dataesr/scientific-paragraphs-categorization huggingface dataset:
1 mm in the vertical direction  (Fischetti et al. , 2009). The (GM/CA-CAT) dual canted undulator beamlines at the APS that played a major role in the 2012 Nobel Prize has developed a 'minibeam' apparatus that conditions the focused beam (20 mm Â 65 mm) to either 5 mm or 10 mm (FWHM) diameter with high intensity. Recently a quad mini-beam collimator has been implemented which is able to deliver high intensity (5 Â 10 10 and 3 Â 10 9 ) with a minimum focal size of 5 and 1 mm at the sample position. There are now some 24 micro-focus macromolecular crystallography beamlines delivering beams of 5-20 mm on the sample over a broad energy X-ray range from 3. 5 to 35 keV  (Smith et al. , 2012). The increase in X-ray brilliance has required major improvement in the X-ray detectors. At the second-generation sources such as SRS (Daresbury), Photon Factory and NSLS the early data were collected on photographic films until the image-plate systems were introduced.
Partially occupied waters and residues with multiple conformations were built in manually after inspection of 2F o À F c and F o À F c electron density maps. Only H atoms visible in F o À F c difference maps at ! 2 were included in the final model. tion data at RT were collected from the D-exchanged crystal to 2. 3 A ˚resolution (Fig. 5 ) over a period of 15 days using LADI-III. Data were indexed and integrated using LAUEGEN  (Campbell et al. , 1998) , wavelength-normalized using LSCALE  (Arzt et al. , 1999)  and scaled and merged using the CCP4 program SCALA  (Winn et al. , 2011). Data-collection and processing statistics for the neutron data are given in Table  4. Structural refinement using the neutron data is currently in progress and will be reported elsewhere. In addition, perdeuterated AcNiR has since been produced in the Deuteration Laboratory at the ILL, and larger crystals of $ 1 mm 3 have been grown (Fig.
Molecular sensing: heme-based gas sensors In biology, substrates have distinctive sizes, shapes and charge distributions that are specifically recognized by their target biological partner proteins. The discrimination between the gases O 2 , NO and CO by heme proteins is a remarkable example of biological specificity because these molecules are apolar and of very similar size. Molecular recognition of these gases is essential for respiration, cell-signaling, aero/chemotaxis and regulation of gene expression. Cytochrome c 0 (CytCp) belongs to a family of pentacoordinate (5c) heme proteins that discriminate between these diatomic gases efficiently helping protect bacteria from nitrosoative stress and/or NO shuttling during denitrifcation. resolution X-ray structure of CytCp from Achromobacter xylosoxidans (AxCytCp) (PDB code 2YKZ)  (Antonyuk et al.
Neutron diffraction data collection and processing for AxCytCp The largest crystal of AxCytCp with volume $ 1. 5 mm 3 (3. 2 Â 0. 7 Â 0. 65 mm) was soaked in D 2 O buffers one month prior to neutron data collection in order to exchange labile H atoms for D atoms. Using exposures from 3-18 h, diffraction data at RT were collected from the D-exchanged crystal to 2. 1 A ˚resolution over a period of ten days using LADI-III. Data were indexed and integrated using LAUEGEN  (Campbell et al. , 1998) , wavelength-normalized using LSCALE  (Arzt et al. , 1999)  and finally scaled and merged using the CCP4 program SCALA  (Winn et al. , 2011). Data-collection and processing statistics for the neutron data are given in Table  5. Structural refinement using the neutron data is currently in progress and will be reported elsewhere.
Materials and Method We chose ILA ACTIVVE ® device (NOVALUNG ® ) with MINILUNG ® membrane and a double line femoral catheter (NOVAPORT TWIN 24F). A training for each member of the team was conducted (physicians and nurses) and we wrote a detailed procedure between February 2014 and July 2014. We wrote a procedure for: the preparation of the device, laying the catheter, monitoring, removal of the catheter and the machine, any malfunctions. ). Between august 2014 and February 2015, data were collected for each patient receiving ECCO2R. Indication, mortality at J28, duration of ECCO2R, complications and success of the technique were evaluated.
citri pv. citri pathotypes may provide new targets to aid in the prevention of bacterial diseases and possibly inform new strategies to treat and manage citrus canker outbreaks. Most notably, it would also allow the improvement of our understanding of how bacterial pathogens evolve in terms of host range variations when coevolving with their host(s) in agrosystems, and more generally on plant bacterial disease emergence  [13]. Here we use NGS data from 42 strains of X. citri pv. citri representing the three pathotypes and selected on the basis of our current knowledge of the bacterium's genetic diversity as well as one outgroup strain of X. citri pv. bilvae (also pathogenic to rutaceous species but with a distinct symptomatology  [14] ), to construct a phylogeny using aligned nonrecombinant genomic regions from all strains.
Presence/absence analysis We used orthologs identified by BLAST best reciprocal hits (BRH) (Additional file 4) in order to estimate the core-genome, pan-genome and number of singletons in our dataset, as well as to catalog gene presence and absence between pathotypes that are differentially present or absent in all strains of a pathotype. Genes related to IS elements and phages were excluded from the analysis due to their similarity, which makes orthology difficult to assign. We estimate that there are 2513 genes in the core-genome, 10,011 genes in the pan-genome and 2445 singletons spread across the 43 X. citri pv. citri strains. We identified four gene islands that are differentially present or absent between the pathotypes (Table  3 , Fig. 1 ). Several genes previously identified as playing roles in pathogenicity or biofilm formation are found on these islands including the A w -specific avrGf1 gene on Island 1 (previously identified as being differentially present between strain IAPAR 306 and A w strain Xcaw12879  [12] ), and xrvA, mobL, XAC1496, XAC1499 and XAC1509 on Island 3 that are absent from A*.
); it cannot cause symptoms to disrupt plant tissues to liberate nutriments and/ or exit (T3E, enzymes, toxins etc. ); it cannot uptake and/or use nutriments (CUT system, transport, enzymes etc. ). More generally deficient sensing, signal transduction or regulation may be involved in the inability to cause disease. In our dataset, the low level of polymorphism along any given branch of the tree (the majority of inferred mutated genes contain only a single polymorphism specific to the pathotype branch) does not provide enough power to estimate selective constraints accurately in a pathotype-specific manner  [49]. Several genes contain more than one nonsynonymous mutation per pathotype or across pathotypes, making them interesting candidates as potential targets of selection. Genes that are already known to play a role in pathogenicity are also prime candidates for the evolution of host range, especially genes that have differences in an A-specific manner.
Contig mapping The assembled contigs for the 43 strains were mapped onto the complete reference genome of X. citri pv. citri strain IAPAR 306  [54]  using BLAST  [55]  with manual curation. Contigs of less than 200 bp were removed. The contigs were initially filtered for plasmid sequences with BLAST  [55]  against a database of whole plasmid sequences from X. citri pv. citri strain IAPAR 306, X. euvesicatoria strain 85-10 [19], Xanthomonas fuscans subsp. fuscans  [56]  and the plasmids from a further two X. citri pv. citri strains, C40 and JK2-10. To map to the reference contigs were required to be at least 90 % identical to the reference over at least 20 % of their length and be the top hit to a given region. In cases of duplicate contigs, the top scoring hit was mapped to the reference. The mapped genomes for all the strains were aligned using Mugsy  [57] , and the resulting aligned blocks were ordered according to strain IAPAR 306.
GC content, GC skew and diversity A Python script was used to calculate GC content, GC skew and sequence diversity. Sliding windows of 8 kb were passed along the alignment, and the average values were plotted using Circos  [61]. Sequence diversity was measured using Hamming distance  [62]. Recombination analysis RDP v4. 16  [63]  was used to detect regions that have undergone recombination. The alignment was reduced to a length of 56,705 by extracting SNP columns from the whole genome alignment blocks. IAPAR 306 was used to order the SNPs so only SNPs (including gaps) from alignment blocks that were present in strain IAPAR 306 were included in the SNP alignment. The SNPs from regions not present in strain IAPAR 306 were examined but no pathotype-differentiating SNPs between A* and A w were found.
Phylogeny A phylogenetic tree was reconstructed from the full genome alignment (Fig. 2 ). Detected regions of recombination as well as gap columns and 20 bp either side were removed as these regions are often at the edges of contigs and are more likely to contain sequencing errors or regions of poor alignment. Model selection was performed with jModeltest 2. 1. 7 [64] , and the SYM model chosen using the Bayesian Information Criterion. The phylogeny was reconstructed using PhyML  [65]  with chi-square branch support. A phylogeny from an alignment containing regions of recombination and a reduced distribution of A strains was also constructed to compare with a recently published phylogeny of X. citri pv. citri strains  [17]  (Additional file 3). The A strains used were those containing recombination Event 16, which was reported to be present in all A strains in the published dataset.
To match the phylogeny in the recent publication, recombination-containing phylogeny was constructed using PhyML under the GTR model, with chi-square branch support values. The trees were visualized with Figtree v1. 4. 1  [66]. Both phylogenies and alignments were deposited in the Dryad online repository (http://dx. doi. org/10. 5061/dryad. 8t53k).
Presence/absence analysis Gene annotations were performed using an automated pipeline implemented by MaGe  [70, 71]. Predicted proteins were compiled into a database and an all-againstall BLASTP was performed. Proteins associated with IS elements, and phage-related proteins were flagged and removed. Best reciprocal hits (BRH) to Xanthomonas citri strain IAPAR 306 were assigned from each of the other strains. Proteins from other genomes that were unassigned in the first round BRHs were then used as queries against the remaining genomes until all genomes had been examined. For each group of BRH assignments (Additional file 4), the distribution of the proteins in A, A* and A w were examined to find those that were completely present in at least one of the pathotypes while being completely absent in at least one of the others.
Acknowledgements The authors would like to thank the teams at the  Microbial Genome Annotation & Analysis Platform  for their assistance. The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  ([FP7/2007-2013]) under grant agreement  n°263958  ( RUN-Emerge  project). Sequencing was financed through the Genoscope  AP 09/10  project # 18. This Work was supported by  France Génomique National  infrastructure, funded as part of " Investissement d'avenir" program  managed by  Agence Nationale pour la Recherche  (contrat  ANR-10-INBS-09 ). The  European Union (ERDF) ,  Conseil Régional de La Réunion and CIRAD  provided financial support.
Lifetime of PÀ The transient spectra of the three strongly coupled systems are shown in Fig. 6 , together with their decay kinetics. The spectra do not evolve over the decay, indicating that they are dominated by a single transient species. The decays are not single exponentials due to the heterogeneities of the samples at the high concentrations that were used to induce strong coupling. The angle dependence of the decay was also measured for TDBC and was found to be invariant, indicating that the lifetime is not dependent on probed k-vector. This indicates that there is no bottle-neck along the PÀ branch shown in Fig. 6  for this sample. Such decay bottle-necks have been seen in other conditions and samples for strongly coupled TDBC. 24 able  1  below summarizes the dynamical data for the strongly coupled molecules.
Acknowledgements The authors acknowledge support from the  ERC  (Grants  227557 ), the  International Center for Frontier Research in Chemistry (icFRC, Strasbourg) , the  ANR Equipex " Union " ( ANR-10-EQPX-52-01 ), the  Labex NIE  projects ( ANR-11-LABX-0058_NIE ),  CSC  ( ANR-10-LABX-0026_CSC ) and  USIAS  within the  Investissement d'Avenir program   ANR-10-IDEX-0002-02.
Confocal measurements Confocal microscopy was used separately to determine the microstructure of the actin cytoskeleton before and after inhibition of the actin polymerization and acto-myosin contractility. Confocal image stacks (Z-stacks) were acquired with a Leica TCS SP8 using Argon laser (488 nm) and a 40x immersion objective. To quantify the distribution of the actin fibres in the cell, the mean fluorescence intensity of three regions of the cell (nucleus, perinucleus and periphery) was analyzed using the ImageJ software 1. Regions of interest were defined by dividing the entire z-stack of confocal images into three sub-stacks where the mean fluorescence intensity is then calculated.
Thus it is not possible to describe the whole frequency domain with the SGR model. Explanations have been proposed in other works  [36, 37]. In these papers, it appears that the frequency dependent behavior can be explained by alternative mechanisms such as the collective behaviors of molecular non-covalent interactions of proteins. Next, measurements were made at different cell locations, as shown in fig. 3. Data was obtained by indenting on top of the nucleus, perinucleus and periphery (the cell edge). Confocal microscopy images were made and positions of the indentations are shown, together with a height map of the actin microstructure. Similar results are obtained for the three locations but the moduli increase as moving towards the edge (N to P to E). We described our data with the simplified model and the fitting parameters of the moduli of T24 cells (G 0 N , a and b only) are represented in fig.
Inhibiting the actin polymerization with LatrunculinA Figure  5  shows the viscoelastic properties of T24 cells before and after treatment with Latrunculin A (0. 1 µM) at three different locations. Measurements were carried out before (t = 0) and after treatment (t = 20 min and t = 30 min). The reversibility of the treatment was verified (after the medium was rinsed, cells are stable for about 30 min and mechanical properties were recovered; data not shown). Confocal images corresponding to the two conditions (fig. 5 ) show that the actin filaments are indeed disrupted (for example, actin fibres that go from the bottom of the cell to the top disappear after treatment). However, there are still actin fibres at the basal side, this might be due to the low drug concentration we used (it was chosen so that the cell does not retract completely in order to perform AFM measurements).
We thank the  ANR  for grant No. 12-BS09-020-01  (TRANSMIG), the  Nanoscience foundation  for support of the AFM platform. This work has been partially supported by the  LabeX Tec21  ( Investissements d'Avenir -grant  agreement  No. ANR-11-LABX-0030 ). Open Access This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/4. 0),which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Developing the Internet Study Published genetic studies on exercise-induced injuries primarily focus on soft tissue injuries  [9] , and there is only one study demonstrating association between genetic polymorphisms and increased risk of bone stress injuries  [10]. In an attempt to address this, we have designed a study to analyze Australian runners using genome-wide association techniques to identify gene variants that contribute to increased risk of, or protection from, Achilles tendinopathy and/or bone stress injuries. To achieve a large sample size, the study must provide a reliable and convenient method of data collection from prospective participants, allowing them to participate in the research from home and with their own device. We therefore developed an Internet activity survey to prospectively recruit participants relevant to our test groups.
Retrospective surveys of sporting injuries have been shown to have some limitations for injury epidemiology research because of issues with injury recall  [11, 12]. In order to counteract these issues, participants were only asked to recall injuries that had occurred in the previous 2 years. Surveys should be evaluated for reliability, a critical measurement property for health-related and physical activity variables. Reliability refers to the consistency of answers obtained by the same participant when a measurement is repeated on different occasions  [13]. Test-retest reliability is measured by having the same participants complete a survey at two different points in time to see how stable the responses are. Consistency is then quantified with a kappa coefficient statistic for categorical data  [14].
Internet survey instruments are increasingly being used as a preferred method of conveniently collecting data from a wide range of participants from various locations. The reliability of survey instruments delivered on the Internet has been previously demonstrated, showing that in the instance of retrospective tobacco exposure and risk, this method of data collection is reliable  [15]. Furness et al  [16]  also demonstrated success using an Internet survey instrument for the study of injuries collected in a retrospective manner in surfing athletes, whereby they recruited 1348 surfers. This high level of response enabled the researchers to produce a comprehensive dataset that is the largest study of surfing injuries in Australia  [16]. The purpose of the study reported here is to test the test-retest reliability of an Internet survey platform from a convenience population of first responders, and pilot test participants who accepted an invitation to describe their recreational running epidemiology.
Self-Report Questionnaire The questionnaire administered was designed to enable recruitment as part of the wider study entitled, "The Genetics of Exercise-Induced Injuries in Tendon and Bone. " This study has very broad aims in the range of wanting to recruit very large numbers of participants to provide injury epidemiology among recreational runners, as well as performing genetic assessments for the injury risk factors in a smaller subsample of the overall injury epidemiology study. The platform used to deliver the survey was the Internet and commercial survey software (SurveyGizmo). The Internet survey was advertised through appropriate forums relevant to the intended population to analyze sporting injuries and training practices. Participants provided us with data on their demographics and running injuries, but the survey provides a platform for determining whether a participant met the wider genetics study's inclusion and exclusion criteria.
They were also asked to stipulate any previous hip, knee, or ankle surgery over their lifetime. In addition, participants were asked to report on their general health, provide any knowledge of existing conditions or diseases, and any known antibiotic or prescribed drug administration. They were asked to describe their regular dietary practices including sport supplement use, as well as any body weight fluctuations. Participants were also asked to report their age, sex, height, weight, and ethnic background to collect demographic data for further epidemiology analysis. Some of the key variables, important to clarify inclusion or exclusion from the wider genetics study previously mentioned, were then selected for test-retest reliability here (Table  1 ). Questions of interest included those that addressed diagnosis of the injuries, as these variables may result in less than optimal reliability due to the retrospective design of the study  [11].
Test Group 2 After data from test group 1 suggested that reliability was more than moderate for 19/19 of the variables analyzed, we then sought to maximize the variability in response and strength in reliability of our questionnaire by soft launching the survey to a wider population using a different test-retest method. We invited a larger convenience sample of participants by promoting the wider genetics study through a local running club of 900 members via email platform as described earlier for group 1. The same inclusion criteria were applied and participant information was provided at the commencement of the survey, and checking the box "I ACCEPT" resulted in access to the Internet survey and provided informed consent. In response to the invitation, 122 participants accessed and consented to the conditions of the study as logged by SurveyGizmo.
Principal Findings The wider study, for which this survey will provide epidemiology information and a participant cohort to recruit from, will be the first, to our knowledge, to examine the genetic predisposition of tendon and bone injury in adult recreational runners. Recruitment for the larger study will involve the use of this survey, tested here initially for test-retest reliability. The results indicate that the self-reported questionnaire, delivered using the Internet commercial software, provided stable and reliable answers for many of the most important measures required for recruiting to the larger study on tendon and bone injury. The Internet delivery of a retrospective injury study is a convenient method for remote collection of data from participants and has been used successfully in the analysis of sports-induced injuries in surfing  [16]  and strongman athletes  [18].
Acknowledgments These studies were supported by funding from the  Collaborative Research Network for Advancing Exercise and Sports Science (CRN-AESS ; RD, NV, JK, and DCH). The authors thank the  CRN-AESS Scientific Committee  members who contributed to this work:  Professor Nuala Byrne  ( Bond University ),  Professor Matthew A Brown  ( University of Queensland, Diamantina Institute ) and  Professor Maria A. Fiatarone Singh  ( University of Sydney ).
Acknowledgements. We thank the  Solomon Islands' Ministry of Fisheries and Marine Resources (MFMR)  and the  Ministry of Environment ,  Climate Change ,  Disaster Management  and  Meteorology  for providing logistical assistance and research permits (MECDM). We particularly acknowledge the assistance offered by  Josef Hurutarau ,  Joe Horokou ,  Geoff Mauriasi ,  Agnetha Vavakaramui ,  Melchior Mataki  and  Rose Babaua  from MECDM, as well as  Peter Lausu  and  Rosalie Masu  from  MFMR. Mike Donoghue  and the late  Lui Bell  of the Secretariat for the  Pacific Regional Environment Programme , and  Sue Taei  of  Conservation International , provided valuable advice on regional policies for conservation of cetaceans. We thank  Mike Donoghue ,  Robert Brownell Jr  and  Phil Clapham  for editorial review of the manuscript and  Mark J.