dataesr/scientific-paragraphs-categorization huggingface dataset:
). The membranes were finally washed thrice with 0. 1% PBsT and detected by eCL method. Next, to determine the expression of β-actin, the same membranes (for each tested protein) were incubated with mouse anti-β-actin-HRP monoclonal antibody for 1 h at room temperature, washed (3x10 min 0. 1% PBsT), and detected by eCL system. Chemiluminescence was visualized using Image station 4000 (Carestream Health, Rochester, Ny, usA). Densitometry analysis of the western blots was performed using Carestream MI software 5. 0. 6. 20 (Carestream Health). All blots were normalized to that of β-actin, and the fold-change protein level expression is reported in comparison to that of the β-actin. ELISA. For the quantitative determination of 17-β-estradiol, osteopontin (OPN), TGFβ, VEGF, thrombospondin, and 25-OH vitamin D, eLIsA kits were used according to the manufacturer's instructions (Demeditec Diagnostics GmbH, Germany; R&D systems, Inc.
In addition, control wells loaded with either ethanol or DMSO based on the solubility of the tested agents were maintained. Absorbance of each solution was read using synergy H4 (BioTek Instruments usA) at a wavelength of 540 nm. entire washing procedure was performed on Biotek eL-406 washing station. The results were calculated as IC 50 value (inhibitory concentration 50%) -the dose (nM or µg/ml) of tested agent which inhibits proliferation of 50% of the cancer cell population. IC 50 values were calculated in Prolab-3 system based on Cheburator 0. 4, Dmitry Nevozhay software for each experiment  (35). each compound in each concentration was tested in triplicate in a single experiment, which was repeated at least thrice. Statistical evaluation. statistical analysis was performed using statistica version 10 (statsoft Inc.
Data collection For each non-admission throughout the study period, the on-call RRT intensivist prospectively filled out a register specifying information concerning the time and provenance of the request, the reason for it and the reason for the non-admission. The reasons for requesting could have variable degrees of severity and are listed in Table  1. There could be several reasons for a single request. A simple medical advice was defined as medical advice not requiring an ICU hospitalisation. An unspecified reason was defined as a request for which the reason was not collected in the register. Reasons for non-admission could be a patient considered 'too well to benefit' from an ICU admission, a patient considered 'too sick to benefit', or the lack of bed availability. Data in the tables and figures were prospectively collected.
A p-value of <0. 05 was considered statistically significant. Statistically significant variables after univariate analysis and clinically relevant variables were entered into the multivariate analysis. Kaplan-Meier survival curves were plotted, and the log-rank test was used to compare the 'later admission' group with the 'immediate admission' group and the patients initially not admitted presenting with respiratory events with those not presenting with respiratory events. Statistical tests were performed using the SPSS statistics software package (SPSS, Version 16. 0 Chicago, IL, USA).
MACROORGANISMS HOST HIGHLY DIVERSE MICROBIAL COMMUNITIES The number of studies on the diversity of microbial communities associated with marine macroorganisms has increased exponentially during the last 5 years but there is surprisingly no synthesis considering various phyla. Here, we gathered information from the literature (82 studies) to highlight that these communities represent a significant part of the total marine microbial diversity. We collected sequence number (sampling effort) and OTU richness data obtained using sequencing approaches (i. e. , clone-libraries and next-generation sequencing, NGS) and according to the following criteria: (i) at least one value of sampling effort and richness was reported per species and per study, (ii) a 97% similarity cut-off was used for OTU definition and (iii) availability of the total number of sequences and total richness or of the mean across replicates (more details are provided in Appendix and Supplementary Table  S2 ).
66), confirming that microbial diversity has not yet been fully explored in marine host-associated microbiota. However, collected data come from studies using different technologies and bioinformatic tools while various mechanisms are involved in the assembly of host-associated microbial communities. These two limitations prevent direct comparisons across taxa in our approach. Nonetheless, collected data support the conclusion that these communities represent a non-negligible part of the total richness of marine microbes. The sampling effort refers to the number of sequences obtained using clone-libraries (green) and pyrosequencing (red). OTU richness corresponds to the number of OTUs observed at 97% identity. Only one value of sampling effort and OTUs richness was retained per study and per species.
The product of GTT by SS defines the SD, i. e. , the estimated distance over which gut bacteria can be transported by their host. We collected data from the literature to evaluate the dispersion potential of gut microbes by estimating the SD for several groups of marine macroorganisms. We used information at the species level or provided a range at the smallest possible taxonomic unit depending on the data (Supplementary Table  S1  and Figure  3 ). The maximum SD estimated for benthic invertebrates such as crabs and shrimps is around 25 km. These unexpectedly high values arise from long GTT in crabs (>95 h) and relatively fast SS for shrimps (∼2 km. h -1 ). As a group, decapods exhibited a mean SD of 14. 3 ± 8. 1 km. Gammarids can only support SD lower than 10 km. These estimates are derived from combinations of disconnected studies and the real dispersion potential depends on GTT and swimming behavior, which are influenced by temperature and foraging behavior for the former aspect and by currents and habitat structure for the latter.
Baas Becking himself recognized that considering that "everything is everywhere" requires that microbial cells are transported and distributed homogeneously over the globe  (de Wit and Bouvier, 2006). Here is the first link with our StR hypothesis. Indeed, we provide evidence that motile macroorganisms constitute a dissemination vector for some environmental microbes, enhancing their dispersal to homogenize microbial communities at large scale. In a previous analysis of the original Baas Becking' paper, de  Wit and Bouvier (2006)  mention that despite the development of novel culture-independent approaches it would be impossible to obtain evidence for the "everything is everywhere" tenet. However, a recent study comparing a deeply sequenced water sample (∼10 M 16S rRNA reads) with 356 ICoMM datasets show the existence of a persistent microbial seed-bank throughout the global ocean  (Gibbons et al.
Study design This was a multicenter prospective study involving 6 centers located in Europe (Italy: Rome, Bologna and Palermo; France: Paris), North America (USA: Indianapolis), and Asia (Japan: Gifu). The study was approved by the Institutional Review Board of the coordinating center (Catholic University, Rome) and thereafter, by the Ethics Committee of each participating center. The trial has been registered in a publicly accessible registry (ClinicalTrials. gov identifier: NCT02307253).
Statistical analysis was performed using Stata software version 13 (Stata Statistical Software: Release 13, Stata Corp. , College Station, TX, USA). or enlarged lymph nodes (43 cases, 17. 5%) were enrolled. The mean size of the target lesion was 32. 6 ± 12. 2 mm. Among patients with solid lesions, 158 (64. 2%) were located in the pancreatic head, 27 (11%) in the uncinate process, and 18 (7. 3%) in the bile duct or the right liver lobe. Baseline characteristics are detailed in Table  1.
The C region is an elongated ␣-helical monomer, containing some disordered content We defined the C region of DISC1 based on two constructs encoding AA 691-836 and 684 -836 of full-length DISC1. Upon purification, the recombinant C region exists as both a prominent and a minor species according to SEC, however, only the more prominent, lower molecular weight species was stable (Fig. 3D ). AUC SE analysis showed this species to have a molecular mass of 20. 8 Ϯ 0. 2 kDa, strongly indicative of a monomer (Fig. 3E , predicted molecular mass: 20. 1 kDa), whereas AUC SV analysis of the species indicated it to possess an elongated shape (weighted average frictional ratio: 1. 45). CD showed this region to be helical, with some disordered content (ϳ25% random coil, based on deconvolution using the CDSSTR method in DichroWeb with reference dataset 4 (18 -21), Fig.
Construct generation A cDNA encoding for full-length human DISC1 (RefSeq accession number NP_061132. 2) was codon optimized for expression in E. coli (GeneArt, Thermo Fisher Scientific, Regensburg, Germany) and then cloned between the AscI and NotI sites of the pET-derived pESPRIT002 vector  (26)  for use in the ESPRIT screen. Ensuing constructs had their BAP tags removed by BspEI enzyme digestion prior to biophysical characterization. Additional subregions of DISC1 were subcloned from this vector and inserted into the pESPRIT vector at its AatII and BspEI sites. The identity of all constructs was confirmed by sequencing.
Circular dichroism For circular dichroism experiments, protein was desalted into 25 mM sodium phosphate, pH 7. 0, 150 mM NaF, 1 mM tris(2-carboxyethyl)phosphine. Circular dichroism spectroscopic measurements were carried out on a JASCO J-815 spectrometer (JASCO, Gross-Umstadt, Germany). A 1-mm optical path length cuvette was used. The temperature was controlled at 20 °C. Spectra were recorded from ϭ 260 to 185 nm at 1 nm resolution, 50 nm/min scan speed, and an integration time of 0. 5 s. For signal improvement, 10 accumulations were averaged. The obtained spectra were transformed to mean residue ellipticity after subtraction of the buffer spectra. Deconvolution of the data were performed on DichroWeb  (18, 19)  using the CDSSTR method and reference dataset 4  (20, 21).
Analytical ultracentrifugation Sedimentation velocity centrifugation experiments at 50,000 rpm and 20 °C were carried out in a Beckman Optima XL-A (Beckman-Coulter, Brea, CA), equipped with absorption optics and a four-hole rotor. Samples (volume 400 l) were pipetted into standard aluminum double sector cells with quartz glass windows. Measurements were performed in absorbance mode at detection wavelength 230 nm. Radial scans were recorded with 30-m radial resolution at ϳ1. 5 min intervals. The software package SEDFIT version 14. 1 was used for data evaluation. After editing time-invariant noise was calculated and subtracted. Continuous sedimentation coefficient distributions c(s) were determined with 0. 05 S resolution and F ratio ϭ 0. 95. Suitable s-value ranges between 0 and 20 S and f/f 0 between 1 and 4 were chosen.
Buffer density and viscosity had been calculated with SEDNTERP version 20111201 beta  (29). The partial specific volumes of the DISC1 protein fragments were calculated according to the method of Cohn and Edsall  (30, 31)  as implemented in SEDNTERP. Sedimentation equilibrium experiments were performed in standard aluminum double sector cells with quartz glass windows. Equilibria were established at multiple speeds. After equilibrium was reached, concentration profiles were recorded with 10-m radial resolution and averaging of seven single registrations per radial value. Data evaluation was performed using SEDPHAT version 10. 55b  (32).
Acknowledgments-The ESPRIT platform of the Grenoble Instruct Centre (ISBG: UMS 3518 CNRS-CEA-UJF-EMBL) receives financial support from the French Infrastructure for Integrated Structural Biology (ANR-10-INSB-05-02) and the Grenoble Alliance for Integrated Structural & Cell Biology (ANR-10-LABX-49 -01) within the Grenoble Partnership for Structural Biology (PSB).
This work was supported by the  European Community 's  Seventh Framework Program  Grant  FP7/2007-2013  under  BioStruct-X Grant  agreement  283570 , as well as the "Biostruct" and "iBrain" graduate schools at the  Heinrich Heine University , the Seventh Framework Program  MC-IN "IN-SENS" Grant   60761  (to C. K. ), the  Brain Behavior Research Foundation NARSAD   Independent Investigator Award Grant   20350  (to C. K. ),  Alexander von Humboldt Stiftung  Grant  1142747  (to N. J. B. ),  Forschungskommission der Medizinischen Fakultät der Heinrich-Heine-Universität Düsseldorf  Grant  9772547  (to N. J. B. ),  Fritz Thyssen Stiftung  Grant  10. 14. 2. 140  (to N. J. B. ), and grants from the  Impuls und Vernetzungs-Fonds der Helmholtzgemeinschaft Portfolio programs "Technology and Medicine" and "Drug Research"  (to D.
The aim of this study was to investigate variation in flower and fruit production of Lodoicea growing in closed palm forest and in degraded shrubland, and to determine the main factors influencing this variation. Specifically, we asked the following questions: (1) "Are soil nutrients associated with inflorescence and flower number, and fruit set?" (2) "What is the relationship between pollen availability and healthy and abnormal fruit production?" (3) "What is the relationship between genetic diversity and flower and fruit production?" and (4) "Are habitat fragmentation and reduced adult tree density related to female fecundity?" In addition to exploring variation in numbers of flowers and fruits, we present data on seed size in Lodoicea. We discuss the implications of our results for the future sustainable management of Lodoicea and drivers of plant reproduction in general.
| Field survey We used the method described above to study the reproductive output of 57 female Lodoicea trees, chosen to represent varying degrees of isolation from male trees. To achieve a balanced representation of female trees along a gradient of distance to the nearest male, females were randomly selected within distance classes. Thirty-nine of the trees were in palm forest, while 18 were in degraded shrubland. Trees with obvious signs of poaching were excluded from the study. For each tree, we examined all inflorescences, recording the numbers of undeveloped ovules, developing fruits, abnormal fruits, and successfully shed mature fruits. We then aggregated these data to obtain "all flowers" (the sum of unfertilized flowers plus normal plus abnormal fruits), abnormal fruits, and "all fruits" (the sum of all developing fruits plus any mature fruits that had been shed).
ACKNOWLEDGMENTS We thank  Seychelles Islands Foundation ,  Ravin de Fond Ferdinand Nature Reserve  and  Seychelles National Parks Authority , and all of their staff. In particular  Marc Jean-Baptiste ,  Wilna Accouche ,  Nancy Bunbury ,  Estephan Germain  and  Allen Cedras  for providing logistical support in the field, and valuable advice. Gerry Rose ,  Fabio Lesperance , and  Arnold Moosa  helped greatly with field work. Björn Studer  ( Soil Protection ),  Sabine Güsewell  ( Plant Ecology ), and  Britta Jahn-Humphrey  ( Sustainable Agroecosystems ) made nutrient analysis.
When proving invariance properties of a program, we face two problems. The first problem is related to the necessity of proving tautologies of considered assertion language, whereas the second manifests in the need of finding sufficiently strong invariants. This paper focuses on the second problem and describes a new method for the automatic generation of loop invariants that handles polynomial and non deterministic assignments. This technique is based on the eigenvector generation for a given linear transformation and on the polynomial optimization problem, which we implemented in the open-source tool Pilat.
Application and results The plug-in Pilat, written in OCaml as a Frama-C plug-in (compatible with the latest stable release, Aluminium) and originally generating exact relations for deterministic C loops, has been extended with convergent invariant generation and non deterministic loop treatment for simple C loops. It implements our main algorithm of invariant generation in addition to the optimization algorithm of figure  5 , and generates invariants as ACSL  [1]  annotations, making them readily understandable by other Frama-C plugins. The tool is available at  [7]. More generally, we evaluated our method over the benchmark used in  [21]  for which we managed to find an invariant for every program containing no conditions. Though this benchmark has been built to test the effectiveness of a specific abstract domain, we managed to find similar results with a more general technique.
Our results are given in table 1. As ellipsoids are a suitable representation for those examples, we have choosen 2 as the input degree of almost all our examples. The optimization script is based on Sage  [23]. Note that the candidate generation is a lot faster than the optimization technique, mainly because of two reasons : • computing min is time consumung for a big number of constraints; • it is imprecise and its current implementation is incorrect (it outputs a lower approximation of the answer). We have to compute verifications in order to find a correct answer.
Thermodynamic analysis of the Ti-Si-Ni-N system equilibrium Prior to experimental investigation, a preliminary thermodynamic analysis of the equilibrium in the Ti-Si-Ni-N system was performed with the help of the ThermoCalc software  [42]. The relevant thermodynamic descriptions of the Ti-Si-N and Ti-Si-Ni systems reported by S. Sambasivan et al. and T. Tokunaga et al. , respectively, were used for these calculations  [43, 44]. The so-calculated equilibrium diagrams at 1100°C are shown in Figure  1a  and Figure  1b. The particularity of the Ti-Si-Ni system is the formation of a Si-rich ternary liquid phase at this temperature. This liquid phase originates from the NiSi-NiSi2 eutectic reaction at only 956°C, as shown in Figure  2   [45]. The phases stability diagrams for the (1-x) TiSi2 + x Ni mixtures were calculated as a function of nitrogen content at 1100°C for x = 0.
While the single tryptophan Trp-214 is fairly distant, two tyrosines, Ty r-138 and Ty r-161, are in close proximity. The picture has been prepared with the AutoDock software package  [21]  (http:// autodock. scripps. edu/resources/ references). The Power of SPecTroScoPy nonlinear fitting/deconvolution process using the impulse response model functions (Eqn. (3) and Eqn. (  4 )) () () ( ) () t f t r t i par 2 1+ = (3) () () ( ) () t f t r t i perp - = 1 (4) convoluted by the Gaussian instrument response function, I(t) ∝ i(t) ⊗ G(t). The model functions thus obtained were fitted to the experimentally measured (I par ) and (I perp ) signals. The full width at half maximum (fwhm) value of a Gaussian apparatus function was found to be about 375 ± 12 fs fwhm at 330 nm.
8-4. 3 Å neutron wavelength range  58. Twenty images (24 hours per image) were collected in two crystal settings to help fill the blind region. Laue images were indexed and integrated using the LAUEGEN 59 suite of programs, wavelength normalized to account for the spectral distribution of the quasi-Laue beam using LSCALE  60  and then scaled and merged using SCALA  61. An X-ray data set was collected on the same crystal using the Rigaku HomeFlux X-ray setup equipped with a MicroMax-007 HF X-ray generator, Osmic VariMax optics and an R-AXIS IV+ + image-plate detector. The diffraction data were indexed, integrated and scaled using the HKL-3000 software suite (Table  1 ) provides the data processing statistics for the neutron and X-ray datasets. An initial model of COx consisting of PDB file 1MXT  19  with all alternate conformations and water molecules removed was refined against the X-ray data.
The joint refinement feature of PHENIX allows the refinement of the occupancy of the H/D atoms that have been added at exchangeable sites to determine the level of exchange of H for D that has occurred at each site. DOD and OD type waters were modeled according to the presence of 2F o -F c and F o -F c nuclear density and several further cycles of joint refinement and modeling performed. The final data refinement statistics are shown in Table  1. Omit maps were calculated by removing the omit atom followed by three cycles of coordinate, atomic displacement parameter and occupancy refinement. Omit maps for main chain D atoms were calculated by removing sets of 50 main chain atoms consecutively along the protein sequence, followed by three cycles of refinement. F o -F c density was inspected and the N-peak distances determined by placing an atom at the center of the peak and optimizing the atomic position using the real-space refine option in COOT.
All the geometries were fully optimized with the B2PLYP-D3BJ functional in conjunction with the Weigend-Ahlrichs Def2-TZVPP basis set  64. The suffix D3BJ refers to the inclusion of the D3 empirical dispersion correction  65  with a Becke-Johnson 66 damping function as recommended in ref. 67. The joint X-ray/Neutron structure of COx is deposited in the Protein Data Bank with the PDB ID: 5KWF. The conserved water molecule known as Wat541 has alternate numbering in the other cholesterol oxidase structures discussed in this manuscript. In 4U2S it is numbered as W1362 (anaerobically reduced structure) and in 4U2T is is numbered as W818 (aerobic isopropanol soaked).
Acknowledgements The authors want to thank Proyectos  FONDECYT 1120001  and  1160106  and  Centers of Excellence with Basal/CONICYT Financing ,  FB0807 , ( CEDENNA ) for nancial support. This work was done under the  International Collaborative Program LIA-MIF 836 (CNRS/CONICYT ). We also thank  Prof. Albert Escuer  ( Universitat de Barcelona, Spain ) for providing the magnetic measurements. P. F. C. acknowledges the doctoral grant  21110612  from  CONICYT. Brazilian EPR  facilities are supported by grants from  CeRTEV, Center for Research, Technology and Education in Vitreous Materials ,  Fapesp 2013/ 07793-6.
Initial Finite Element Modelling of Shaky Bridge The finite element (FE) analysis software Strand 7 (Strand7 Pty Ltd 2014) was used to build a detailed FE model of the structure (Figure  2(a) ). The overall geometry of the model reflects the actual shape of the structure and the cross-sectional details match the as-built geometry of each section, measured by the authors for this work using slide calipers, dumpy level and a staff. All members were modelled as beam elements and the suspension cable is modelled using a number of beam elements, similar to other existing works  (Xu Y. L and Xia Y, 2012; Kilic et al. , 2015; Soyluk et al. , 2013). Since the bridge deck is significantly stiff, this approach is deemed adequate for the scope of the investigation. The connecting clamps between cables and hangers were simplified to beam elements, as shown in Figure  2     The material properties were modelled as per specification in the David Rowell patent document.
e. DOD). Therefore it is clear that distinguishing structural frequencies from excitation frequency from output-only vibration data (without having any information about excitation) is a challenge. In this regard, wavelet packet decomposition as outlined above is employed for system identication. Figure  8  Fourier spectra of vibration data under various pedestrians walking The vibration data under RW walking is utilised. First, the acceleration at the mid-span of the bridge is decomposed using wavelet packet transform (WPT). Depending on the sampling frequency (i. e. , 50 Hz) and lower frequency of interest, a scale level (s) of 6 is chosen for the WPT. The wavelet basis is selected as db5, an orthogonal basis that is suitable for oscillating vibration data. WPT of vibration data results in various low and high frequency coefficients  (Mallat, 1998)  that are mono-component (i.