatant was generated by the University of Michigan Vector Core. Virus-containing supernatant was used to infect SJSA-1 cells. The cells were sorted 96 h post-infection for GFP fluorescence and used for all subsequent experiments.
Analysis of p53 mutation Mutation of p53 was determined by sequence analysis. Total RNA was extracted with RNeasy Mini Kit from Qiagen Inc (Valencia, CA). Complementary DNA (cDNA) was prepared by reverse transcription using SuperScript III First-Strand Synthesis SyperMix system from Invitrogen Corporation (Carlsbad, CA) following the manufacturer's protocol. Primers to amplify and sequence cDNA for exons 2 to 11 of human p53 were used from Aziz et al. [23]. The amplified p53 cDNA was sequenced by the University of Michigan Sequencing Core. Mutation Surveyor (SoftGenetics LLC) software was used to compare experimental sequences against Refseq Gen-Bank as well as by visual inspection of sequence tracings.
Computational modeling The crystal structure of tetrameric p53 and the DNA of the BAX response element (PDB entry: 4HEJ)  [32]  was used in the computational modeling. For the molecular dynamics (MD) simulations, we used the MOE program  [31]  to determine the protonation state of ionizable groups on p53 under standard physiological conditions. The MOE program was also used to perform the mutation of C176F in p53. In modeling of C176F, we selected the Phe rotamer that has no van der Waal clashes with neighboring atoms. PMEMD from Amber (version 12)  [33]  was used for MD simulations. The Amber 99SB force field parameters  [34]  were used for the amino acids. The force field parameters for the zinc ion were taken from Lu et. al  [35]. To prepare the topology and coordinate files, counter ions were first added to neutralize the charges in p53/DNA and the system was then placed in a 13Å octahedral box of water (the TIP3P  [36]  water model).
In the two other models, two p53 wild-type monomers form a dimer and two C176F p53 mutant monomers form another dimer to interact with DNA. We denote these arrangements as FCCF, FCFC, CFCF, CFFC, FFCC, and CCFF, with C representing the wild-type p53 (C176) monomer and F the C176F mutated p53 monomer (S5 Table  and S2 Fig). We used the motional fluctuations of the p53 backbone atoms in these models from the p53 wild-type tetramer crystal structure to assess the structural stability for these 6 models containing a C176F heterozygous mutation. Our data showed that the FFCC model appears to be least stable and the FCCF tetramer appears to be the most stable. In each of the dimers, we also calculated the salt-bridge interaction distances between R181 and E180 as another indicator of the structural stability of the dimer.
Introduction The substantial dataset of Large Hadron Collider (LHC) proton-proton (pp) collisions at √ s = 8 TeV collected by the ATLAS experiment provides a distinct opportunity to search for new heavy resonances at the TeV mass scale. This paper presents a search for narrow diboson resonances (WW, WZ and ZZ) decaying to fully hadronic final states. The fully hadronic mode has a higher branching fraction than leptonic and semileptonic decay modes, and is therefore used to extend the reach of the search to the highest possible resonance masses. W and Z bosons resulting from the decay of very massive resonances are highly boosted, so that each boson's hadronic decay products are reconstructed as a single jet. The signature of the heavy resonance decay is thus a resonance structure in the dijet invariant mass spectrum.
8 × 0. 8. The subsequent high-level trigger consists of two stages of software-based trigger filters which reduce the event rate to a few hundred Hz. Events used in this search satisfy a single-jet trigger requirement, based on at least one jet reconstructed at each trigger level. At the first filtering stage of the high-level trigger, jet candidates are reconstructed from calorimeter cells using a cone algorithm with small radius, R=0. 4. The final filter in the high-level trigger requires a jet to satisfy a higher transverse momentum (p T ) threshold, reconstructed with the anti-k t algorithm  [24]  and a large radius parameter (R=1. 0). This search is performed using the dataset collected in 2012 from 8 TeV LHC pp collisions using a single-jet trigger with a nominal p T threshold of 360 GeV.
The final-state particles produced by the generators are propagated through a detailed detector simulation  [39]  based on GEANT4  [40]. The average number of pp interactions per bunch crossing was approximately 20 while the collision data were collected. The expected contribution from these additional minimum-bias pp interactions is accounted for by overlaying additional minimum-bias events generated with Pythia 8, matching the distribution of the number of interactions per bunch crossing observed in collision data. Simulated events are then reconstructed with the same algorithms run on collision data.
Exclusion limits on new diboson resonances Limits on the production cross section times branching ratio of massive resonances are set in each diboson channel as a function of the resonance mass using the EGM W as a benchmark for the WZ selection, and the bulk G RS model for the WW and ZZ selections. In most of the mass range, the observed limit is somewhat better than the expected limit, but in the region near 2 TeV the excess of events in the data leads to observed limits which are weaker than expected. Figure  6 (a) shows the observed 95% CL upper limits on the cross section times branching ratio on the EGM W → WZ hypotheses as a function of the W mass. EGM W → WZ for masses between 1. 3 and 1. 5 TeV are excluded at 95% CL. Figures  6(b ) and 6(c) show the observed 95% CL upper limits on the cross section times branching ratio for the bulk G RS → WW and ZZ, respectively.
Acknowledgements We thank  CERN  for the very successful operation of the LHC, as well as the support staff from our institutions without whom ATLAS could not be operated efficiently. We acknowledge the support of  ANPCyT , Argentina; YerPhI, Armenia;  ARC, Australia ;  BMWFW  and  FWF , Austria; ANAS, Azerbaijan; SSTC, Belarus;  CNPq  and  FAPESP, Brazil ;  NSERC ,  NRC and Trust ,  United Kingdom. The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from  CERN  and the ATLAS Tier-1 facilities at  TRIUMF (Canada) ,  NDGF (Denmark, Norway, Sweden) ,  CC-IN2P3  (France),  KIT/GridKA (Germany) ,  INFN-CNAF (Italy) ,  NL-T1  (Netherlands),  PIC (Spain) ,  ASGC (Taiwan) ,  RAL (UK)  and  BNL (USA)  and in the Tier-2 facilities worldwide.