dataesr/scientific-paragraphs-categorization huggingface dataset:
Structural Organization of tRNA Array Units The organization of tRNA between tRNA array units was compared as follows: 1) Each tRNA array unit was first converted into an amino acid (aa) sequence, in which each tRNA gene was turned into the corresponding aa isotype; 2) then, incremental patterns (incremental path of 1) of 20 amino acids (corresponding to the tRNA genes) were extracted from each aa sequence and an overall amino acid pattern database associated with tRNA array units was constituted; and 3) the fuzzpro program (http://emboss. sourceforge. net) was used for pattern matching analysis between each incremental pattern and the pattern database, allowing 0-19 maximal pattern mismatches. These represented all putative local alignments of 20 adjacent tRNA genes between tRNA array units.
2015). On the contrary, one disadvantage of having a highly clustered tRNA gene organization is the difficulty finely tuning the transcription of each tRNA gene under different growth conditions. One last compelling theory is that controlling the expression of individual and clustered tRNA species enables different levels of translational control, which may be useful for specific gene products or under certain growth conditions. Another important question that remains is: Does the presence of tRNA arrays enhance the efficiency, fidelity or specificity of the translation? For that purpose, the structural organization (same order in amino acids) of the arrays was analyzed as a protein motif or pattern within proteomes of organisms harboring array units compared with nonarrayed organisms. However, there is no difference between the two sets of organisms suggesting that the structural organization of the arrays is not directly linked to the translation efficiency (data not shown).
Acknowledgments This work was supported by  Aix-Marseille Universite(AMU) ,  Centre National de la Recherche Scientifique (CNRS) , and the  Vietnamese Ministry of Education and Training  (PhD fellowship to T. T. T. T. ). The authors thank  Patricia Chan  ( Lowe Lab, University of California Santa Cruz ) for her kind advice on the tRNA gene detection procedure as well as to Sebastien.
Continuous relative measurements at GPK1 In order to obtain local tidal parameters for solid Earth and ocean loading tides, a continuous record at GPK1 was collected GPK1 with a Scintrex CG5 gravimeter. The time span covers the period from 16 April 2013 to 21 May 2013 (Fig. 7 ). The analysis of the data set using ETERNA 3. 4  (Wenzel 1996)  shows that the determination of large tides in the semi-diurnal and diurnal bands is satisfactory with  results in close agreement with those obtained from the superconducting gravimeter C026 in Strasbourg (cf. Fig. 8 ). However, the determination of smaller amplitude tides shows more discrepancies. Notice also the strong differences in the tidal uncertainties with respect to the SG observations for the same time period. We also found a factor close to 35 in the standard deviation (SD) of the Scintrex CG5 and the GWR C026 gravity residuals.
Data processing The repetition of a micro-gravimetric network, where x 0 and t 0 are the reference point and time, leads to the following formula for the gravity double differences at point x and time t: Dg t-t 0 x-x 0 ¼ g x -g x 0 t -g x -g x 0 t 0 ð5Þ To process the data, we developed a software written using a Python language called PyGrav in order to homogenize and concatenate current processing codes like Matlab scripts, MCGravi  (Beilin 2006) , CGxTool  (Gabalda et al. 2003) , or ETERNA  (Wenzel 1996). This code is very appropriate for all kinds of gravity surveys (static, time-lapse) and allows in particular an easy reprocessing of repeated micro-gravity networks. It has a user-friendly interface for handy and fast treatment of the raw gravity data at every station of the network (see Fig.
12 ). Fully manual or automatic selection is possible according to specific thresholds in tilt, standard deviation, or duration of the gravity observations. Each selected measurement is then corrected for tides and air pressure and the software allows to remove the instrumental drift on all the chosen loops of the network. This is done using the least-square inversion scheme described in  Hwang et al. (2002). This first step leads to the gravity simple differences between the reference point and any point of the network; the standard deviation is computed following  Hwang et al. (2002)  as the square root of the posteriori variance resulting from the inversion scheme. When different repetitions of the network are done, gravity double differences are computed according to Eq. 5; the standard error (uncertainty) on a gravity change between two surveys and for a specific station is the square root of the quadratic sum of respective station standard errors for each survey.
Data analysis The calculations of mesohylar cell number (types 1 and 2 vacuolar cells) were carried out on the serial semithin sections. Six sponge specimens were used for each regeneration stage. For each specimen, we analyzed digital photos of 8 sections (four photos from four serial sections, in order to avoid overestimation due to the overlapping of cells). We determined the number of vacuolar cells throughout the regenerate stages and estimated each cell type over an area of 1mm 2 using ImageJ Software (http://rsb. info. nih. gov/ij/index. html).
Specimens were then rinsed three times in blocking buffer for 3-5 hours in a tube rotator and incubated in Alexa Fluor labeled anti-mouse secondary antibody (Molecular Probes). After 12 hours of incubation in the secondary antibody, specimens were rinsed and the DNA was stained with TO-PRO-3 (Molecular Probes) at concentration 1 μM in PBS for 2 hours. Rinsed pieces of the sponges were mounted in DABCO-glycerol. Images were obtained using a multiphoton confocal microscope Leica TCS SP5 MP with white laser WLL. Pictures were processed with LAS AF Lite (Leica Microsystems) and ImageJ software (http://imagej. nih. gov/ij/).
This work was supported by  13-04-01084   Russian Foundation for Basic Research  (http://www. rfbr. ru/rffi/eng/about) to AVE, IEB, and  DBT  for data collection and analysis; 1. 38. 209. 2014Saint-Petersburg State University grants (http://spbu. ru/images/orders/2015/496_1. pdf) to AVE and IEB for data collection and analysis; and  ANR-ll-IDEX-DOOI-02 French Government A Ã MIDEX  project (http:// amidex. univ-amu. fr/)to AVE and  CB  for preparation of the manuscript. regeneration mechanisms in metazoans, and is a strong basis for future investigations with molecular-biological approaches.
Electrophysiological recordings Two-electrode voltage-clamp recordings were performed at room temperature (18-22°C) using a Geneclamp 500 amplifier (Molecular Devices, USA) controlled by a pClamp data acquisition system (Axon Instruments, USA). Whole cell currents from oocytes were recorded 1-4 days after injection. Bath solution composition was ND96 (in mM): NaCl, 96; KCl, 2; CaCl 2 , 1. 8; MgCl 2 , 2 and HEPES, 5 (pH 7. 4). Voltage and current electrodes were filled with 3 M KCl. Resistances of both electrodes were kept between 0. 7-1. 5 MO. The elicited currents were filtered at 1 kHz and sampled at 500 Hz using a four-pole low-pass Bessel filter. Leak subtraction was performed using a-P/4 protocol. K V 1. 1-K V 1. 6 and Shaker IR currents were evoked by 500 ms depolarizations to 0 mV followed by a 500 ms pulse to -50 mV, from a holding potential of -90 mV.
Molecular modelling and Protein-Protein Docking Three-dimensional structure models of Kbot21 toxin and Kv1. 2, Kv1. 4 and Kv2. 1 channels. The homology model of Kbot21 was built using the NMR structures of the BmBKTx1 peptide  [26]  (PDB code: 1Q2K). In order to partially account for the flexibility of the scorpion peptides, all the 21 NMR solutions presented in the PDB file were used as templates to build 21 models of Kbot21. The structural models were generated by simply mutating the 13 th (Val to Arg) and 24 th (Asn to Asp) amino acids using SCWRL4 program  [27]  followed by 50 and 500 steps of energy minimization using steepest-descent and adopted basis Newton-Raphson methods respectively. The Kv1. 2 is a potassium channel belonging to the Shaker-like subfamily. Its full length crystallography structure was solved for the first time by Long et al.
[28]. However, in our study we used the crystal structure of Kv1. 2-Kv2. 1 paddle chimera channel due to its better quality  [29]. In our study we were restricted only to the pore domain. The homology models of Kv2. 1 and Kv1. 4 were build with MODELLER 9v8  [30]  using only the pore domain of the channel crystal structure (PDB code: 2R9R)  [29]. Sequences of human Kv2. 1 and Kv1. 4 were retrieved from Uniprot database (http://www. uniprot. org/) under Q14721 and P22459 codes, respectively. Twenty structures were generated for each subtype and their respective DOPE  [31]  scores were calculated. The models of Kv1. 4 and Kv2. 1 with the lowest DOPE values were selected and retained.
Protein-Protein Docking Solutions of protein-protein docking between Kbot21 and the Kv1. 2 potassium channel were generated using ZDOCK software  [32]. The 21 models of Kbot21 generated were used to run an ensemble docking. Consequently, a total of 42000 poses was returned. A clustering analysis was carried in order to remove redundancy due to the highly geometrical similarity of some complexes. Cα Root Mean Square Deviations (RMSD) of the whole set of docking solutions were calculated. The poses belonging to the same cluster were grouped together based on a RMSD cut-off of 4 Å. The most represented clusters (>10 members) were then processed for the refinement using molecular mechanics for only the centre of each cluster. The refinement consists of 50 steps of Steepest-descent energy minimization followed by 800 steps of adopted basis Newton-Raphson minimization.
Sequences were analyzed for known classes of RNA based on Rfam  [29]  (version 11, obtained from ftp://ftp. sanger. ac. uk/pub/ databases/Rfam/11. 0/). The best hit with at most two mismatches was used to classify the reads. Analysis of miRNA content was carried out using miRdeep2  [30]  with the following settings: 1) reads map perfectly to the genome, 2) cut off -v 1, 3) employing the "-s option" using all mature sequences from mirbase (version 20)  [31] , 4) only read lengths (18 to 30 nt) were analyzed. Folding analyses of the novel pre-miRNAs detected in nodule fluids were carried out using the RNAfold Vienna package with default settings  [32].
It is possible these are of human origin but are edited or that they derive from other organisms or dietary sources as shown in several studies  [38, 39]. Similarly the source of many reads that map to O. volvulus genome and are annotated as tRNA fragments  [34]  cannot be reliably assigned (Table  2 ). Here we focus on the miRNAs detected in the serum from humans testing positive for O. volvulus that can be assigned a nematode origin. From the combined datasets we identify a total of six O. volvulus miRNAs. The nematode origin of these is evident from a number of criteria: 1) they map perfectly to regions that fold into hairpin structures within the O. volvulus genome; 2) they are not other classes of sncRNA and 3) they are not present in the sera of European controls. Of the six miRNAs identified, all were identical to the O.
Common and distinct circulating miRNA signatures in filarial infections We recently identified 16 miRNAs in the serum of mice infected with the filarial nematode L. sigmodontis and four of these are identical to the O. volvulus miRNAs detected in human serum (mir-71, two miR-100 members, and one bantam family member) and one is derived from the other arm of the hairpin of a O. volvulus miRNA (miR-87). A further seven of the L. sigmodontis miRNAs are identical to O. ochengi miRNAs found in the nodule fluid and three (miR-50-3p and Bantam-b,c) differ by 1 nt outside of the seed region (Figure  3 ). Strikingly multiple miR-100 and bantam family members are present in the datasets. These also dominate the secretion product of the gastrointestinal nematode H. polygyrus  [9]. The O. volvulus miR-100 and bantam miRNAs identified have distinct sequences outside of their seed regions from the miRNAs in H.
polygyrus (Figure  4 ). To compare relative quantities across the datasets and to qualify our limit of detection, we used total host miRNA read counts in the same samples as a normalizer. The individual parasite miRNAs are detected at a range of 26 to 12,863 per million bovine miRNA reads (O. ochengi nodule fluid), 5 to 127 per million human miRNA reads (serum/   4. We anticipate these relative proportions will vary depending on the intensity of infection. Importantly, this provides a baseline for comparing relative levels of parasite miRNAs between studies and understanding the limits of detection in each study. A recent analysis of serum from humans infected with O. volvulus using deep sequencing reported 20 putative O. volvulus miRNAs that have no overlap with those we identify here  [5].
Thirteen of the reported sequences were < 17 nt long, or detected in only one read and thus are not analysed by our criteria. Of the seven additional sequences three of these perfectly align to human ribosomal RNA and two of these (PC-5p-31768_12, PC-3p-46055_7) are found as a part of longer sequences in European control serum. One of the sequences, let-7, is also found in our datasets but we do not confidently assign this to nematode origin given its conservation in the mammalian host.
As observed in the L. sigmondontis dataset the O. volvulus miRNAs are much less abundant than host miRNAs in serum or plasma: in the Ghana samples we mapped 743 reads to 6 different nematode-derived miRNAs, compared to approx. 2. 5 million human miRNAs reads in the same library. Low-abundance is a challenge when detecting any type of parasite-derived molecule in host fluid. An advantage of the miRNAs is that these can be amplified by PCR prior to detection. Nonetheless, methods for enriching parasite material are likely to be advantageous in terms of maximizing the specificity and sensitivity of detection. In this regard, we have shown nematode miRNAs are secreted within extracellular vesicles in vitro  [9]. Further work is required to understand whether parasite and host miRNAs exist in similar or distinct complexes in host fluids, and/or whether these can be further purified prior to RNA extraction to reduce the scope for crosscontamination.
Acknowledgements Funding was provided by the  Institute for Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Germany  as part of a consortium grant funded by the  Bill and Melinda Gates Foundation  to the  University Hospital of Bonn  as well as a  Wellcome Trust RCDF  ( WT097394AIA ) to  A. Buck. Funding for Cameroonian human sera and nodule fluid was provided by the 7th  Framework Programme  of the  European Commission  (project identifier  HEALTH-F3-2010-242131 ). We thank  Kat Gordon  and  Kashyap Chhatbar  for helpful discussions on this work. Author  details 1 Centre for Immunity, Infection and Evolution, Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh, UK. 2 Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK.
Statistical Analysis One-way variance analysis was used to calculate the significances of REG3β-positive lesions per tissue (percentage values), as previously described  (34). To compare REG3β mRNA expressions, BrdU incorporation and caspase 3/7 activity after treatment with different concentrations of the REG3β, we used the one-way variance analysis; the p value was calculated using delta Ct, as described by Yuan et al. (35). Two-way variance analysis was used to compare lesion numbers per field in Kras G12D mice carrying the indicated REG3β (REG3β +/+ or REG3β -/-) at 14 weeks of age. Values are expressed as mean ± SEM. All tests of significance were two-tailed and the level of significance was set at 0. 05. The examined cell lines represent at least three independent experiments. All statistical tests were performed using IBM SPSS statistics 21.
Thus, we complemented these studies by measuring the effects of REG3β on pancreatic cell death. For this purpose, we activated the apoptotic program of pancreatic cancer cells by serum starvation for 24, 48, and 72 h. At the same time, cells were also incubated with or without recombinant REG3β protein at a concentration of 100 ng/ml. Apoptosis was determined by measuring cell viability and caspase 3/7 activities at the end of the experiment. Figures  6B  and 7C  show that the treatment of both MiaPaCa2 and Panc1 cells with REG3β for 48 and 72 h increased their resistance to apoptosis as evidenced by increased cell viability and decreased caspase 3/7 activity. Thus, we conclude that REG3β promotes cell growth and protects against cell death in PDAC cells. This data is relevant to better understanding the role of this protein during the process of initiation, since it is wellestablished that both of these processes are crucial for normal cells to acquire the ability to undergo ADM and form PanIN lesions in response to oncogenic KRAS.
Acknowledgments This work was supported by  La Ligue Contre le Cancer ,  INCa ,  Canceropole PACA ,  DGOS (labellisation SIRIC ) and INSERM to JLI,  National Institutes of Health  grants  DK52913 , the  Mayo Clinic Center for Cell Signaling in Gastroenterology  ( P30DK084567 ), the  Mayo Foundation  to RU, by  Fraternal Order of Eagles Cancer Award  to GL and the  FIS grant  from  Instituto de Salud Carlos III  ( PI13/01224 ) to EFP.
Case identification and outcomes In January 2009, the VIP cohort was linked to the Northern Sweden Regional Cancer Registry, part of the Swedish Cancer Registry, using the Swedish personal identity number. We identified 1423 incident PCa cases in the VIP cohort, 1377 of which had cryopreserved blood available for analysis. Clinical data were retrieved from the National Prostate Cancer Register. We reviewed hospital medical charts of men diagnosed with cancer to identify men who later had documented evidence of metastatic disease (ie, a positive bone scan) during the follow-up period. There were 126 patients with metastatic PCa diagnosed during follow-up who subsequently died from PCa, according to the Cause of Death Registry. Cause of death was assessed by medical chart review or, when charts were not available (n = 4), the Swedish Cause of Death Registry.
Acknowledgment statement We thank  Åsa Ågren ,  Västerbotten Intervention Project ,  Umeå, Sweden , for data management; Britt- Inger Dahlin , research nurse,  Department of Urology, Umeå University Hospital (Sweden ) for chart review; and the  Västerbotten County (Sweden)  for providing the blood samples. We also thank  Gun-Britt Eriksson ,  Mona Hassan Al-Battat , and  AnnaPeri Erlandsson  for expert assistance with immunoassay measurements of the blood samples at the  Wallenberg Research Laboratories at Lund University, Malmö, Sweden. All participants gave written informed consent at the time of recruitment, and the project was approved by the  Research Ethics Board at Umeå University  (research authorization number  2009-1436-31 ).
These data indicate that absence of MsrA and MsrB leads to non-specific protein damage  [25]  but Met ox 169 reduction still occurs. The partial oxidative damage of NirA could explain the slightly reduced transcriptional activation capacity of NirA found in the msrA msrB double deletion strain (S1B Fig). Because FLAG-NirA carries reduced M169 in the msrA msrB double deletion background it remains to be determined which activities would be required for the very rapid NirA-NES Met ox 169 reduction associated with activation of NirA by nitrate. As methionine oxidation could generally affect NirA protein stability under non-induced conditions, we tested the amounts of FLAG-NirA in crude extracts obtained from argininegrown (NI) or NO 3 -grown (IND) cells. We found that NirA levels were basically equal under both conditions and this result indicates that overall stability of NirA is not influenced by the Met169 oxidation state (Fig  2C ).
Confocal microscopy of NirA-GFP however, showed that the transcription factor was constitutively nuclear in the fmoBΔ background (Fig  2A ). This result is consistent with M169 oxidation in the NES under NI conditions having a specific role for NirA localization and function. However, despite the constitutive nuclear localisation of NirA, the fmoBΔ background does not lead to constitutive expression of NirA-dependent genes (Fig  2B ). Induction by nitrate, on the other hand, occurred as in the wild type and may even be slightly enhanced (+70%) in the fmoB mutant (Fig  2B ). These results confirm that the oxidation status of NirA-NES is determined specifically by FmoB, one out of seven flavin-containing monooxygenases predicted in the A. nidulans genome. These data also confirm that the NES oxidation status controls the nuclear-cytosolic shuttling process but not necessarily the transcriptional activity of NirA.
15 μg of extracts were loaded per lane. Intensity of signals were calculated with ImageQuant software (Molecular Dynamics) against actin (ActA) (Ab 691001, MP Biomedicals) as loading control. Western blot analysis GFP-and FLAG-tagged of nirA strains, were carried out by preparing total cell extracts according to the methods described by  [46]. Grained mycelia were resuspended in protein extraction buffer (20 mM Tris-HCl, pH8, 150 mM NaCl, 0,01% Triton X-100) containing protease inhibitor cocktail (P8340, Sigma). 30 μg per lane of total protein extract was loaded on a 10% acrylamide/bis-acrylamide gel in the presence of β-mercaptoethanol and SDS as denaturing agents. GFP-NirA membranes were incubated with anti-GFP primary Ab (Roche, 11814460001) and with Anti-Mouse IgG (H+L) secondary Ab (Jackson, 115-001-003).
Mass spectrometric analysis In-gel protein reduction, alkylation and trypsination were performed as described previously  [48]. NanoHPLC-MSMS protein sequencing was performed on the UltiMate system from Dionex. Eluting peptides were directly introduced into the MS and ionized via Pico Tip (New Objective, Cambridge, USA) to be further transferred online to a heated capillary of an ion trap mass spectrometer (LCQ Deca XPplus, Thermo Finnigan). Analysis of MS/MS spectra with respect to peptide identity was routinely performed by applying both the MASCOT (Matrix Science)  [49]  and the SEQUEST  [50]  (Bioworks3. 1) search engines using the MSDB (MSDB 09082006) and the Global Proteome Machine database (Aspergillus nidulans), respectively. The following settings were used for the generation of DTA files and for database search: MW range, 450 -3500 Da; threshold, 10000; minimum ion count, 10; precursor mass tolerance, ± 3 Da; fragment mass tolerance, ± 0.
μm. (B). Comparison of niaD mRNA levels between the control strain (alcA p -FnirA) and the msr double deletion mutant (alcA p -FnirA msrABΔΔ). Numbers below the niaD hybridization panel are relative values compared to the niaD IND expression in the control strain (alcA p -FnirA) that was arbitrarily set to 100. (C). NirA is fully functional in thioredoxin mutants. Transcription of the NirA target gene niiA was tested in strains carrying a deletion in the single A. nidulans thioredoxin gene (trxAΔ, accession number ANID_00170) under noninduced and induced conditions and compared to wild type (WT), nirA c 1 and a strain in which the trxA deletion has been complemented by a functional ectopic copy (27). Growth conditions were as in B, except that induction by nitrate was proceeding for 2 hours instead of 20 minutes.