dataesr/scientific-paragraphs-categorization huggingface dataset:
Potential radiation and time-saving In an unpublished study on the local use of the technology in his own institution, one of the pioneering authors on WBCT provided, during the open session of the WBCT ISG in the 2017 IFFAS congress, 16 the following numbers: since 2012, more than 8000 scans have been performed, most of them bilateral. The use of conventional XR has dropped by 83% (now only used for early postoperative, non-weight-bearing) and the use of CT by 96% (now only used for acute injury with severe soft-tissue damage). The same author also published data relative to savings in radiology technician allocated time, which was estimated to have dropped by 15 800 hours per year from 22 550 in the XR + CT setup to 6750 with the WBCT setup. 16 The total radiation exposure was estimated in the same study to have dropped by a dose equivalent to that of 6000 XR or 6000 mSV, which is comparable with 750 years of United States equivalent background dose.
Mitochondrial Oxygen Consumption Oxygen uptake by isolated mitochondria was measured polarographically using a Clark-type electrode at 25 • C (Oxygraph and Oxygraph Plus Software; Hansatech, Norfolk, England) in an incubation medium containing 0. 45 M mannitol, 10 mM phosphate buffer (pH 7. 2), 5 mM MgCl 2 , 10 mM KCl, and 0. 1% (w/v) BSA  (Ostaszewska et al. , 2014). D-lactate, pyruvate, and S-D-lactoylglutathione (5 mM each) were used as substrates, and the oxygen consumption in the presence of 80 µM ADP was recorded. Measurements with inhibitors were performed in the presence of 10 µM antimycin A, 750 µM salicylhydroxamic acid (SHAM), or 5 mM α-cyano-4-hydroxycinnamate (CINN).
Statistical Analysis Values are the mean ± standard deviation (SD) of three to five independent biological replicates. Protein gel blot/activity analysis was performed using data from at least two independent experiments with a minimum of three biological replicates. Tissue extracts or mitochondria, constituting one biological replicate, were prepared from a single culture. Experimental data were analyzed using Microsoft Excel 2010 (Microsoft Corporation, Redmond, WA, United States). Significant differences were identified using Student's t-test at P ≤ 0. 05 unless indicated otherwise.
Background. The majority of oral antibiotics are prescribed in outpatient primary and urgent care clinics for acute respiratory infections. Effective antibiotic stewardship must include proper prescribing for outpatients as well as for those in a hospital or longterm care facility. Methods. Major databases, including MEDLINE and the Cochrane Library, were searched for prospective human clinical studies, including children and/or adults published between January 1966 and November 2017 that evaluated Myxovirus resistance protein A (MxA) as a biomarker for diagnosing viral infections as well as both C-reactive protein (CRP) and procalcitonin (PCT) as potential biomarkers for identifying and differentiating true bacterial upper respiratory infection (URI) from colonization. Results. Ten prospective human studies, totaling 1683 patients, were identified that evaluated MxA as a viral biomarker in children and/or adults.
METHODS Major databases, including MEDLINE and the Cochrane Library, were searched for prospective human clinical studies, including children and/or adults published between January 1966 and November 2017 that evaluated Myxovirus resistance protein A (MxA) as a biomarker for diagnosing viral infections as well as both C-reactive protein (CRP) and procalcitonin (PCT) as potential biomarkers for identifying and differentiating true bacterial upper respiratory infection (URI) from colonization.
3 software, and the average of these three measurements was considered as one single value. SkMDC myotubes were labelled with mouse monoclonal anti-myosin heavy chain antibody (MF20, 1:50 dilution) and resolved with secondary antibodies conjugated to Alexa-Fluor 488 (1:400 dilution, Invitrogen, Cergy-Pontoise, France). Images were captured with a high-resolution cooled digital XC30 camera coupled to a BX-50 microscope (Olympus, Rungis, France) at a resolution of 0. 64 μm/pixel. Myotube diameter was measured on 100 myotubes in each condition (from three independent experiments). For each myotube, five random measurements were performed along the length of the myotube using the image processing software ImageJ 1. 47v, and the average of these five measurements was considered as one single value.
Nano-LC-MS/MS analysis Proteins (80 μg) from CM of each condition (CTR vs. DEX, n = 3 independent experiments) were concentrated in the stacking gel of 1D electrophoresis gels (12% acrylamide) as described. 14 Briefly, gels were stained in Coomassie Brilliant Blue G-250 solution and excised lanes were reduced (DTT) and alkylated (iodoacetamide). Proteins were then digested by trypsin, and peptide mixtures were analysed in duplicate by online nanoflow liquid chromatography using the Ultimate 3000 RSLC (Dionex, Voisins le Bretonneux, France) and eluates being electrosprayed into a LTQVelos mass spectrometer for nano-LC-MS/MS analysis. Thermo Proteome Discoverer v1. 3 was used for raw data file processing and MASCOT for database search (http://www. matrixscience. com). For protein identification, the Uniprot Mus musculus (07/2016, 51 518 seq) protein database was used; protein identification was considered valid if at least one peptide with a statistically significant Mascot score assigned it (with Mascot score ≥ 36 for P value < 0.
05 with a false discovery rate at 1%). The acquired spectra were loaded into the Progenesis LC-MS software (version 4. 1, Nonlinear Dynamics, Newcastle, UK), and label-free quantification was performed. Briefly, for each migration lane from the SDS-PAGE, the profile data of the MS scans as well as MS/MS spectra were transformed to peak lists with Progenesis LC-MS using a proprietary algorithm and then stored in peak lists comprising m/z and abundance. One sample was set as the reference, and the retention times of all other samples within the experiment were automatically aligned to create maximal overlay of the twodimensional feature maps. At this point, features with only one charge, with retention time windows lower than 6 s or with retention time lower than 20 min and higher than 80 min, were masked and excluded from further analyses.
Fibre cross-sectional area Cross-sections of GA muscle were labelled with anti-laminin-α 1 (L9393, Sigma-Aldrich) to outline the fibres and resolved with corresponding secondary antibodies conjugated to Alexa-Fluor 488 (Invitrogen, Cergy-Pontoise, France). Images were captured with a high-resolution cooled digital XC30 camera coupled to a BX-50 microscope (Olympus, Rungis, France) at a resolution of 0. 64 μm/pixel. Five fields, each containing 100 fibres, were analysed per muscle. Cross-sectional area was determined for each fibre, using the image processing software ImageJ 1. 47v.
Human subjects Patients with proven Cushing's syndrome and healthy controls matched for age and sex were recruited from the Endocrine Clinic of the St-Luc Academic Hospital (Brussels, Belgium). Exclusion criteria included pseudo-Cushing, paraneoplastic or cyclic Cushing's syndrome, adrenocortical carcinoma, or pituitary irradiation during the last 6 months. All subjects underwent standard medical examination, and blood samples were collected from patients at the time of recruitment, in standardized conditions. This study (ClinicalTrials. gov identifier: NCT03229395) was approved by the local Ethical Committee of the Université Catholique de Louvain (Belgium) and was performed in accordance with the principles of the revised Declaration of Helsinki. All subjects were fully informed regarding study participation, and they provided written informed consent prior to inclusion in the study.
Acknowledgements We thank  Pr M. Sandri  ( Venetian Institute of Molecular Medicine, Padova, Italy ),  Dr. L. Grobet  ( Department of Morphology and Pathology, University of Liege, Belgium ), and  Dr. S. J. Lee  ( Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA ) for the genetically modified mice. We thank  Pr O. Ritvos  for sActRIIB-Fc soluble receptor. The authors certify that they comply with the ethical guidelines for authorship and publishing of the  Journal of Cachexia, Sarcopenia and Muscle. 45is work was funded by grants from  Fonds de Recherche Clinique  to MG and the  Saint-Luc Foundation  to  JPT (Cliniques Universitaires Saint-Luc, Belgium)  and a grant from the  FRS-FNRS/Télévie  to LB, NMD and  JPT (InterCachectomics Consortium ).
Shatrovskiy (2017)  examined both these specimens and described the second specimen, male from Singapore, as Cycreon armandi. Extensive sampling of insects associated with inflorescences of Malayan aroid plants was performed recently by  Low et al. (2014 Low et al. ( , 2016)) ,  Hoe and Wong (2016)  and  Hoe et al. (2018)  in order to study their pollination biology, and  Takizawa (2010)  in order to study the association of species of Chaloenus Westwood, 1861 (Chrysomelidae) with these inflorescences. As a result, a high number of Cycreon specimens from both Peninsular Malaysia and Borneo was accumulated. In this study, we use this material to redescribe and illustrate the genus Cycreon in detail, to revise the systematics of the genus, and to sum up the available data on the biology of the genus.
Material and methods Examined specimens and depositories. A total of 1444 specimens of Cycreon were examined. Label data are reproduced verbatim; notes on the label data or additional information are written between square brackets []. List of examined specimens is available in DarwinCore-formatted spreadsheet file at Zenodo repository (https://doi. org  /10. 5281/zenodo. 1258208). This file was also used to prepare the distribution map using QGIS software and freely available GLOBE altitude data and DIVA-GIS country borders data. The authors did not examine holotypes of C. sculpturatus and C. armandi as these are not accessible for the examination, and adopted the information about them from  Shatrovskiy (2017). In addition, A. Shatrovskiy kindly provided a new photograph of ventral view of the head of C.
sculpturatus used to illustrate the shape of the mentum of this species (Fig. 5P ). Morphological studies. Specimens were dissected, with genitalia embedded in a drop of alcohol-soluble Euparal resin on a piece of glass glued to a small piece of cardboard attached below the respective specimen. Habitus photographs were taken using a Canon D-550 digital camera with attached Canon MP-E65mm f/2. 8 1-5 macro lens. Pictures of genitalia were taken using a Canon D1100 digital camera attached to an Olympus BX41 compound microscope; combined pictures were were made with Helicon Focus software. Scanning electron micrographs were taken using Hitachi S-3700N environmental electron microscope at the Department of Paleontology, National Museum in Prague. Pictures used for plates were adapted in Adobe Photoshop CS6.
2018: fig 4). The excised clypeus and anterior margin of mentum is unusual in the Megasternini. Excised mentum is only known in the Central American genus Nitidulodes, which is also associated with aroid inflorescences  (Hansen 1991 , Bloom et al. 2015). Excised clypeus is only present in Cycreon. Moreover, the strong variation of mentum and clypeus shape between different species of Cycreon is also unusual within Megasternini. Usually these characters are very similar in congeneric species and differ at most between genera. We suppose that this interspecific variation in Cycreon may indicate species-specific food and hostplant preferences. The data by  Hoe et al. (2018)  indicate some kind of specificity in host plants, which would be in agreement with this assumption. For example, various genera and species of Schismatoglottideae were sampled in Mulu National Park (Malaysia, Sarawak) from December 2017 to February 2018, but Cycreon beetles were only found in sampled species of Schismatoglottis (beetles were present in all sampled plants), whereas not a single specimen was found in inflorescences of Anadendrum, Aglaonema, Alocasia, Bucephalandra and Lasia.
Acknowledgements We are indebted to  H. Takizawa  and  Y. N. Minoshima  ( Japan ) for providing us with the material from their collections. This work was supported by the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No. 642241  to EAV, and by the  Ministry of Culture of the Czech Republic  ( DKRVO 2018/13 ,  National Museum ,  00023272 ) to MF. The work of EAV at the  Department of Zoology, Charles University , Prague was partly supported by grant  SVV260434/2018. WSY acknowledges the funding from the  Ministry of Education of Malaysia  through Vote No. NRGS/1089/ 47 2013-( 03 ). The study of AGK was performed in the frames of the state research project  AAAA-A17-117030310210-3  and partly supported by the programme of the  Presidium of the Russian Academy of Sciences  "Evolution of organic world.
Genetic map construction A new Pacific oyster linkage map was constructed in four successive steps: (i) First, a low-density map was built for each family using the SNP and microsatellite markers dataset. These two maps were used to provide accurate ordering of markers, since both mapping populations comprised approximately 300 individuals with very few missing genotypes (0. 5%). (ii) In a second step, we tried to reach a consensus order for the markers that were included in the two previous maps, in order to determine a set of anchor loci for each linkage group. (iii) Third, we included RAD markers and determined the order of all loci in each mapping family after setting a fixed order for the anchor loci. (iv) Finally, we integrated the two high-density linkage maps to produce a consensus genetic map for the Pacific oyster.
All linkage mapping analysis were performed using JoinMap 4  (van Ooijen, 2006). Markers showing significant segregation ratio distortion after Bonferroni correction (p < 0. 05) were removed from the analysis. Markers were grouped using an independence LOD threshold of 16 for the SNP and microsatellite marker datasets and a LOD threshold of 10 for the RAD marker datasets. Additional ungrouped markers were assigned at a LOD threshold of 5 using their strongest cross-link information. We used the regression mapping algorithm to build the maps using a recombination frequency threshold of 0. 4, a minimal LOD score of 1 and a goodness-of-fit jump value of 5. The ordering of markers was optimized using the ripple function after each added locus. Map distances in centiMorgans (cM) were calculated from recombination frequencies using Kosambi's mapping function.
This resulted in 60,912 cleaned full-length (i. e. >1300 bp) BAC-End sequences (BES) pairs. Each sequence from each pair was trimmed to only conserve 1000 bp between positions 10 and 1010, and clipped into 19 evenly-spaced 100-mers overlapping by 50 bp. This clipping procedure aimed at constructing a high quality short-read paired-end dataset from our BES dataset. Clipped BES were used for an additional round of contig extension and scaffolding with SSPACE  (Boetzer et al. , 2011). For each LG, we used unambiguously anchored scaffolds and contigs originating from splitted scaffolds matching to this LG. Clipped BES were aligned to scaffolds using Bowtie2  (Langmead & Salzberg, 2012) , allowing at most 3 mismatches per 100-bp read. Scaffolding parameters to SSPACE were set to a minimum of 5 links (-k) to validate a new scaffold pair and a maximum link ratio of 0.
The dAPC analysis performed with the R package Adegenet  (Jombart, 2008) , using the global SNP dataset containing the two populations from both species with only one randomly selected SNP per RAD locus. In order to evaluate the influence of recombination rate variation on genetic differentiation between species, we used a nonparametric quantile regression approach. Recombination rate and F ST values (averaged between the Asian and European species pair) were averaged in 500 kb windows to increase the number of informative sites per window. We excluded windows with recombination rate values exceeding 9 cM/Mb (i. e. corresponding to the 98 th percentile of the distribution of estimated recombination rate). This cutoff aimed at removing outlying recombination rate values estimated along chromosome IX (Figure  1 ).
Inference of the demographic divergence history We inferred the demographic divergence history between C. angulata and C. gigas in both their native and introduced ranges using a version of the program δaδi  (Gutenkunst et al. , 2009)  modified by  (Tine et al. , 2014). The observed joint allele frequency spectrum (JAFS) of each population pair was obtained by randomly selecting one SNP for each pair of RAD loci associated to the same restriction site in order to avoid the effect of linkage between SNPs, and then by projecting the data to 20 chromosomes per population to reduce the JAFS size. We first considered four classical models of divergence including models of strict isolation (SI), isolation-with-migration (IM), ancient migration (AM) and secondary contact (SC). We also considered extensions of the three divergence-with-geneflow models assuming two categories of loci occurring in proportions P and 1-P and having different migration rates: IM2m, AM2m and SC2m  (Tine et al.
Construction of an integrated high-density linkage map The microsatellite and SNP datasets used for constructing the low-density linkage map contained 133 informative markers in family F2-19 (293 progeny, Table  S1 ) and 137 informative markers in family F2-21 (282 progeny, Table  S2 ). Ten linkage groups were found in each family in agreement with the haploid number of chromosomes of the species, and the two maps generated by the first round of regression mapping respectively contained 98 and 105 mapped markers in family F19 and F21. The integrated map obtained after identifying homologous LG pairs between families contained 136 markers successfully ordered after the first round of regression mapping. This sex-averaged consensus low-density linkage map displayed a strong collinearity with the two maps from which it was derived (Supplementary Figure  S2 , left panel), indicating that the ordering of markers was highly consistent between the two families.
Acknowledgements This work was supported by  Interreg SUDOE "Aquagenet"  ( SOE2/P1/E287 ) and  ANR  " GAMETOGENES " ( ANR-08-GENM041 ) projects, as well as from  GIS-IBiSA and Ifremer. We would like to thank  Brieg Pontreau  for his help in microsatellite genotyping, the hatchery team of  Ifremer La Tremblade  for its help in the production of the biological material, and  Hélène Holota  from  Inserm UMR 1090 TAGC  for her kind assistance during the sonication of RAD libraries. We are also grateful to  Patrick Gaffney  for providing BAC clones and  Pascal Favrel  for managing BAC-end sequencing with the Genoscope. Golden Gate  SNP genotyping was performed at the  Genome Transcriptome Facility of Bordeaux  (grants from  Conseil Régional d'Aquitaine n°20030304002FA  and  20040305003FA , from the  European Union   FEDER n°2003227  and from the  Investissement d'Avenir   ANR-10-EQPX-16-01 ).
Macrophyte data We surveyed lake macrophytes in 16 different regions covering six continents across the Earth (Table  1 ). Overall, 27-30 lakes were investigated in each region. In each region, we randomly chose ca. 30 lakes with similar geographical distribution from the pool of candidate lakes. The selected lakes ranged from floodplain lakes in Brazil and China to glacial-origin relatively stable lakes situated at boreal and temperate zones (e. g. , Finland, Estonia, Sweden, Norway, Denmark, New Zealand, Poland, and US states of Minnesota and Wisconsin). Although the lakes differed in their environmental conditions among the regions, all lakes were mostly natural lentic systems (i. e. , reservoirs were excluded). However, most of the lakes suffered from various anthropogenic pressures such as nutrient enrichment, alien invasive species, water-level fluctuations, and decreased connectivity.
The inclusion of different types of lakes was considered an important factor increasing the range of environmental conditions, resulting in environmental filtering effects. Detailed descriptions of study lakes can be found in the Supporting Information (Appendix S1). The macrophyte data consisted of presence-absence observations of hydrophyte species, i. e. , species which grow exclusively in freshwaters. These hydrophytes consisted of submerged (elodeids and isoetids), free-floating (ceratophyllids and lemnids), floating-leaved, and emergent species  (Cook 1999). Emergent hydrophytes included only those species strongly bound to aquatic environments and found to grow in water at the time of survey, like Alisma plantago-aquatica, Butomus umbellatus, Glyceria fluitans, Juncus bulbosus, Mentha aquatica, Sagittaria sagittifolia, and Schoenoplectus lacustris  (Tanner et al.
1986; Crow 1993; Willby et al. 2000; Thomaz et al. 2003; Kosten et al. 2009a ). In addition to non-aquatic emergent and shore species, charophytes and aquatic bryophytes were removed from the data sets, because only hydrophytes were exclusively surveyed in all the regions. We also excluded hybrids, subspecies, and genus level identifications when species from the same genus were recorded from the data. We refer to this set of aquatic species as macrophytes hereafter. All macrophytes were empirically surveyed using similar methods within each region. This enabled us to compare the strength of the community-environment relationships across the 16 regions and to minimize the potential negative influences caused by different survey methods within each region. The macrophyte surveys were executed mostly between 2001 and 2013.
2011; Søndergaard et al. 2013 ). However, data on maximum colonization depth were not available for all study lakes. Moreover, lake area is often highly correlated with shoreline length which mirrors species-area relationship relatively well for many aquatic organisms  (Søndergaard et al. 2005; Lewin et al. 2014 ). These three local variables are among the most important explaining variation in lake macrophyte community structure, and often correlate with other water chemistry and hydromorphological variables that were not available for all the study lakes  (Jones et al. 2003; Lacoul and Freedman 2006; Kosten et al. 2009a ). Local variables were surveyed For the columns from total phosphorus to precipitation, the values are mean (min-max, SD). The actual estimated maximum lake ages (left side value) were changed to a ranked variable ranging from the youngest to oldest (right side value), because there was no information on the maximum age estimates for all 30 lakes in each region and the age estimates showed high level of variation in some study regions and determined similarly within each study region (Appendix S1).
Acknowledgements Open access funding provided by  University of Oulu including Oulu University Hospital. JA appreciates financial support from the  Ella and Georg Ehrnrooth Foundation. BAL was supported by  National Research, Development and Innovation Office-NKFIH ,  OTKA PD120775 Grant  and by the  Bolyai János Research Scholarship of the Hungarian Academy of Sciences. S. K. was supported by  NWO Veni  grant  86312012. Sampling of the coastal 1 3 Brazilian lakes was financed by  NWO  grant  W84-549 ; The  National Geographic Society  grant  7864-5 ; and  CNPq  grants  480122 ,  490409 ,  311427. We thank the  SALGA team , especially  Gissell Lacerot ,  Nestor Mazzeo ,  Vera Huszar ,  David da Motta Marques , and  Erik Jeppesen  for organizing and executing the  SALGA  field sampling campaign and Bruno Irgang † and  Eduardo Alonso Paz  for help with identification.