dataesr/scientific-paragraphs-categorization huggingface dataset:
AVF encodes a single precursor polyprotein 2130 amino acids (aa) in length. In BLASTP query, the AVF polyprotein was 82% identical to the polyprotein of MsMV1 (99% coverage, Evalue = 0. 0, accession ATJ00054. 1). The next closest species was Nectarine marafivirus M (49% identities, 98% query cover, E-value = 0. 0, accession YP_009222597. 1). The Pfam database search and analysis of the AVF polyprotein (http://pfam. xfam. org/) resulted in five significant Pfam-A matches corresponding to five viral domains characteristic for the genus Marafivirus, family Tymoviridae: viral methyltransferase (PF01660; E-value 7. 9e-55), tymovirus endopeptidase (PF05381; E-value 3. 8e-19), viral (superfamily 1) RNA helicase (PF01443; E-value 5. 3e-52), RNA dependent RNA polymerase (PF00978; E-value 5. 9e-13) and tymovirus coat protein (PF00983; E-value 4.
Notably, MsMV1 was not verified in plant samples as it was digitally deduced from alfalfa transcriptomic data published elsewhere and deposited to NCBI GenBank  [12]. In addition, judging from the comparison with AVF, the reported sequence of MsMV1 appears to be missing the 5' terminus and thus its genome length (6675 nt) is most likely inaccurate. Therefore, bioinformatic data alone, without experimental validation, might not be sufficient as the only criteria for characterization of new viral genomes. The final classification of AVF and MsMV1 as new marafivirus species is under consideration by the ICTV Tymoviridae study group. Primary research by Zhang et al. [12] , whose transcriptomic data has been later adopted by Kim et. al. [11]  for identification of MsMV1, originated from China and employed alfalfa standard varieties Maverick (FDC1) and CUF101 (FDC9) introduced to China from the United States.
Beyond identification and confirmation of AVF as a new viral species infecting alfalfa, the RT-PCR assay with virus-specific primers developed in this work may be of practical use for detection of the virus. Notwithstanding, we conclude that AVF represents a unique virus species with a close resemblance to the members of the genus Marafivirus, family Tymoviridae and a more evident relation to the unclassified Medicago sativa marafivirus 1. The genome sequence of AVF was deposited in NCBI GenBank on 12/24/2017 as accession MG676465.
For quantitative histomorphometry, liver tumors in HE-stained sections were subscribed and their area was automatically measured in image pixels. The size of each tumor was recorded. The total tumor area per total liver area ratio was also calculated for each mouse liver section. IHC-positive cells or pixels were counted in hepatocellular adenoma images of x20 representative high power fields and results were recorded as number of cells or pixels per image as previously described. The ImageJ image processing and analysis program (NIH, Bethesda, MD) with cell counter, color threshold and histogram plug-ins was used for all histomorphometrical assessments.
Qi et al  [36]  studied the expression of AURKB and its correlation with cell proliferation in 40 oral squamous cell carcinoma cases. They showed the elevation of AURKB and Ki67 expressing cell fractions in carcinomas compared to normal epithelial tissue, with a linear correlation between the two datasets. They also found a prominent kinase expression in cases with lymph node metastasis. In our present study, the hepatocellular adenomas that were developed had low neoplastic cell proliferation and apoptosis levels, a finding however that has been reported also previously  [37]. Lee et al  [38]  reported that DEN-induced hepatocellular proliferating lesions including adenomas have only 11 PCNA-positive proliferating hepatocytes in every 100 abnormal hepatocytes counted; the relatively low proliferating index, which is a typical feature of human hepatocellular adenoma as well  [32] , probably reflects the low proliferation rate of hepatocytes that in normal conditions rest in the G0 phase of the cell cycle.
2014). The parameters of data acquisition were as follows: TR = 1500 ms, TE = 35 ms, number of acquisitions -128, number of excitations -8, time of acquisition -3 min 45 s. Using the localizing axial T2-weighted images of the brain, two voxels of 2x2x2cm (8cm 3 ) were located in the gray and white matter. The voxels were placed in the following 2 regions: posterior cingulate gyrus -PCG (Fig. 1 ) and left parietal white matter -PWM (Fig. 2 ). The total acquisition time was 3 min 45 s for each voxel. Post-processing of MRS data was carried out on commercial workstations using algorithms provided by the manufacturer (GE workstation, ADW 4. 4). Each spectrum was automatically fitted to four peaks corresponding to the levels of N-acetylaspartate (NAA) (2. 02 ppm), total creatine (Cr) (3. 03 ppm), choline-containing compounds Additionally, the correlations between metabolite ratios and hormonal concentrations (TSH, fT3, fT4) as well as anti-TG and anti-TPO levels were also assessed.
AHL identification by high performance liquid chromatography-Fourier transform-high resolution mass spectrometry To identify the AHLs produced by the selected Vibrio strains by HPLC/FT-HRMS, a litre of whole culture of each strain was grown in MB medium to stationary phase (OD 600 2. 8) and extracted twice with an equal volume of dichloromethane, evaporated and resuspended in CH 3 CN  [47, 48]. For the analysis, each extract was purified by solid phase extraction  [49]  and analyzed by high-performance liquid chromatography coupled with Fourier-transform and high resolution mass spectrometry (HPLC/FT-HRMS)  [50, 51]  using full scan (FS) and selected ion monitoring (SIM) modes in a Thermo Scientific Accela LC system coupled to a LTQ Orbitrap. The software Xcalibur 3. 0 was used for data processing in both cases.
Based on the results obtained with the different Vibrio species tested, it was noted that V. owensii VibC-Oc-106 was the most virulent species since it produced a higher mortality on the brine shrimp nauplii. Additionally, the virulence of V. coralliilyticus VibC-Oc-193 was also preliminarily tested on Venerupis philippinarum (Manila clams), since the other two strains produced a very slow mortality in this invertebrate model and the assay could not be maintained in our laboratory facilities. For each aquarium, death symptoms on the clams (wide open valves and decontracted adductor muscle) were observed during seven days. The results indicated that V. Regarding the number of CFU of Vibrio spp. in water in all the experiments conducted, in each case the concentration of bacteria showed similar values throughout the experiment (data not shown).
each loading test lasted 19 days. Parameters and methods of testing: stem subsidence. a digital displacement gauge (dTh-a5 5 mm; Kyowa electronic Instruments Co. , Tokyo, Japan), placed at the stem shoulder, was used to measure stem subsidence over time. data was collected using the metshod described by Kaneuji et al. 14  The 16-hour loading period for each day was divided into early, middle and late phases and the first two files from each phase (a total of 20 000 values) were collected and used. data was transmitted automatically to a computer through data collection and analysis software (Sensor Interface pCd-300a; Kyowa electronic Instruments Co. ). Subsidence was defined as the mean of maximum values for sine waves from the 20 000 values during each phase of the loading period. perpendicular movement of the tantalum balls at the tips of the stems was measured by micro-CT and was used as the final amount of subsidence.
We graphed continuous data on stem subsidence for all models through the experiment. Parameters and methods of testing: compressive force at the bone-cement interface. a rod in the tube from outside the fixator was connected to a load cell (Tr20I 500N/ fs, Tr20I 200N/fs; Kyowa electronic Instruments Co. ) and the pressure transducer after cement hardening. This rod made contact with the cement at the medullary canal. Compressive force on the cement was measured over time after calibration. The load and no-load periods in a day were classified into three periods (early, middle and late). The compressive force in each period was defined as the mean of the collected 960 maximum values of sine waves in the two consecutive files after the start of each period (60 values/min × 8 mins × 2 times).
a total of 57 averaged values (3 × 19 days) were used for analysis of stem subsidence and the compressive force, respectively. The measured values were automatically inputted to a computer. Continuous data of compressive force were graphed throughout the experiment. The relationship between stem subsidence and compressive force at the cement-bone interface were investigated using pearson's correlation coefficient. a significance level of 1% was used. Statistical analysis was performed using Statview ver. 5. 0 (SaS Institute Inc. , Cary, North Carolina). Parameters and methods of testing: tantalum ball movement by micro-CT analysis. before and after loading, 3d images of the areas within an approximate radius of 2 cm from the markers were obtained using a micro-CT (Microfocus x-ray System CT) scanner (ToSCaNer-32250 µ hd; Toshiba IT & Control Systems Corporation, Tokyo, Japan), to measure moving distance and direction of the balls in the cement and at the stem tip.
For the vertical distribution analysis, the percentage of individuals identified in the litter and fermentation layer compared to the one identified in depth layer was calculated. The adults/preadults ratio (A/P -expressed as an absolute value) providing information on the demographic structure of the studied communities was also calculated. The resemblance degree of Mesostigmata communities from the 5 ecosystems was tested by Cluster analysis (UPGMA method) using Sorensen's coefficient of similarity. All statistical calculations for this research were done in MVSP 3. 2 software.
After  Salmane (1999) , both are hygromesophillic species and after  Karg (1993) , R. silesiacus is hygromesophilic and O. placentula euryhygrophilic, but certainly both are well adapted to the peculiar conditions of the Danube Delta. Hypoaspis nolli -the edifying species in all investigated sites -is characteristic to wet meadows and considered to be flood resistant  (Salmane 1999 , Griegel 2008). Its development in all investigated sites is presumably owing to similar biopedoclimatic conditions or to trophic resources which coincide (Table  2 , 3). All these results are encouraging and further research that will be made in the frame of the BIODIVERS Research Programme will include investigations into the dynamics and some other forests as well as other types of ecosystems; thus the obtained results will constitute an important database on the diversity and density of soil Mesostigmata in the DDBR.
A. CRT correction for CeBr3 and LYSO detectors The CRT was measured in another study  [5] , in which two (32  32  25) mm CeBr3 crystals were used in coincidence. Each detector was coupled to a Philips Digital Photon Counter tile, DPC-3200-22 sensor with the windowless Fluoral™ technology  [6]. We used the DOI measurement in order to correct for the delay time introduced by the scintillation photon travelling along the crystal at a speed of c/n, assuming that the gamma ray travels at the speed of light in vacuum c. Without corrections, the measured CRT for CeBr3 was 519 ps FWHM. As shown in Fig. 5 , the result was obtained by fitting the raw CRT curve with Gaussian distribution. Fig. 5. FWHM of the raw data CRT: no DOI corrections were applied. The FWHM is deduced from the Gaussian fit  [5].
After a preliminary period to establish the hours over which the dogs were active, follows were largely carried out between 07:00 and 16:00 hrs. Two observers were present for the duration of all followsone either a member of the Ethiopian Wolf Conservation Programme (EWCP) monitoring staff or an official BMNP scout, the other the primary researcher. Data were recorded at between 3 and 5-minute intervals, with additional records of unusual or noteworthy behavior, including attempts at predation and interactions with wolves. Each record included GPS position, habitat type (using EWCP guidelines) and focal animal identity. Presence of additional non-focal animals was documented, separated into sex and age classes where possible. Behavior was categorized into 27 categories  [33]. Associations of focal.
Data analysis This study gathered 1,862 records over 132 observational follows, of which 1,629 records were of focal animals. Of those, 25 were female, comprising ~19% of the dataset, and all-bar-one focal animals were adult. The follow was the unit of analysis for summarizing the prevalence of different activity classes, and for understanding individual behavior. Where possible (n=94), the home village of each focal animal was identified by following animals to or from their village. It was not possible to sample villages evenly (with 2, 15, 3, 6, 6, 18, and 44 focal animals from Alando, Doda, Gata, Mulamo, Tarbo, Wola and Sodota, respectively). Of the 27 classes into which behavior was originally categorized, for analysis this was collapsed into 5 main classes: foraging, eating, travelling, interactions and stationary behavior.
Acknowledgements The authors would like to thank the  Ethiopian Wildlife Conservation Authority  and  Bale Mountains National Park  for permissions and support. They gratefully acknowledge the support provided by the  Ethiopian Wolf Conservation Programme , without which this work would not have been possible. L. R. Perry would like to thank the EWCP and BMNP staff,  Eric Bedin  and  Neville Slade  for help with fieldwork, and  Brasenose College, Oxford , which partially funded this work.
This technique consists in the specific isolation and sequencing of short leading strands from asynchronously growing cells, generating a landscape of replication initiation probabilities within a cell population (Supplementary Fig. 2a ) (reviewed in ref. 17  ). SNS-Seq has been applied to identify ORIs in several systems  [18] [19] [20] [21] [22] [23]  , contributing to build up the notion that the usage of sites of replication initiation in large genomes is intrinsically flexible and related to the transcriptional and epigenetic programme. Analysis of SNS-Seq datasets derived from HMGB1-KO MEFs showed limited changes in the replication initiation profile of cells containing reduced number of nucleosomes relative to their wildtype (WT) counterparts (Figs. 1a  and 2a ). Note that the lower overlap between WT and HMGB1-KO ORIs (63%) relative to that obtained between replicates (78-80%) (Fig.
However, their abnormal accumulation in chromatin has been correlated with genome instability  [52] [53] [54]. We found that H1-TKO cells displayed significantly increased nuclear immunoreactivity than their WT counterparts (Fig. 4d  and Supplementary Fig. 6b-c ). Treatment of cells with RNAseA before immunostaining decreased most of cytoplasmic signal and some of the nuclear signal, while RNAseH treatment strongly reduced nuclear fluorescence, demonstrating Fig. 2  Replication initiation landscape and dynamics in cells with 50% reduction in histone H1 levels. a Representative IGV snapshot showing the SNS-Seq coverage and identified ORIs from two biological replicates derived from 300 to 1500 nt SNS purified from wild-type (WT) mES (blue tracks) or H1-TKO mES cells (red tracks). Data from MEFs WT and HMGB1-KO SNS-Seq are also shown for comparison (green and orange tracks).
All cell lines have been tested for mycoplasma contamination. For cell-cycle analyses cells were incubated for 20 min with 250 µM IdU (Sigma) and fixed in 70% ethanol. After 30 min incubation in 2 M HCl with 0. 5% Triton X-100 samples were neutralized for 2 min in 100 mM Sodium Tetraborate, pH 9. 5, and then incubated for 1 h with primary antibodies (mouse anti-BrdU/IdU, BD Bioscience) and 30 min with secondary antibodies (anti-mouse IgG Alexa-Fluor 647, Thermo Fisher Scientific), both at room temperature. After that cells were stained with cycle buffer (PI/RNAse, BD Pharmingen) for 30 min at room temperature in the dark. Samples were analysed using a FACSCanto A machine (Becton Dickinson), FACSDiva v6. 1. 3 analysis software, and the FlowJo v10 programme. RNAPII-dependent transcription was inhibited by incubating cells in the presence of either 100 mM DRB for 3 h (Sigma Aldrich) or 10 mg/ml α-amanitin for 6 h (Sigma Aldrich).
Reactions were inactivated for 10 min at 75 °C. Ligation of adjacent fragments of the secondstrand synthesis was performed by adding 2 μl of Taq DNA ligase 40 U/μl (New England Biolabs), incubating for 30 min at 50 °C and inactivating the enzyme for 10 min at 75 °C. Finally, RNA primers were removed by treating samples with 1 μl RNAse A/T1 Mix (Thermo Scientific) for 30 min at 37 °C, and DNA was extracted with phenol/chlorophorm, ethanol precipitated and resuspended in 20 μl of TE. DNA libraries were prepared at the Fundación Parque Científico de Madrid (FPCM), with the NBNext kit (New England Biolabs) following manufacturer's instructions. Each library was sequenced by 75 single-end runs on a NS500 system (Illumina) at the FPCM. SNS-Seq data processing. SNS-Seq reads were aligned to the mm10 version of the genome using the standard BWA-MEM algorithm.
Reads with low quality and multihits were removed with the Samtool view (parameter -q 1). ORI peaks were determined with the scanquantile programme  19  , with a P value threshold of 1E -16. The required genome segmentation used by this peak-calling script was based on replication timing data from mES  39  , which accurately matches the read coverage differences between segments. Finally, the peaks separated by less than 200 bp were merged (keeping the lowest P value), and the peaks with a P value higher than a threshold were removed; this threshold was fixed depending on the read depth and the background of each track. Common peaks were obtained with the intersectBed (BedTools), with parameters -wa -f 0. 1: nonreciprocal, and with a minimal fraction of 10% of overlap. The heatmap, pairwise comparison between origins per segment, and Venn diagrams were generated with custom R scripts; the dendrogram of the heatmap was calculated with the standard hierarchical clustering implemented on the heatmap.
Visual acquisition of the DNA fibres was done in a Axiovert200 (Zeiss) Fluorescence Resonance Energy Transfer microscope and the images were analysed with the image processing programme ImageJ v1. 51a using the conversion factor of 1 μm = 2. 59 kb. Statistical analyses were performed in Prism v5. 0. 4 (GraphPad Software) using the non-parametric Mann-Whitney rank sum test. *P < 0. 05, **P < 0. 01, ***P < 0. 001, ****P < 0. 0001. Protein extraction and western blotting. Cells were lysed with RIPA buffer (25 mM Tris-HCl pH 7. 5, 180 mM NaCl, 1% deoxycholate, 1% NP-40, 0. 1% SDS) and extracts were sonicated in a Bioruptor (Diagenode) during 10 cycles 30 s HIGH, 30 s OFF, and then cleared by centrifugation (15 min, 4 °C, 21,100 × g). Primary antibodies used were rabbit anti-P-MCM2-S53 (Abcam ab70367, dilution 1/1000), rabbit anti-MCM2 (gift from Juan Méndez, CNIO, Spain, dilution 1/5000), rabbit anti-P-CHK1-S345 (Cell Signalling, 2348 S, dilution 1/500), mouse anti-CHK1 (Santa Cruz sc-8404, dilution 1/500), rabbit anti-γH2AX (Cell Signalling 9718S, dilution 1/1000), rabbit anti-H2AX (Cell Signalling 7631S, dilution 1/1000), rabbit anti-RNAseH1 (Proteintech 15606-AP, dilution 1/2000), mouse anti-α-TUBULIN (Sigma T-5168, dilution 1/4000), rabbit anti-HMGB1 (Abcam ab18256, dilution 1/ 1000) and mouse anti-SLBP (Sigma WH0007884M1, dilution 1/500).
1 software (Agilent Technologies). Analysis was performed with the Agilent Genomic Workbench 5. 0 software. The log 2 -ratio timing profiles were smoothed using the Agilent Genomic Workbench 5. 0 software with the Triangular Moving Average option (500 kb windows). To determine the replication domains in different conditions, algorithms from CGH applications in the Agilent Genomic Workbench 5. 0 software were used, particularly the aberration detection algorithms (Z-score with a threshold of 1. 8) that define the boundaries and magnitudes of the regions of DNA loss or gain corresponding to the late and early replicating domains respectively. Then, a comparative analysis of replication domains was performed between the different cellular conditions, in order to determine DNA segments with significant replication timing changes.
Coverslips were mounted in Prolong Diamond (Life Technologies) and visual acquisition was performed in a LSM510 AxioImager M1 microscope (Zeiss) using either a ×63 or a ×100 oil objective. Nuclear segmentation was based on DAPI staining. Statistical analyses were performed in Prism v5. 0. 4 (GraphPad Software) using the nonparametric Mann-Whitney rank sum test. *P < 0. 05, **P < 0. 01, ***P < 0. 001, ****P < 0. 0001. Nascent DNA and RNA labelling. For nascent DNA labelling, cells were incubated in culture medium supplemented with 10 μM EdU for 20 min, rinsed in cold PBS before fixation in 3. 7% formaldehyde for 15 min. EdU incorporation was revealed with Click-iT® EdU Imaging kits (Invitrogen) using Alexa Fluor 647 dye according to manufacturer's instructions. Coverslips were staining at room temperature with 2 ng/μl of DAPI (Merck) in PBS for 5 min and then mounted in Prolong Diamond (Life Technologies).
Cells were analised using the ImageJ v1. 51a software and scored as early-, middle-, or late-S phase according to their EdU replication-foci patterns. Statistical analyses were performed in Prism v5. 0. 4 (GraphPad Software) using the non-parametric Mann-Whitney rank sum test (Supplementary Figure  6 ). *P < 0. 05, **P < 0. 01, ***P < 0. 001, ****P < 0. 0001. For nascent RNA labelling, cells were incubated in culture medium supplemented with 0. 5 mM EU for 1 h and processed as above. EU incorporation was revealed with Click-iT® RNA Imaging kits (Invitrogen) using Alexa Fluor 488 dye according to manufacturer´s instructions. The mean EU fluorescence intensity per cell was obtained using ImageJ v1. 51a software by averaging the mean grey value of EU signal measured in each nucleus. Nuclear segmentation was based on DAPI staining.
Acknowledgements We are grateful to  Arthur Skoultchi ,  Félix Prado ,  Juan Méndez ,  Pablo Huertas  and  Andrés Aguilera  for reagents and advice, and to  Fernando Azorín  for sharing data with us before publication. We also thank  Fernando Azorín ,  Juan Méndez  and  Félix Prado  for comments on the manuscript;  Silvia Jimeno-González  and  José Carlos Reyes  for advice on transcription elongation experiments;  Daniel Gómez  and  Alberto Ferrera  for help in some stages of the project and members of the  Crisanto Gutierrez and M. G. laboratories  for discussions. This work was supported by the  Spanish Ministry of Economy and Competitiveness ,  MINECO  ( BFU2013-45276-P  and  BFU2016-78849-P , co-financed by The  European Union FEDER funds)  to M. G. , and by  ANR  grant ( ANR-14-CE10-0008-02 ) and  Ligue Contre le Cancer Comité de Paris  ( RS16/75-108 ) to J.
20 strain. Although a direct comparison of here presented results and literature data is not completely correct due to obvious experimental differences, it can be stated that both here obtained wild type strains show great potential towards production of 2-PE, which constitutes a promising starting point for future optimization studies. As demonstrated by the former reports mentioned above, optimization of culturing parameters may significantly improve the bioconversion processes performance. The bioconversion cultures of K. lactis 6. 10 and P. cactophila 7. 20 strains were accompanied by an additional run of GC-MS analyses, to determine if any new aroma compounds appeared in the culturing media, apart from those pre-selected after the primary cultivation run. The analysis revealed no new aroma compounds being synthesized in the amino acid-supplemented minimal medium, apart from disulfide dimethyl, an aroma compound of sulfurous, vegetable, cabbage and onion flavour, particularly desired in meat and cheese-containing foods.