dataesr/scientific-paragraphs-categorization huggingface dataset:
It is highlighted here that the choice of statistical model fitting technique may significantly influence the shape of the resulting fragility function. As an example, Fig. 5  shows the fragility functions obtained using GLM and LS for the Special-Code building assessed for the 150 unscaled records with FRACAS. It can be observed that the GLM and LS approaches result in large discrepancy between the fragility curves derived for DS2, with the GLM approach showing a greater variability in the results. The GLM better captures the fact that there are only a limited number of data points (observations) available for the higher damage states. It is noted, that despite the intensity of the chosen records being significant, too few data are available to derive the collapse damage state curve for the Special-Code building (without scaling the records).
g. ,  [35] ). EC8 Section 3. 2. 3. 1. 2 does instead provide guidance on the relevant range of structural periods over which to carry out the matching, specifying this range in terms of the structural fundamental period of vibration (T 1 ) as 0. 2T 1 to 2T 1. In the case of the considered case-study structure (Pre-Code building), the latter period range lies well within the adopted period range for matching. In the case of the natural records, the software REXEL  [35]  is used to select unscaled accelerograms from the three databases included in the software, namely Selected Input Motions for displacement-Based Assessment and Design (SIMBAD,  [28] ), the European Strong-motion Database (ESD)  [36]  and the Italian Accelerometric Archive (ITACA)  [37]. It is worth noting that  the EC8 approach for ground motion selection is not sufficiently conservative for the derivation of fragility functions and this guideline has not been developed for this purpose.
However, as discussed above, the main aim of the simple exercise carried out in this section is to demonstrate FRACAS' ability to capture recordto-record variability. In particular, three suites of input accelerograms are adopted to assess the effect of record-to-record variability on the fragility curve produced for the Pre-Code building: 1. Twenty natural accelerograms (unscaled) to be compatible with the target spectrum over the period range 0. 05-2 s (thereafter referred to as REAL-EC8:475). 2. The same accelerograms as in REAL-EC8:475 adjusted using wavelets so that their spectra better match the target (MATCHED-EC8:475). The program SeismoMatch  [38]  was adopted to adjust earthquake accelerograms to match a specific target response spectrum, using the wavelets algorithm proposed by Hancock et al.
[39]. 3. Twenty accelerograms generated using SIMQKE  [40] , a method (and associated software) that can generate responsespectrum-compatible statistically-independent synthetic motions showing very little dispersion in their spectra and matching the target closely (SIMQKE-EC8:475). Table  3  presents basic information on the ground motions used within the first two record sets. Within FRACAS these sets of accelerograms are scaled several times for the capacity spectrum assessment at increasing IM levels. The elastic spectra for the three suites of accelerograms are shown in Fig. 9a -c together with their average, and the target spectrum. Stafford and Bommer  [41]  postulate that, when deriving fragility curves accounting for ground motion variability, the peak-totrough variability in their response spectra should not be too small.
Acknowledgments The FRACAS procedure has been implemented in a Matlab program through a collaborative effort between  University College London  ( UCL ) and  Bureau de Recherches Géologiques et Minières (BRGM) ,  France. Pierre Gehl 's contribution to this study was partially funded by a  Carnot Mobility  grant. AIR Worldwide and the  UK Engineering and Physical Sciences Research Council (EPSRC)  are thanked for supporting Stylianos Minas' Engineering Doctorate through the  UCL Centre in Urban Sustainability and Resilience  ( EP/ G037698/1 ). Appendix A. Parameters  for all derived fragility curves Table A. 1.
Sequence Alignment ABI traces were assembled with Geneious 5. 4. 3  [76]  and manually adjusted. All sequences were unambiguous. The identity of sequences was verified using blast search  [77]. Sequences were aligned using MUSCLE  [78]  as implemented in Geneious 5. 4. 3. Alignment parameters were default. In addition to sequences of 10 specimens (five species) generated in our lab, we downloaded a set of 46 sequences (representing 42 species from seven subtribes within the tribe Bambusoideae plus two outgroup taxa) from GenBank. We chose this single gene because of the taxonomic coverage in GenBank. No other genes were published with a similarly high representation at the time of analyses. Accession numbers and vouchers of all samples are given in Table  1  and S1.
Phylogenetic Analyses For phylogenetic analyses, we used a Bayesian approach and a Maximum likelihood (ML) analysis as described previously  [79]. Here, we adopted a conservative perspective and considered only those clades as well-supported that had a posterior probability of at least 0. 95 and bootstrap support equal to or above 70%. The Bayesian (B/MCMC) analyses were performed using MrBayes 3. 1. 2 [80]. Posterior probabilities were approximated by sampling the trees using a Markov chain Monte Carlo (MCMC) method. The sequences were tested for the most appropriate model of DNA substitution analyses by the program MrModeltest version 2. 3  [81]. Using AIC, GTR+ Γ was determined as the most appropriate maximum likelihood model of evolution for our dataset. MrBayes estimated the proportion of invariant sites, the gamma distribution shape parameter, base frequencies, and the substitution rates.
No molecular clock was assumed. A run with 10,000,000 generations starting with a random tree and employing 4 simultaneous chains was executed. Every 100 th tree was saved into a file. The first 2,500,000 generations (i. e. , the first 25,000 trees) were deleted as the "burn-in" of the chain. We plotted the log-likelihood scores of sample points against generation time using TRACER v1. 5 (http://tree. bio. ed. ac. uk/software/tracer/) to ensure that stationarity was reached after the burn-in by checking whether the log-likelihood values of the sample points reached a stable equilibrium value  [80]. Of the remaining 150,000 trees (75,000 from each of the parallel runs) a majority rule consensus tree with average branch length was calculated using the "sumt" option of MrBayes. Posterior probabilities were obtained for each clade.
Lemur Phylogeny and Ancestral States Reconstruction Published nucleotide sequences for several mitochondrial genes (12s rRNA, cytochrome c oxidase subunit II (COII), cytochrome b (cyt-b), D-loop, as well as the Pastorini fragment (PAST) covering NADH3, NADH4L, NDH4 and 5 tRNAs) were obtained from GenBank (see Table  2  for accession numbers). These loci were chosen on the basis of taxonomic coverage; other candidate loci were discarded because of poor representation. In instances where a subspecies had recently been elevated to species level (within Hapalemur) the most recent names were adopted and the taxonomy, presented by Mittermeier et al. [47] , was followed. We included a total of five (out of six recognized) Hapalemur species (H. alaotrensis, H. aureus, H. griseus, H. meridionalis, H.
Statistical Analyses Differences of ground shoot HCNp, protein concentration, and cyanide per protein among the five bamboo species included in this study were statistically analyzed using post-hoc analyses (Tukey's HSD; P < 0. 05) after one-way ANOVA. We tested for significant differences of the above-mentioned traits between branch shoots of C. madagascariensis and C. capitata using ttests. Only these two species had developed branch shoots at the time of our fieldwork. All statistical analyses were carried out using the Statistical Package for Social Sciences (SPSS) 16. 0 (SPSS for Windows, SPSS, Chicago, IL, USA).
[93]. Since the topologies of the ML and B/MCMC analyses did not show any strongly supported conflicts, only the 50% majority-rule consensus tree of Bayesian tree sampling is shown. Those nodes that received strong support (i. e. , posterior probability (pp) ! 0. 95 in B/MCMC analysis as well as ML bootstrap ! 70%) in both the ML and Bayesian were considered significant (Fig  2 ). Based on our dataset, several genera (i. e. , Bambusa, Cephalostachyum, Nastus) and subtribes (Bambusinae, Hickelinae, Melocanninae) are not supported as being monophyletic. Nevertheless, Malagasy Hickelinae and Cephalostachyum sp. (Melocanninae) were strongly supported as being monophyletic and appear to be derived within the woody bamboos (tribe Bambuseae). This clade contained all species that we tested positive for cyanide (i.
Maximum likelihood and maximum parsimony analyses of the combined data set yielded a tree that did not contradict the Bayesian tree topology and only the 50% majority-rule consensus tree of Bayesian tree sampling is shown (Fig  3 ). The maximum likelihood search in GARLI v0. 94  [82]  using the GTR+I+ Γ model, which was determined the best fit model for the combined dataset using Modeltest, resulted in one maximum likelihood tree with a lnL = -25633. 2494. The bootstrap values recovered with the maximum likelihood criterion (ML bs) are included in Fig 3. Of all 5523 characters, 3406 were constant, 556 were parsimony-uninformative and 1561 parsimony-informative. The maximum parsimony (MP) analysis resulted in one most parsimonious tree with a length of 4533 steps, a CI of 0. 5908 and a RI of 0.
madagascariensis. As we exclusively quantified cyanide in the bamboo species co-occurring in the Ranomafana area, we cannot draw general conclusions about the evolution of cyanogenesis in bamboos. Our results are largely consistent with previous phylogenies  [93, 102] , but with the addition of several new taxa and specimens. Based on this dataset, the support of most branches is weak. Some genera (i. e. , Bambusa, Cephalostachyum, Nastus) and subtribes (Bambusinae, Hickelinae, Melocanninae) are not supported as being monophyletic, which is consistent with earlier findings using the same sequence fragment  [75]. It is, however, noteworthy that all Malagasy Hickelinae clustered together in the molecular phylogeny including the high cyanogenic species C. madagascariensis, C. capitata, N. elongatus, and the low cyanogenic Cephalostachyum sp.
Acknowledgments We thank  Dr. Anna T. C. Feistner ,  Dr. Razafimahaimodison Jean Claude  and  Dr. Frank P. G. Princée  ( all Centre ValBio ) as well as the MICET (the  Madagascar Institute pour la Conservation des Environments Tropicaux ) and  ANGAP (Association Nationale pour la Gestion des Aires Protégées)  for logistic help,  Razafindrakoto Georges  ( Centre ValBio ) for superb assistance in the field, and  Peter Bayer  ( Essen, Germany ) for kind support. We would like to thank three anonymous reviewers for their suggestions to improve previous versions of this manuscript.
The ancillary sub-complex comprising SecD and SecF stimulates protein translocation through SecYEG 8 assisted by the transmembrane proton-motive force (PMF)  16, 17. The periplasmic domain of SecD consists of a P1-head and a P1-base domain, which are thought to contact the substrate and move in response to proton translocation; thereby facilitating the passage of polypeptides across the membrane  17. Here, we present an interdisciplinary analysis of HTL architecture combining small-angle neutron scattering (SANS), electron microscopy (EM) and biochemical and biophysical data in an integrated approach. Absolute-scale contrast variation SANS revealed a dynamic HTL complex and a lipid-filled central cavity surrounded by protein. The surrounding protein components were then visualized by cryo-EM.
The procedure enabled the dissection of the contribution of the protein, lipid and detergent components to the HTL structure based on their respective chemical composition and partial specific volume (CMP = 39. 0%, 21. 7%, 13. 1% D 2 O, respectively, for protein, DDM and lipid). The lipid CMP was calculated from the lipid composition of the inner E. coli membrane. The measured CMP of the native HTL complex (24 ± 0. 2% D 2 O) indicated a substantial contribution from non-protein components. The protein component contribution was calculated and subtracted from the complex contrast variation line to yield the CMP of the non-protein component (16. 5 ± 0. 3% D 2 O), allowing the lipid/DDM volume ratio to be calculated. The SANS data indicates that the composition of native and cross-linked HTL in DDM is consistent and mono-disperse, with single copies of each protein subunit.
A total of 300 micrographs were recorded at room temperature on a BioTwin CM120 electron microscope (FEI) at a magnification of 71,550× and a defocus of ∼ 2 μ m at 120 kV, using a 4 k × 4 k CCD camera. Two consecutive images of the same area were taken at 45° and 0° tilt angles under low-dose conditions. The contrast transfer function (CTF) was analyzed and corrected using BCTF (Bsoft package ref. 39). 11,653 HTL, 9,908 DFYY and 10,986 Δ YidC tilt pairs were selected manually using Tiltpicker  40. Untilted images were aligned using iteratively refined 2D class averages as references and were subjected to multivariance statistical analysis (MSA) and Hierarchical Ascendant Classification for clustering into 400 class-averages with IMAGIC-5  41. 400 volumes were calculated from the 2D classes and were aligned, averaged and clustered using Xmipp MLtomo  42  to compensate for the missing cone, resulting in 10 RCT reconstructions for each sample.
2,500 micrographs were recorded on a 4 k × 4 k direct electron detector (Falcon I, FEI) at 1. 36 Å/pix and coarsened three times resulting in a final pixel size of 4. 08 Å. HTL-amphipols were plunge-frozen using holey-carbon grids (Quantifoil 2/2) and imaged on a Titan Krios (FEI) equipped with a 4 k × 4 k direct electron detector (Falcon II) at a pixel size of 1. 01 Å using 36 electrons per Å 2. We also collected data at 300 kV, but we then could not identify the particles in the vitreous ice with confidence. Image Processing. The CTF was determined using Bsoft  39  , and the image phases were flipped accordingly. Using EMAN2  44  , 84,732 particles were boxed, subjected to 2D MSA and classification and compared to projections of the refined HTL RCT volume. At this step, 300 2D class-averages corresponding to 23,749 particles of crosslinked HTL and 35,521 particles of HTL-amphipols were rejected based on visual inspection and lower correlation with the projections from the RCT model.
The RCT volume was used to assign the projection angles to the remaining 800 2D class-averages of HTL and 1,000 class-averages of HTL-amphipols to calculate the 3D reconstruction from the cryo-EM data with the BP RP program of Spider  43. The resulting initial cryo-EM volumes contained 60,983 HTL particles and 119,346 HTL-amphipol particles. For the HTL-amphipol sample, 3D classification resulted in one class with improved features (Supplementary Fig. S5f ), which was subjected to maximum likelihood 3D refinement until convergence in Relion  45. The final reconstructions of crosslinked HTL and of HTL-amphipols after gold-standard refinement  21  contained 53,648 and 23,381 particles respectively. After high-resolution noise substitution  46  , the resolution of the structures was 14 Å for the cross-linked HTL and 15 Å for HTL-amphipols, based on the Fourier shell correlation criterion 0.
Ions with unrecognized charge state were excluded. CID normalized energy 38%, activation of q 0. 25, activation time 30 ms, AGC 10,000; HCD normalized energy 65%, activation time 40 ms, AGC 50,000, resolution 7500. Data Analysis. Data were analysed by LipidSearch software (version1. 0, Thermo Fisher Scientific). Database: Orbitrap, search type: Product; Exp Type: LC-MS; Precursor tol: 5 ppm; Product tol: 0. 2 Da; Intensity threshold, relative 1%; m-Score Threshold: 10. 0. Class: PE, PG, CL; Ion: -H and -2H. Each sample was run 4 times. All the reported lipid ions were identified at least twice. Small angle neutron scattering of holo-translocon. Sample preparation. Native HTL was purified as described (ref. 5). SANS data collection. HTL complexes were concentrated and buffer exchanged into the appropriate D 2 O buffers using a 50 kDa MWCO centrifugation filter (Millipore).
100 or 0. 200 cm optical path. The temperature was kept between 4 and 8 °C. Scattering patterns were radially averaged and corrected for buffer scattering and detector responses using standard software from the ILL (ftp://ftp. ill. eu/pub/cs/sans/SansManual_ and_2012update. pdf) and from JCNS (www. qtikws. de). The scattering data from H 2 O buffer was used to place the data on an absolute scale. SANS data analysis. Guinier analysis of the data was accomplished using Igor Pro software (WaveMetrics, Lake Oswego, OR) with SANS macros developed at the NCNR (NIST, Gaithersburg, USA). The Guinier approximation straight line fit was used on the low-Q portions of the data to obtain values and errors for the radius of gyration R g and the forward scattering intensity I(0) of the samples  19. In general, the Guinier approximation is considered valid for q.
The theoretical scattering length of the protein component was calculated using MULCh  50. The oligomeric state of the protein was determined directly from the 0% D 2 O data as ρ ρ ∆. ≥ ∆. V V ( ) ( ) P. The molar mass of the protein component alone, calculated from the extrapolation to 0% D 2 O of √ (I(0)/C) at the lipid/ DDM match point (16. 5% and 18% D 2 O respectively for the native and the cross-linked HTL) putting a zero value at 39% the match point of the protein, indicated that the HTL complex included one copy of each subunit. Contrast match point Match total for the particle occurs at D 2 O concentration ρ ∆. = V ( ) 0. It is significantly lower than that of protein alone indicating the presence of a component (DDM/detergent mixture) of lower CMP. Incorporating into the above equations the experimental √ (I(0)/C vs %D 2 O line permitted the determination of the volume and CMP of the lipid/DDM component.
Hoechst 33342 (Invitrogen) was used to stain DNA. Samples were examined with a Zeiss LSM 780 microscope equipped with a Zeiss 63X/1. 4 oil Plan-Apochromat objective. Images were captured using a GaAsP spectral detector interfaced with ZEN 2011 software. Images were processed using algorithms of MetaMorph 7. 1 software. Image background was treated with "Background and Shading correction". Merged images were obtained using "Color combine" and spectral colocalisation was performed using "Linescan". FLIM-FRET. Time-domain FLIM was performed with a multiphoton microscopy system, based on a Zeiss LSM 510 Meta NLO equipped with a Ti: Sapphire Chameleon-XR pulsed laser (Coherent). Time-resolved detection was afforded by the addition at a non-descanned output of a fast hybrid photomultiplier (HPM-100-40) and SPC-830 time-correlated single-photon counting (TCSPC) electronics (Becker & Hickl).
For EGFP excitation, laser power at 900 nm was adjusted to give average photon counting rates of the order 10 4 -10 5 photons s -1 (0. 0001-0. 001 photons/excitation event) and with peak rates approaching 10 6 photons s -1 , below the maximum counting rate afforded by the TCSPC electronics to avoid pulse pile-up. FLIM acquisitions were performed on living mitotic cells (2 min acquisitions for single micrographs; 20 s acquisitions for the movie). Images were taken with a Zeiss 63X/1. 4 oil Plan-Apochromat objective. For the movie and foci trajectory study, images were aligned with ImageJ 1. 44 software, using "StackReg" plugin ("Rigid body" option).
Acknowledgements We thank  Maithé Coppey-Moisan  ( Institut Jacques Monod, Paris, France ) for pmCherry vectors,  Cécile Gauthier-Rouvière  ( Centre de Recherche de Biochimie Macromoléculaire, Montpellier, France ) for pEGFP-RhoA-V14 vector. We thank  Paul Barber  ( University of Oxford, UK ) for TRI2 software. This work was possible thanks to  Montpellier RIO Imaging  facility. We are grateful to  Robert Hipskind  ( Institut de Génétique Moléculaire de Montpellier, Montpellier, France ) for helpful discussions. This work was supported by the  Agence Nationale de la Recherche  (grant number  08-BLAN-0037-02 ), and the  Fondation ARC pour la Recherche sur le Cancer. A. L. was supported by the  Centre National de la Recherche Scientifique , the  Région Languedoc-Roussillon  and the  Fondation pour la Recherche Médicale.
(Figure  2A ). This mutation, inherited from his healthy mother, was previously reported in SCID patients  (1). No other missense and nonsense mutations, as well as insertions and deletions, were found in coding exons or exon-intron boundaries in genomic DNA. Since the phenotype of the patient clearly pointed to an IL-7R deficiency due to the absence of CD127 expression and naive CD4 and CD8 T-cells (Table  1 ; Figure  1B ), we revaluated the coding sequence of the IL7R gene. Apart from the c. 353G>A mutation, we only found another heterozygous synonymous mutation that affects codon 111 (c. 333T>A, p. V111V) (Genbank NM_002185. 3). This mutation was inherited from his healthy father, but its absence from various mutation repositories (dbSNP v. 146, Human Gene Mutation Database Professional, ClinVar, 1000 Genomes Project) indicates that it is a rare polymorphism.
333T>A and c. 353G>A mutations. (B) Representation of the exon 3 truncation in the paternal mutated allele (c. 333T>A), in which the last 49 nucleotides of exon 3 are skipped. cDNA was obtained from the IL-7R-deficient patient, and RT-PCR was done using following set of primers corresponding to IL7R that amplified a part of exon 2, exon 3, and a part of exon 4 (IL7R-Exon2-F-5′-GACCTGTGCTTTTGAGGACC and IL7R-Exon4-R-5′-TCATCCTTTTCCTGGCGGTA). RT-PCR gel shows two bands corresponding to maternal allele (360 bp) and the paternal allele (311 bp) that lacked the last 49 nucleotides of exon 3. Sequencing trace of the IL7R cDNA sequence illustrates the presence of the truncated version, as well as the presence of the maternal allele in the non-truncated version of the mature mRNA. (C) Structural analysis of IL7R-IL7 complex was done using the structure prediction of IL7R-IL7 as reference PDB code: 3UP1 (2).
The C-terminus IL-7R protein that is truncated after residue 119 is colored in gray. Structure image was done with the Pymol software package (PyMOL Molecular Graphics System). 1 ). Analysis of IL-7 induced pSTAT5 (Y694) in T-cells from the patient was also reduced in comparison with healthy donors (Figures  1C, D ). At molecular level, IL7R mRNA expression in T-cells in samples post-HSCT was severely reduced in the patient compared with healthy donors (Figure  1E ). The immunological findings after HSCT of this patient were compared with another IL-7R deficient patient (P2B) (3) who experienced complete immune reconstitution 19 years post-HSCT (Table  1 ). The protocols of this study were approved by the Institutional Review Board of Hospital Universitario 12 de Octubre (Madrid, Spain).
Estimating the integrated L 0 Here, we describe the technique to estimate the global L 0 using telemetry data from the Gemini South 8 m telescope and its multiconjugate adaptive optics (MCAO) system, GeMS  (Neichel et al. 2010). It is based on the auto-correlation of slopes acquired from the laser guide star (LGS) WFSs. The first step in the method consists in computing a set of simulated or theoretical auto-correlation functions for different values of L 0 s that are later used to fit the auto-correlation function obtained from LGS telemetry. The object-oriented MATLAB adaptive optics (OOMAO) package (Conan & Correia 2014) has been used to simulate the phase screens. OOMAO is based on a small set of classes representing the source, atmosphere, telescope, wavefront sensor, deformable mirror and an imager of an AO system.