dataesr/scientific-paragraphs-categorization huggingface dataset:
Cell profiling The expression profile of NRSF, YY1, TARBP2, Alx1, and NFAT-5 in HeLa, Co115 and H4 cells was determined by Western-blot analysis using commercial antibodies for NRSF (ab75785; Abcam), YY1 (ab12132; Abcam), TARBP2 (ab42018; Abcam), Alx1 (ABIN785202; antibodies-online GmbH) and NFAT-5 (ABIN183505; antibodies-online GmbH). For DT40 and HeLa cells, expression profile was determined by RNA-seq analysis using data available in databases, GEO datasets SRX286375 and SRX083286, respectively. During the analysis, we observed only one discrepancy between the RNA-seq data and the Western-blot analyses. Indeed, our HeLa cells were found to express NFAT-5 whereas the RNA-seq analyses done on another HeLa cell batch led to the opposite conclusion. Transient GFP expression assay and flow cytometry analyses 8 x 10 4 cells were seeded onto a 24-well plate one-day prior transfection and then transfected with jetPEI, according to the manufacturer's instructions using 0.
CHIP-seq peak analyses Annotations from RepeatMasker were used to select positions of Hsmar1 and Hsmar2 in the hg19 human genome version. Those containing a Δ8 segment (Sil+), a damaged Δ8 segment (U), or no Δ8 segment (Sil-) and their location in a genic or an intergenic region were inventoried using home made perl scripts (S1 Table ). Here, genic regions corresponded to those for which maximal efficiency of the mariner silencer was observed from our experimental data (i. e. from the TSS of each gene to 5 kbp downstream of its 3'end). Intergenic regions corresponded to any region of the genome that was not genic. ChIP-seq peaks files (EzH2, H3K27me3, H3K27ac, H3K4me3, and H3K9me3; no data about H4K20me3 were available for all cell lines) were located within UCSC resources for ENCODE data and downloaded at https://genome.
The names of each of the 34 mariner elements are shown on the right side of the figure. Their names, accession numbers and host species for each element are: Tvmar1, AY282463 Trichomonas vaginalis; Ahmar1, AB056896 Adoxophyes honmai; Armar1, AB056894 Ascogaster reticulatus; Cpmar1, U11641 Chrysoperla plorabunda; Mpmar1, U11649 Mantispa pulchella; Damar1, U11656 Drosophila ananassae; Himar1, U11646 Haematobia irritans; Hsmar2, U49974 Homo sapiens; Bytmar1, AJ507226 Bythogrea thermydron; Acmar1, AB081476 Apis cerena; Ammar1, U19902 for Apis mellifera; Ccmar1, U40493 Ceratitis capitata; Demar1, U08094 Drosophila erecta; Famar1, AY226507 Forficula auricularia; Gpmar1, U18308 Glossina palpalis; Aamar1, AB006464 Attacus atlas; Dtmar1, X79719 Dugesia tigrina; Funmar1, AB055188 Fungia sp. Kusabiraishi; Hbmar1, U04455 Heterorhabditis bacteriophaga; Hcmar1, M63844 Hyalophora cecropia; Hsmar1, U52077 Homo sapiens; Cemar1, M98552 Caenorhabditis elegans; Cemar2, X77804 C.
Acknowledgments We thank colleagues who very kindly supplied pieces for our puzzle:  Dr L. Elnitski  ( NIH, Rockville, MA USA ) for providing plasmids for transient expression assays,  Dr L. B. Hersh  ( University Kentucky, USA ) for providing the plasmid vector expression for the human NRSF and the pKL-7 plasmid,  Dr W. P. Yu  ( National Neurosciences Institute, Singapor ) for providing the plasmid vector expression for the fugu  NRSF ,  Dr M. Cerrutti  ( CNRS, Saint Christol-les-Alès, France ) for providing the plasmid containing the pEI1-[NeoR] cassette,  Dr V. Gouilleux  ( University of Tours, France ) for providing the H4 cells,  Dr G. Sui  ( Harvard Medical School, ME USA ) for providing DT40 and DT40yy1-cells,  Dr M. Esteller  ( CNIO, Madrid, Spain. ) for providing Co115 cells and  Dr L Sinzelle  ( CNRS UPS3201-Université d'Evry Val d'Essonne ) for her technical support for the experiments made with Xenope cells.
This work was funded by grants from the C. N. R. S. , the I. N. R. A. , the  Groupement de Recherche CNRS 2157 , the European Project  SyntheGeneDelivery  ( N°18716 ), and the  Ministère de l'Education Nationale, de la Recherche et de la Technologie. SB holds a post-doctoral fellowship from the overheads of the European Project SyntheGeneDelivery and PA holds a senior researcher fellowship from the  STUDIUM. The funders had no role in study design, data collection.
Mosquito collections A total of 10 sites were classified according to the habitat (urban, suburban or rural) and the type of breeding site (aboveground or underground) (Table  1 ). Fourth instar larvae were sampled from May to October 2010 using the dipping method  [24]  with ten dips in different places of the breeding site. Larval density was expressed as numbers of larvae per litre and estimated according to a range of five classes: class 1 for larval density = 0, class 2 for larval density = 10 (1-10), class 3 for larval density = 50 , class 4 for larval density = 100 (51-100), class 5 for larval density = 500 (> 100). Ecological data characterizing each breeding site were recorded: the presence of vegetation (Additional file 1: Table  S1 ), temperature, pH, salinity and percentage of O 2 (Table  1 ).
Data analysis Chi-square test was used for comparisons of rates (autogeny, stenogamy and the molecular forms of Cx. p. pipiens), Kruskal-Wallis H test to study the spatial variation of rates (autogeny, stenogamy) and Mann-Whitney test to evaluate the influence of blood meal on fecundity and fertility rates. All statistical tests were conducted using the IBM® SPSS® Statistics for windows v. 21 (IBM Corp. Armonk, NY). P-values > 0. 05 were considered non-significant.
Funding This work was funded by the  Institut Pasteur  ( ACIP grant   A-08-2009 ) and the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (grant n°A  NR-10-LABX-62-IBEID ). AKR was supported by  PhD fellowship « Biodiversity, Evolution and Ecology of Health  » from the  Algerian Ministry of Higher Education and Scientific Research.
2 ). Moreover, livers, spleens and kidneys were removed after 1, 2 and 3 doses of EGF-SubA and analyzed histopathologically. In mice treated with 25 µg/kg EGF-SubA, we occasionally observed hemorrhagic foci and hepatic necrosis as well as very subtle changes in spleens and kidneys (data not shown). More pronounced changes were observed in the mice treated with 50 µg/kg of EGF-SubA. Splenic abnormalities included small accumulations of reticular fibers in the white pulp; renal abnormalities ranged from subtle edematous changes in deep cortical layer tubules to more pronounced focal deposits of eosinophilic material in some tubules, with obliteration of their lumina. The most noticeable changes we observed in the livers of mice treated with 50 µg/kg of EGF-SubA (Fig. 3 ). After one or two doses of the toxin we observed pronounced hepatocyte anisocytosis and occasional hemorrhagic foci.
Acknowledgements We thank  Ewa Werner , karolina  Hajduk ,  Anna Czerepinska  and  Elzbieta Gutowska  for valuable technical assistance. This study was supported by grants:  DI2011 021141  (M. G. ) and  DI2013 006643  (A. D. ) from  Polish Ministry of Science and Higher Education  and  FP7-REGPOT-2012-CT2012-316254-BASTIOn  from the  European Commission 7th Framework Programme  (J. G. ).
To achieve this profile, they used an external localized force applied directly on the backfill while imposing a settlement to the wall foundation. In the literature, numerical modelings of the DSRWs behavior are based on the finite element method (FEM)  [6]  or on a discrete element method (DEM) in order to keep the discrete nature of the wall composed of individual blocks. This latter method can take into account the specific arrangement of the blocks and can get a better local insight of these retaining structures. Harkness  [7]  modeled Burgoyne's field experiments using UDEC code (DEM, ITASCA code)  [8] , confirming the qualitative results Burgoyne obtained. Also based on Burgoyne's tests, Powrie et al. [9]  and later Claxton et al. [10] , performed numerical simulations, studying the influence of the mechanical properties and geometry of blocks on the wall stability.
Recently, Oetomo et al. [11]  modeled the behavior of slope DSRWs by two methods. The first technique involved a fully DEM approach where both the wall and the backfill grains were modeled as individual bodies. The second method was based on a mixed discrete-continuum approach where the wall was modeled using individual blocks while the backfill was modeled by a continuum approach. The software PFC2D and UDEC (ITASCA codes) were used for the fully discrete approach and the mixed discrete-continuum approach respectively. The objective of these works was to retrieve the critical loading heights observed through full-scale experiments performed by Villemus et al. [3]  and Colas et al. [4]. All these before-mentioned studies showed the capability of DEM to retrieve the mechanical behavior of slope DSRWs.
Basic aspects about 3DEC This software is based on an explicit solution method for the solvation of the equations of the dynamics and can model discontinuities in a material by the discrete element method. The system is then modeled by an assembly of polyhedra where relative displacements and rotations are allowed between them. These blocks can be either rigid or deformable and, in this instance, the deformability of the blocks is handled by means of the finite difference method. Consequently, 3DEC allows geotechnical or construction problems to be solved by a mixed discrete-continuum approach  [13]. In the past, this code was used to get more insight into the behavior of plane DSRWs where pathologies observed on site and the behavior of specific DSRWs toward failure could have been reproduced  [7, 9, 10, 14].
Acknowledgments The present work is part of the research project  MapCoD  ( Materials and processes for sustainable constructions ) and was financially supported by the  program Projet d'Avenir Lyon-Saint Etienne of University of Lyon which is part of the program  " Investments for the Future "  ANR-11-IDEX-0007  ( National Agency of Research). The authors want to acknowledge these institutions for their support and would like also to thank  Kimberly Morin-Coulomb ,  Stéphane Cointet  and  Laureen Giraud  for performing the experimental tests.
Findings: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.
In addition, AdapterRemoval v2 allows for the simultaneous trimming of multiple different (pairs of ) adapter sequences, selecting the best match per read (pair), and can furthermore transparently read and write gzip and bzip2 compressed FASTQ files. AdapterRemoval v2 further allows for simultaneous demultiplexing and adapter trimming, using a simple maximum-number-ofmismatches comparison for the provided barcodes, and correctly trims paired-end reads extending past the end of the insert. Such reads are terminated by the reversecomplemented barcode sequence of the other mate followed by an adapter sequence, both of which must be removed. Finally, AdapterRemoval v2 can reconstruct putative adapter sequences from overlapping read pairs, which can be used to detect experimental errors and help analyze poorly documented data sets.
To evaluate the performance of AdapterRemoval v2, we compared it with AdapterRemoval v1, and with a selection of contemporary adapter trimming software, in terms of the ability to correctly trim adapter sequences, and in terms of throughput when using one or more threads (where applicable). We further compared the ability of AdapterRemoval to correctly merge overlapping sequences, with several other programs. For the latter, we restricted our comparison to programs which are designed to carry out read merging in the presence of adapter contamination, but note the existence of several alternatives which are well suited for datasets containing little or no adapter contamination, e. g. COPE  [9] , fastq-join  [10] , FLASH  [11] , and XORRO (arXiv:1304. 4620).
Methods We compared AdapterRemoval v2. 1. 3 with Adapter-Removal v1. 5. 4  [2] , using parameters equivalent to the defaults for AdapterRemoval v2. x (--mm 3 for both single-end and paired-end reads); with AlienTrimmer v0. 4. 0  [4] , using the natively compiled version, see below; with CutAdapt v1. 8. 3  [12] ; with leeHom rev. dfca9e6  [13] , with and without the '--ancientdna' option; with PEAR v0. 9. 6  [14] ; with PEAT rev. 4e9ebf3  [14] ; with fastq-mcf v1. 1. 2 (https://code. google. com/p/ea-utils/); with FLEXBAR v2. 5  [15] , pre-compiled version; with Scythe v0. 991 (https://github. com/ucdavis-bioinformatics/scythe); with Skewer v0. 1. 127 [16] ; and with Trimmomatic v0. 33  [5]. We furthermore compared AdapterRemoval v2. 1. 3 with Minion from the Kraken suite of tools  [17]. Software was compiled with GCC v4.
We used single indexed Illumina HISeq adapter sequences, "AGATC GGAAG AGCAC ACGTC TGAAC TCCAG TCACN NNNNN ATCTC GTATG CCGTC TTCTG CTTG" and "AGATC GGAAG AGCGT CGTGT AGGGA AAGAG TGTAG ATCTC GGTGG TCGCC GTATC ATT", during read simulations. Reads were simulated against the human chromosome 1 sequence, using the hg38 reference genome. All results are reported as the average obtained from trimming each of the 10 replicate datasets; the order in which programs were run in each replicate was randomized. To benchmark throughput, we furthermore simulated 200 bp long reads. In the absence of a biological read profile, we duplicated each position in the 100 bp default error-profiles for pIRS v1. 1. 1, and simulated 200 bp long reads using this profile, with a mean insertsize of 300 bp, and a standard deviation of 100 bp.
As these error profiles are not representative, we only used these to examine data throughput. For benchmarking trimming of multiple adapters, we generated four additional pairs of adapters by shuffling the nucleotides in the adapters listed above, for a total of five pairs of adapter sequences. We next generated 1 M reads as described previously, and randomly selected an adapter pair for each insert. Trimming performance was measured as described above. For benchmarking of adapter sequence identification, we shuffled the sequence of the default adapter-pair for AdapterRemoval, and generated 1 million reads as described above using the shuffled adapter pair, a variable mean insert size with a standard deviation of 75 bp. We counted the number of correctly called bases from the 5′ end of the resulting adapter sequences (Fig.
3 ). For Minion, we considered the five best sequences for each run, and selected the best match. Benchmarking was carried out on an otherwise idle Intel ® Core ™ i7-4790 K 4 × 4. 00 GHz, with 8 GB of DDR3-2133 RAM, on an ext4 partition on a Samsung SSD 840 EVO 750 GB drive. The scripts used for the performance tests described in this paper, as well as any patches applied to programs used in the tests, are stored in the AdapterRemoval v2 GitHub repository in the 'benchmark' folder.
Results and discussion The performance of AdapterRemoval v2 was compared to a selection of other adapter trimming software, as described above (Fig. 1  and Additional File 1: Table  S1 ), for both single-end and paired-end operations, as well as for merging of overlapping paired-end reads. AdapterRemoval v2 was found to offer high sensitivity (0. 979), at the cost of lower specificity (0. 814) when trimming single-end data sets containing either a single adapter sequence, or containing multiple adapter sequences. Similar high sensitivity (0. 965) low specificity (0. 731) was observed for data sets containing multiple, different adapters. This is a consequence of Adapter-Removal not requiring a minimum length of the overlap with the adapter sequence, resulting in an excess of short (1-3 bp) fragments trimmed from the 3′ termini of singleend reads.
999) when considering paired-end data, when using default parameters. High sensitivity (0. 959) and specificity (0. 999) was also observed for data sets containing multiple adapter pairs. For merging of overlapping pair-end reads, AdapterRemoval offers comparable similar sensitivity (0. 938) and specificity (0. 955) to the alternatives examined here. When comparing the throughput of each program (Fig. 2  and Additional File 2: Table  S2 ), we observed that AdapterRemoval v2 offers the highest throughput next to Trimmomatic, for the trimming of 100 bp single-end (434 vs 414 k reads/sec) and paired-end (336 k vs 418 k reads/ sec) reads, and scales well with multi-threading. For the merging of overlapping reads in the presence of adapter sequences, AdapterRemoval greatly outperforms all alternatives by an order of magnitude (295 vs 47 k reads/sec for leeHom).
Availability and requirements • Project name: AdapterRemoval • Project home page: https://github. com/MikkelSchubert/adapterremoval/ • Operating system(s): POSIX (tested on Linux and OSX) • Programming language: C++ • Other requirements: Optional support for gzip compression, bzip2 compression, and multi-threading requires zlib, libbzip2, and libpthreads, respectively • License: GPL v3.
Alkaline phosphatase-conjugated anti-IgG antibody (Promega) was used as the secondary antibody, and Western Blue (Promega) was used to detect the signals. The band intensities of the Western blots were quantified using ImageJ software. Immunofluorescence studies. Mouse kidneys were fixed by perfusion through the left ventricle with 0. 2 M periodate lysine and 2% paraformaldehyde in PBS. Tissue samples were soaked for several hours in 20% sucrose in PBS, embedded in Tissue-Tek OCT Compound (Sakura Finetechnical), and snap-frozen in liquid nitrogen. Goat anti-AQP2 (C-17, Santa Cruz, sc-9882; 1:500) was used as the primary antibody. The mpkCCD cells were fixed with 4% paraformaldehyde and permeabilized with 0. 1% Triton-X/PBS. The filters were detached from the holders and incubated with the following primary antibodies: goat anti-AQP2 (N-20; 1:500), rabbit anti-AQP2 (phospho S269; 1:500), and Acti-stain 555 phalloidin (Cytoskeleton, # PHDH1-A; 7:1,000).
Alexa 488 and 546 dye-labeled antibodies (Molecular Probes; 1:200) were used as the secondary antibodies. The samples were mounted with Vectashield/DAPI (Vector Laboratories). Immunofluorescence images were obtained using the LSM510 Meta (Carl Zeiss). The fluorescence intensities of AQP2 in mouse kidneys were quantified using Zen 2009 software. The fluorescence intensities of AQP2 in the mpkCCD cells were quantified using ImageJ software. Reverse transcription-PCR analysis. Total RNA from the mpkCCD cells and C57BL/6 mouse kidneys was extracted using TRIzol Reagent (Invitrogen) and purified with RNase-free DNase Sets and RNeasy Kits (Qiagen). RNAs were reverse-transcribed using Omniscript Reverse Transcriptase (Qiagen). Primer sequences used for PCR were summarized in Supplementary Table  1.
Intracellular calcium assay. The culture medium of the mpkCCD cells or dissection solution of mouse kidneys was replaced with loading buffer containing 5 mg ml À 1 Fluo4-AM (Dojindo), 1. 25 mmol l À 1 probenecid (Dojindo), and 0. 04% Pluronic F-127 (Dojindo). After incubation for 1 h at 37 °C, loading buffer was replaced with recording medium containing 1. 25 mmol l À 1 probenecid. The mpkCCD cells and isolated CCD of mouse kidneys were then placed under confocal laser scanning microscopy. Wnt5a (500 ng ml À 1 ) was added, and calcium responses were monitored by the LSM510 Meta. Fluorescence intensities of Fluo4 were quantified from six regions of interest using Zen 2009 software. Cell surface biotinylation assay. The amount of AQP2 in the apical plasma membrane was quantitated by apical surface biotinylation as previously described  58.
Acknowledgements This work was supported by  Grants-in-Aid for Scientific Research (S)  ( 25221306-00  to S. U. ),  Scientific Research (A)  ( 22249032-00  to S. S. ), and  Scientific Research (B)  ( 16H05314  to E. S. ) from the  Japanese Society for the Promotion of Science  and a  Health Labor Science Research Grant  from the  Ministry of Health Labor and Welfare ,  Challenging Exploratory Research  from the  Ministry of Education, Culture, Sports, Science and Technology of Japan  to S. U. and E. S. , the  Salt Science Research Foundation  ( 1422  and  1629 ) to S. U. , the  Takeda Science Foundation  to E. S. , Banyu  Foundation Research Grant  to E. S. , and the  Vehicle Racing Commemorative Foundation  to S. U.
, 2014  Mystacinidae F X  Dobson, 1875; Hand et al. , 1998 Hand et al. , , 2005   Schlosser, 1910 Schlosser, , 1911  using a stage micrometer. Measurements were recorded to the nearest tenth of a millimeter. In the case of fossil bat skeletons with teeth preserved in occlusion, tooth measurements were calculated from scaled X rays, digital photographs, or digital renderings of micro-CT images. Dental Comparisons: The molar teeth of the new fossil were compared with specimens, casts, CT images, and literature descriptions of teeth of bats and other mammals known to have dilambdodont molars (see appendix 1 and citations below). Comparisons with many species of noctilionoid bats were made using the illustrated data matrix of dental characters published by  Dávalos et al. (2014)  and made available online in MorphoBank (www.
morphobank. org) as project P891. MorphoBank is a public online database for assembling and managing morphological matrices (O'  Leary and Kaufman, 2012). Each cell in the matrix is documented with a labeled image that can be zoomed into or downloaded to better observe the structure in question. Morphological observations based on specimens published in MorphoBank project P891 are attributed to "  Dávalos et al. (2014: P891)  Locality and Horizon: Fayum Quarry BQ-2, 23 meter level, Birket Qarun Formation, Fayum Depression, Western Desert, Egypt (Fig. 1 2 ). Family NA C SA E A M IP MA OA Au NZ References & Notes Myzopodidae F X Age: Late Eocene, Priabonian, ~37 Ma. Etymology: From Aegyptus, Latinized Greek for "Egypt, " and nycteris, Greek for "bat. " The genus name refers to the country in which this new taxon was discovered.
ACKNOWLEDGMENTS We thank the  Egyptian Mineral Resources Authority  and the  Egyptian Geological Museum  for their continued support to assure successful fieldwork in the  Fayum Depression. We thank  Elwyn L. Simons  and  Prithijit Chatrath  ( Duke Lemur Center ) for organizing and leading the many fossil expeditions to Egypt upon which this work is based, and the many field crew members who assisted with quarrying and screening at BQ-2. We thank  Philip Myers  and  Priscilla Tucker  ( University of Michigan Museum of Zoology ) for access to bat and comparative mammal specimens. We thank  Philip D. Gingerich  ( University of Michigan Museum of Paleontology ) for providing casts of Tupaia and Ptilocercus dentitions. Suzann Goldberg  and  Paúl Velazco  (AMNH) provided the photographs in figures 3 and 4 respectively, for which we thank them.
In both cases, the yellow-green horizontal lines between frequencies of 0. 1 and 1. 5 MHz correspond to the local plasma harmonics at the spacecraft altitude (in the ionograms these are vertical lines), the central bulge corresponds to the periapsis of the Mars Express orbit, the yellow-green vertical lines between frequencies of 1. 5 and 3. 5 MHz correspond to the ionospheric traces, and finally the data gap in both orbits correspond to the time period when MARSIS was working in the subsurface mode. Since these two orbits were acquired over the same region and separated by only 13 days, the MEX orbit trajectory over the planet was very similar for both cases. Therefore, the dissimilarities in the spectrograms respond to changes in the ionospheric behaviour and are not related to orbital/planetary variations from one orbit to the next.