dataesr/scientific-paragraphs-categorization huggingface dataset:
Strikingly, a fourth ST, ST6, was identified only in the slaughterhouse A staff group and with a rather low prevalence of 7. 1%, corresponding to two cases of asymptomatic infection among the 50 individuals tested, and not in the control group. However, the presence of avian ST6 in the single cohort of in-contact workers with chickens strongly suggested zoonotic transmission of the parasite, especially since this ST has never been identified in previous molecular surveys conducted in Lebanon  [32, 34]. To reinforce this hypothesis, all the ST6 SSU rDNA gene sequences available in the databases and covering the domain amplified by qPCR in the present study were extracted and aligned with those obtained in our survey from humans and animals, for a total of 94 sequences. By analyzing the sequence polymorphism between Blastocystis sp.
Conclusion In this study, the chemical compositions of the damselfly Calopteryx haemorrhoidalis wings were investigated. While a low concentration of melanin and a uniform chemical distribution were observed for the female wings using s-FTIR, the male wings showed substantially higher melanin contents. Differences in the elemental compositions were observed between the two genders. The nanoscale XRF data revealed that the concentrations of Cu, Zn and Ca were substantially higher in the male wing membranes. The results obtained from SEM and XRF analysis clearly indicate the distinct morphology and its connection with chemistry and elemental compositions of hairs and membranes of the male and female damselfly wings. The combination of the different state-of-art techniques that provide complementary, spatially resolved data is a powerful tool to understand the chemical Figure  3.
Scanning electron microscopy. Scanning electron microscopic (SEM) images were collected using a field-emission FEI Nova NanoSEM (ThermoFischer Scientific, Hillsboro, USA) at 3 kV. Prior to the measurement, the wing samples were sputter coated with a thin layer of gold (approximately 3 nm in thickness) using a Dynavac CS300 coating unit (Australia). Quantitative analysis of the SEM images was carried out using ImageJ software (NIH USA Image ver. 1. 51), over 30 different spots from 2 images. There are two insect specimens of male and female examined for SEM analysis. FEI Teneo VolumeScope environmental SEM (ThermoFischer Scientific, Hillsboro, USA) was operated at 5 kV and 0. 1 nA under the low vacuum to image the whole wings without the assistance of gold-coatings. Synchrotron Fourier transform infrared (s-FTIR) microspectroscopy.
In practice, the wing section was held on a gap between aluminum support frames using polyimide (Kapton ® ) tape to fix both sides of the wing section. The s-FTIR chemical maps were then acquired to cover an area of 160 × 160 μm 2 on the wing. For each pixel, the s-FTIR spectrum was recorded within a spectral range of 3800-700 cm -1 using 4 cm -1 spectral resolution and 16 co-added scans. Blackman-Harris 3-Term apodization, Power-Spectrum phase correction, and zero-filling factor of 2 were set as default acquisition parameters using OPUS 7. 2 software suite (Bruker). Two IR maps have been on acquired on fore-and hind-wings of one insect specimen. There are two insect specimens of male and female examined for IR mapping. Spectral pre-processing and hierarchical cluster analysis (HCA). Hierarchical cluster analysis (HCA) was performed on the acquired s-FTIR maps using CytoSpec v.
5 × 1. 5 mm 2 , Silson Ltd, Warwickshire, England). The samples were measured under vacuum at the Nano-Imaging beamline ID16A-NI at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using an excitation photon energy of 17 keV. The fluorescence detector (six element silicon drift detector, SGX SENSORTECH) was placed next to the sample, perpendicular to the beam. The beam focus was 42 × 39 nm 2 , while the photon flux during the measurements was 7•10 10 ph/s. A step size of 400 nm and a dwell time of 0. 1 s were used for scanning the regions of interest. The analysis of the data was performed with the X-ray fluorescence toolkit PyMCA  38. The quantitative results were calibrated using a Thin Film XRF Reference Sample (RF7-200-S2371, Axo Dresden GmbH, Dresden, Germany).
Acknowledgements V. A. B. , M. W. and E. P. I. gratefully acknowledge funding from the  Marie Curie Actions research program  under the  EU   FP7 Initial Training Network SNAL 608184. The Bochum authors kindly acknowledge financial support from the  BMBF  ( 05K16PC1 ), the  Virtual Institute VH-VI-403  and the  DAAD  ( PPP Australia 57141363 ). This research was undertaken on the  Infrared Microspectroscopy beamline at the Australian Synchrotron, Victoria, Australia  and the Nano-Imaging beamline ID16A-NI at the  ESRF, Grenoble, France. Authors gratefully acknowledge the  RMIT Microscopy and Microanalysis Facility (RMMF)  for providing access to the characterization instruments. We also acknowledge the  Bio21 Advanced Microscopy Facility  for the assistance with low-vacuum SEM operation.
Samples were observed with a Zeiss LSM880 Confocal microscope to obtain high-resolution images (voxel 0. 079 × 0. 079 × 1 µm 3 ) using an Airy scan detector with a ×40 oil immersion lens (EC Plan Neofluar 40×/0. 30 oil). Images were processed using ZEN software for Airy scan processing and two sections plane of the Z stack were selected for a maximum projection by choosing for each pixel the highest signal value in any of the sections. Two lasers (488 and 561 nm) were used for excitation of GFP and LipidTOX. The bacteria were imaged at 37 • C and 5% CO 2 with snapshots every 90 min.
, 2001) , restored ILI accumulation to a level similar to that obtained with BCG (Figure  4C ). Immunoblot analyses previously showed that the complemented strain produced HBHA at a level comparable to that of BCG  (Pethe et al. , 2001). The recombinant strain, BCG-HEH, restored as well ILI staining when NOstress, meaning that HBHA-EGFP is able to complement the phenotype in the absence of the nHBHA (Supplementary Figure  S2 ). To quantify ILI formation in BCG and BCG hbhA, we analyzed the ILI content on sections of NO-stressed bacteria by transmission electron microscopy. As shown in Figure  5A , the number of ILI observed as clear white vesicles in the bacteria (black arrows), was higher in BCG than in BCG hbhA. To compute precisely this difference, we developed a script in ImageJ 1  allowing to measure the surface of individual bacteria and the total surfaces of ILI within the bacteria.
Hardware Platform Throughout our hardware design and implementation, we were committed to a low-cost solution. Thanks to the latest developments of single-board computers, power-efficient systems equipped with a high-performance multi-core CPUs, and most modern peripheral networking interfaces are available in the size of a credit card. Being increasingly available and cheap, we chose the popular Raspberry Pi (RPi) [52] (a credit card-sized ARM architecture-based computer with 1. 2 GHz 64-bit quad-core CPU and 1 GB of memory, running Rasbain, a Linux-based operating system. We used RPi version 3 in this project) as the main processing unit of our platform. This allowed most image processing and computer vision techniques to be run smoothly. As already mentioned, we designed and implemented two configurations of our system that we present in the following text.
See Figure  3  for corresponding distances and conversion to other baselines. In our approach, we propose to constrain the so-defined acceptable disparity range further, which corresponds to the third range in Figure  3 (left). Given the used lighting system, we can assume a light diffuse reflection model where the light reflects equally in all directions. Based on the inverse-square law that relates light intensity over distance, image pixels intensities are roughly proportional to their squared disparities. Based on such an assumption, we can use the pixel intensity to constrain the disparity and hence, limit the range of searching for a correspondence. To do so, we used a dataset of rectified stereo images. For each image pair, we performed feature point matching. Moreover, for each matching pair of points (x i , y i ) and (x i , y i ), x being the coordinate in the horizontal axis, we computed the squared disparity, d 2 i = (x ix i ) 2.
Visual Odometry Evaluation Unlike terrestrial odometry datasets that come with ground-truth, there is no such option for underwater odometry. Alternatively, to validate the proposed visual odometry method, we conducted an underwater survey using several scenarios, for instance, long trajectories with loop closures or raster scans. We estimated the overtaken trajectories using Agisoft Photoscan which employs a global optimization approach. We used the best available accuracy settings with large numbers of matching points. We considered the estimated trajectories as a reference for comparison in our experiments. An example of a dense reconstruction of such trajectories is shown in Figure  14. It measures around 5 m × 12 m and contains several loop closures. We followed a standard evaluation procedure, as described in  [62] , where, for all test trajectories, we computed translational and rotational errors for all possible sub-trajectories of one-meter length.
Funding: This work was partially supported by both a public grant overseen by the  French National Research Agency (ANR)  as part of the program Contenus numériques et interactions (CONTINT) 2013 (reference:  ANR-13-CORD-0014 ),  GROPLAN  project  (Ontology and Photogrammetry; Generalizing Surveys in Underwater and Nautical Archaeology ) (http://www. groplan. eu),and the  French Armaments Procurement Agency (DGA) ,  DGA   RAPID LORI project (LOcalisation et Reconnaissance d'objets Immergés ).
1% TFA for 15 min (30 µl min -1 ), before the peptides were separated on the separation column (Acclaim PepMap RP-C18, 75 μm × 250 mm, 2 µm, 100 Å) using gradients from 1 to 35% B (90 min), 35 to 85% B (5 min) followed by 85% B (5 min), with solvent A: 0. 1% FA in water and solvent B: 0. 08% FA in acetonitrile. MS and MS/MS experiments were performed on the Orbitrap Fusion, which was equipped with a Nanospray Flex Ion Source. Data were acquired in the data-dependent MS/MS mode: Each high-resolution full-scan (automatic gain control (AGC) target value 4 × 10 5 , maximum injection time 50 ms) in the Orbitrap (m/z 300-1500, R = 120,000) was followed by high-resolution product ion scans in the Orbitrap (collision-induced dissociation, CID), 35% normalized collision energy, R = 15,000, AGC target value 5 × 10 4 , maximum injection time 200 ms) within 5 s, starting with the most intense signal in the full-scan mass spectrum (quadrupole isolation window 2 Th).
Dynamic exclusion for 60 s (mass window ± 2 ppm) was enabled to allow analysis of less abundant species. Data acquisition was controlled with Xcalibur 3. 0. 63. Peptides were identified by automated de novo sequencing followed by matching to the UniProt/Swiss-Prot database using the software PEAKS Studio (version 7. 5; Bioinformatics Solutions, Waterloo, Canada). The enzyme was set to 'trypsin' and a maximum of one missed cleavage was allowed. Carbamidomethylation was considered as fixed modification and oxidation of methionine and deamidation of glutamine and asparagine residues were chosen as variable modifications. Mass error tolerances for precursor and fragment ions were set to 3 ppm and 0. 015 Da, respectively. The peptide score threshold was decreased until a false discovery rate of ≤ 2% on the peptide spectrum match level was reached and a minimum of two unique peptides were required for protein identification.
Immunofluorescence Macrophages or COS-7 cells transfected with NEU1/PPCA (1:2) and CD36 were grown on sterile coverslips in 24-well plates and stimulated, or not, with kE (50 µg/mL, 1 h). After three washes in PBS, cells were fixed with 2% paraformaldehyde in PBS for 15 min and permeabilized by 0. 2% Triton X-100 in PBS for 10 min. After blocking with 10% goat serum in PBS for 1 h, cells were incubated with rabbit polyclonal anti-NEU1 (2 µg/mL) and mouse monoclonal anti-CD36 (2 µg/mL) in PBS containing 1% BSA overnight at 4 °C. Coverslips were then washed three times with PBS and incubated with Alexa Fluor 488-conjugated goat anti-mouse and Alexa Fluor 568-conjugated goat anti-rabbit antibodies (1/1000) in PBS containing 1% BSA for 1 h at room temperature. Coverslips were mounted, visualized with a laser scanning microscope (LSM 710 NLO, Zeiss) and analyzed by Image J software.
FRET analysis FRET analysis was based on the protocol described by Leavesley et al. [27]. The first part of spectral images processing was done using ZEN software (Zeiss). Images were filtered with median 3 × 3 and the linear unmixing algorithm with measured references spectra of Teal and YFP were processed. Each pixel of the spectral image can then be described by the following equation: I sp = C D × I SpD + C A × I SPA + R; where I SPD and I SPA are the donor and acceptor spectra, respectively, C D and C A are the donor and acceptor spectra contribution, respectively, and R is the residue signal which was unidentified by the algorithm. The second part of analysis was done using homemade ImageJ macro to determine FRET efficiency using the following equation: 1 3 E FRET = C A C A +C D × 100.
Uptake of oxLDL Uptake of DiI-oxLDL was studied as described previously  [28]. Adherent macrophages in 24-well plates (250,000/ well) were incubated, or not, with kE (50 µg/mL), DANA (400 µM), DANA/kE, kE/V14 (1:2 molar ratio) or V14 alone for 1 h at 37 °C. Then, cells were incubated with 10 µg/mL DiI-oxLDL for 4 h at 37 °C. Thereafter, cells were washed three times with PBS containing 2 mg/mL BSA, twice with PBS and fixed with 2% paraformaldehyde in PBS for 15 min. After washes, coverslips were mounted and visualized with an invert fluorescent microscope (AXIO, Zeiss). The main gray value per field was calculated using the "Integrated Density" parameter of Image J software from ten different fields per condition.
2a , left panel, asterisks). In contrast to the coated beads alone (lane 3), several additional bands were also detected over the whole lane 2 after the purification procedure. As illustrated for lane 2 (Fig. 2a , right panel), lanes were systematically excised into 23 bands, in-gel digested with trypsin, and the resulting peptides were analyzed by mass spectrometry and identified from UniProt/Swiss-Prot databases. As expected, MS/MS identifies the two major bands migrating around 50and 60-kDa (Fig. 2a , left panel, asterisks) as IgG and serum albumin. Importantly, MS/MS identification confirmed the presence of NEU1 in lane 2 (Fig. 2b ) between 34-and 55-kDa and around 95-kDa in agreement with its glycosylation profile and its ability to form dimeric structures  [16, 36]. In addition, already known interacting partners of NEU1 and/or proteins already known to be regulated by NEU1 were unambiguously identified such as integrin beta-2, lysosome-associated membrane glycoprotein 2 (LAMP2), matrix metalloproteinase-9 (MMP-9), platelet endothelial cell adhesion molecule (PECAM) and toll-like receptor 2.
Acknowledgements We thank  Dr Alessandra d'Azzo  ( St. Jude Children's Research Hospital, Memphis, USA ) and  Pr Maddy Parsons  ( Kings College London, London, UK ) for providing the human PPCA and Teal cDNAs, respectively. This work was supported by funding from  CNRS ,  URCA ,  Fondation de France ,  Fraunhofer  ( Attract 069-608203 ), the  German Research Foundation (DFG)  grant  HE 6190/1-2.
4 7 Q9H0U4|RAB1B_HUMAN Ras-related protein Rab-1B 37 5 22. 2 1, 4 Q14964|RB39A_HUMAN Ras-related protein Rab-39A 26 5 25. 0 1 O43752|STX6_HUMAN Syntaxin-6 9 2 29. 2 10 Trypsin-digested protein bands from two independent experiments were analyzed by nano-LC-ESI MS/MS and proteins identified with Mascot software in Swiss-Prot and trEMBL databases.
The technical solutions such as building envelope components insulation, solar system, heating, ventilation, and cooling (HVAC) system performance, etc. were selected so that the building complied with national PE requirements. Primary energy values simulated with national input data were then compared with national requirements in other countries, and if a gap existed, the technical solutions were changed to minimize the gap. The requirement of the country corresponding to the technical solutions with highest performance level express the strictest NZEB level. By applying standard energy calculation input data from European standards to buildings with national technical solutions, national NZEB requirements comparison with EC benchmarks was conducted. Developed method based on the economic insulation may be utilized in the development of voluntary European certification scheme for the energy performance.
Normalized Space Heating and Cooling Needs Normalization factors were calculated from the climate files. The base temperature was the only building specific data needed. The objective of the normalization factors is to normalize the space heating and cooling need from one climate to another. The method works if the normalized result equals to space heating and cooling need that is simulated in the other climate. Both dry-bulb outdoor air and solar-air temperature were used to calculate the heating degree days and dry bulb outdoor air temperature to calculate the cooling degree days reported in Table  7. These Degree days (DD) were applied in Equation  (11)  to normalize the heating and cooling need to other climates: E j,Norm = E j • DD re f DD j (11) where, E j, Norm , normalized energy (space heating or cooling) need in the reference climate ( kWh m 2 •a ), E j , energy (space heating or cooling) need in the actual climate ( kWh m 2 •a ), DD re f , heating or cooling degree days in reference climate with dry-bulb air temperature or sol-air temperature ( • Cd), DD j , heating or cooling degree days in the actual climate with dry-bulb air temperature or solar-air temperature ( • Cd).
4. 0  [37] , we verify the consistency of the Higgs sector with experimental measurements of LHC Run 1. In practice, we check that the Higgs-boson mass, gluon and vector-boson fusion production cross sections (computed with the SusHi program version 1. 5  [38] ) and signal strengths agree with data up to deviations corresponding to a global χ 2 (μ) quantity of at most 111. 6, which corresponds to a 2σ level of agreement for the number of considered observables. Additionally, we constrain superpartners masses (of the MSSM sector) from direct search bounds  [17, 30, 31]. We impose that the gluino mass (M g ), the neutralino and chargino masses (M χ0 i and M χ± i ), the slepton masses (M ẽ, M μ and M τ ) and the stop mass (M t) satisfy M g > 1. 75 TeV , M χ0 2 > 62. 4 GeV , M χ0 3 > 99. 9 GeV , M χ0 4 > 116 GeV , M χ± 1 > 103.
In our simulations, we rely on the four-flavour number scheme, making use of the leading-order set of NNPDF2. 3 parton densities  [60]. We include taus when enforcing weak boson leptonic decays, and allow for the presence of up to two extra partons in the final state. The multipartonic contributions are then merged following the MLM prescription  [61]. Parton showering and hadronisation are performed within the Pythia8 (version 8. 230) framework  [62]  and we simulate the response of the detector by means of Delphes 3 (version 3. 4. 1) [63]. We modify slightly the default CMS detector parameterisation that relies on the FastJet program (version 3. 2. 1) [64]  for jet reconstruction on the basis of the anti-k T algorithm  [65] , with a radius parameter set to R = 0. 5. Our modifications imply a tau-tagging efficiency fixed to 60%, for a mistagging rate of a light-jet as a hadronic tau set to 1% (this configuration matches average performances after the object selection enforced below).
Acknowledgments We thank  F. Staub  and  A. Pukhov  for their respective help with the Sarah and MicrOMEGAs packages, as well as  S. Jain  for helpful discussions on the collider front. This research was enabled in part by support provided by the  High Performance Computing (HPC) server Guillimin in McGill University  (hpc. mcgill. ca)and  Compute Canada  (computecanada. ca). JYA and MF acknowledges  NSERC  for partial financial support under grant number  SAP105354  and JYA acknowledges the hospitality of the LPTHE,  Sorbonne University  and  INFN -Laboratori Nazionali di Frascati  where part of this work was completed. The work of BF and AG is partly supported by  French  state funds managed by the  Agency Nationale de la Recherche (ANR) , in the context of the  LABEX ILP  ( ANR-11-INDEX-0004-02 ,  ANR-10-LAB-63 ).
Plant material and DNA sequencing We combined previously studied  (Denk & Grimm, 2010)  and new material to develop a sampling design of 221 individuals completely covering the taxonomic breadth and distribution range of Quercus sect. Cerris in western Eurasia (File S1); some individuals with intermediary morphology were labelled as presumed hybrids. 158 individuals were studied for the first time, and new plastid data were generated for the previously and newly studied individuals. DNAs were extracted from silica gel-dried leaf samples with the DNeasy Plant minikit, following the manufacturer's instructions. The trnH-psbA intergenic spacer was amplified and sequenced following  Simeone et al. (2016). The nuclear ribosomal 5S intergenic spacer (5S-IGS) was amplified with the primer pair 5S14a and 5S15  (Volkov et al.
, 2001; Denk & Grimm, 2010). Individual PCR fragments were ligated into a pGEM-T easy vector (Promega). The ligation mixtures, purified with the Illustra GFX PCR DNA Purification kit (GE Healthcare), were used to transform E. coli strain XL1-Blue electroporation-competent cells  (recA1, endA1, gyrA96, hsdR17, supE44, relA1, lac, [F' proAB, lacIqZ M15, Tn10 (tetr)] ). The positive clones, selected on LB/Ampicillin plates, were identified by colony PCR using the amplification primers. Five to ten recombinant clones per individual were sequenced with the vector-specific universal primers (SP6/T7) at LGC Genomics (Augsburg, Germany). The GenBank trnH-psbA sequences of several East Asian members of sect. Ilex (Q. baloot, Q. floribunda, Q. phylliraeoides, Q. semecarpifolia, Q. baroni, Q. dolicholepis, Q.
spinosa), East Asian species of sect. Cerris (Q. acutissima, Q. variabilis) and further sequence accessions of the investigated group were included in the analyses. In addition, all 5S IGS sequences of Quercus sect. Cerris available on GenBank were included in the final dataset, and the sequences of Q. baloot and Q. floribunda were used as outgroups, based on  Denk & Grimm (2010) ; all GenBank accession numbers are reported in File S1.
Data analyses Eye-checked electropherograms were aligned in MEGA7  (Kumar, Stecher & Tamura, 2016). Highly dissimilar clone sequences showing no BLAST match with the targeted regions  (Altschul et al. , 1990)  were filtered. Final multiple alignments were obtained with ClustalW 1. 81  (Thompson, Higgins & Gibson, 1994)  and checked by eye. The diversity of the investigated regions was evaluated with MEGA7 and DnaSP5. 1  (Librado & Rozas, 2009). Median-joining (MJ) haplotype networks for the trnH-psbA region were inferred with Network 4. 6. 1. 1 (http://www. fluxus-engineering. com/), treating gaps as fifth state. The MJ algorithm was invoked with default parameters (equal weight of transversion/transition), in order to handle large datasets and multistate characters. After removal of identical clones, the total 5S-IGS sequences were used to build a Maximum likelihood (ML) tree with RAxML v8.