dataesr/scientific-paragraphs-categorization huggingface dataset:
Sound production and recordings Playback tracks were created from original recordings made at Santander Harbor (Spain). During these recordings, the hydrophone was positioned at a depth of 2 m, with cargo ships passing at a distance of approximately 500 m. Due to port regulations, the ships were estimated to be sailing at a speed 9 knots. Weather conditions were calm (wind force 3 on the Beaufort scale). A noise generated by one passing ship was randomly picked. The selected noise of 12-min duration was modified using a sound program interface (Cool Edit, version 2. 0, Syntrillium Software Corporation, USA) to obtain two records with two different amplitudes and with frequencies from 20-20,000 Hz: one passing ship had a maximum amplitude of 150 dBrms re 1 μPa, and the other had a maximum amplitude of 138 dBrms re 1 μPa.
Oyster behavior recording As explained by Andrade et al. [21] , the recording apparatus consisted of lightweight electromagnets (56 mg) glued to each valve and connected by flexible wires to a laboratory-made valvometer. The device measures current which varies according to the distance between the electrodes. For this experiment, the sampling frequency was 3. 3 Hz, and according to that frequency, the opening status of each oyster was measured every 4. 8 sec. Data were transmitted via an acquisition card (Ni-USB-6009, National instrument, Austin, TX, USA) and recorded by a computer using a laboratory-made script in Labview (National instrument). Data were also processed automatically using routines and published online on the professional pages of the MolluSCAN eye website https://molluscan-eye.
Intermediate values are possible. Valve partial closure is calculated from the sum of the detected partial closures for a given time for each animal at different thresholds. In the present experiment, the 80% thresholds were used for partial-closure calculation, as this was appropriate. Growth rate can be estimated using valvometry. As calcification in bivalves occurs in the mantle cavity, when daily growth layers are deposited, the minimum distance between the electrodes glued to the shells increases, thereby providing a good index of growth. By plotting these values of minimal daily valve opening as a function of time, one obtains growth curves  [32]. For each condition, no significant difference was observed between the duplicates, and the data were pooled together.
cDNA synthesis and quantitative PCR Gill samples of oysters were individually processed for RNA extraction using TRI Reagent1 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Total RNA quality and quantity were estimated by spectrophotometer (Epoch, Biotek1), and reverse transcription was realized with 4 μg total RNA, oligo dT17, and Moloney Murine Leukemia Virus (M-MLV) reverse transcriptase (Promega, Madison, WI, USA). Nineteen genes were chosen to encode the proteins involved in the various metabolic pathways. For each candidate, specific primers were designed from the sequence of M. gigas available in the National Center for Biotechnology Information (NCBI) database or selected from the literature (Table  1 ). The PCR efficiency of each primer pair was realized by determining the slope of the standard curve obtained from the serial dilution analysis of cDNA.
Real-Time quantitative Polymerase Chain Reactions (RT-qPCR) were performed in an Mx3000P (Stratagene1) with GoTaq qPCR Master Mix (Promega1, Madison, WI, USA) and a concentration of 100 nM for each primer according to the manufacturer's instructions. The amplification program starts with 3 min at 95˚C to activate the DNA polymerase, followed by 50 cycles of 10 sec at 95˚C and 30 sec at 60˚C. Reaction specificities were confirmed by a melting curve (from 65˚C to 95˚C). Five potential housekeeping gene (12s, ef1α, rpl7, gapdh, actb) was tested using BestKeeper, geNorm and Normfinder and 12s gene was sectioned. The expression of transcripts levels in each oyster was quantified by the 2 -ΔΔCt method described by Livak and Schmittgen  [33].
Statistics Comparisons between variables were investigated using analysis of variance (ANOVA) after checking for assumptions of normality and homoscedasticity of error term. For significant differences, the Tukey's Honest Significant Difference (Tukey's HSD) was used for all pairwise comparisons. When assumptions were not met, the Kruskal-Wallis test was applied, and the Dunn test was considered for all pairwise comparisons. Differences between distributions were assessed using a two-sample Kilmogorov-Smirnov test, and differences between variances were assessed using a Levene test. For all statistical results, a probability of p < 0. 05 was considered significant. Data were computed and analyzed using R software  [40]. All data are provided as supporting information (S1 Database).
Shi and Gibson  [56]  already shown that oxidative stress can induce an increase in mdh gene expression. Without ship noise, and in the presence of Cd alone, the expression of sod2, sod1, gpx, and mdh did not change. Cadmium does not directly induce ROS production  [57] , but it can induce oxidative stress indirectly through different pathways  [58]. The absence of enhancement of the oxidative stress defense mechanism at T 14 in presence of Cd alone suggests either weak oxidative stress or an already fixed problem. In this view, the data show that the cat gene coding for the catalase, an enzyme responsible for converting H 2 O 2 to H 2 O and O 2 , was downregulated more with Cd alone than with Cd plus the cargo ship noise. This larger downregulation agrees with the above dataset, which fits well with a low or absent oxidative stress and higher MT proteins levels in the cells.
This study was supported by grants from  Campus France ,  ANR  ( ANR-15-CE04-0002-02  WAQMOS), NEUROMED, the  Institut National de la Santeet de la Recherche Medical (INSERM) , the  GDRI de Neurosciences , n  198 ,  Embassy of France ,  Institut Franc  ¸ais in Morocco, the  MolluSCAN Eye Project , and the  Centre National pour la Recherche Scientifique et Technique (CNRST)  to  M. C. TOTAL R&D  provided a grant (no. FR00008208 ) to A. M. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Gas chromatography-mass spectroscopy (GC/MS) GC-MS was carried out in a Hewlett-Packard 6890 gas chromatograph fitted with a HP-1 fused silica column (polydimethylsiloxane 30 m × 0. 25 mm i. d. , film thickness 0. 25 μm), interfaced with an Hewlett-Packard mass selective detector 5973 (Agilent Technologies) operated by HP Enhanced ChemStation software, version A. 03. 00. GC parameters as described above; interface temperature: 250 °C; MS source temperature: 230 °C; MS quadrupole temperature: 150 °C; ionization energy: 70 eV; ionization current: 60 μA; scan range: 35-350 units; scans s -1 : 4. 51. Components of each EO sample were identified by their linear retention indices on both UB-Wax and SPB-1 columns. Linear retention indices were calculated relative to linear homologous series of n-alkanes C 8 -C 24.
X-ray Photoelectron Spectroscopy (XPS) analyses were carried out with a Versa Probe II spectrometer (ULVAC-PHI) equipped with a monochromated Al Kα source (hν = 1486. 6 eV). The core level peaks were recorded with constant pass energy of 23. 3 eV. The XPS spectra were fitted with CasaXPS 2. 3 software using Shirley background and a combination of Gaussian (70%) and Lorentzian (30%) distributions. Binding energies are referenced with respect to the adventitious carbon (C 1s BE = 284. 6 eV). Scanning electron microscopy (SEM) images were acquired with a ZEISS Ultra 55+ Electron Microscope equipped with EDX detector. in propylene carbonate)  35  , ferrocyanide/ferricyanide (0. 01 K 3 Fe(CN) 6 , 0. 2 M K 4 Fe(CN) 6 in water). 54 As a counter electrode for polysulfide electrolytes, brass plates was activated in 1.
Acknowledgements The work was supported by the  Agence Nationale de la Recherche , project  QuePhélec  ( ANR-13-BS10-0011-01 ). We also acknowledge support from the  European Research Council  (grant number  321305 ) and the  EPSRC  (grant numbers  EP/L017008/1  and  EP/M506631/1 ). IDWS is a  Royal Society Wolfson Research Merit  award holder. The authors would like to thank  Dr. Stéphanie Pouget  ( CEA/INAC/MEM/SGX ) for help with the XRD and  Dr. Mahfoudh Raissi  ( Univ. Nantes/CEISAM)  for the photovoltaic measurements.
Finally, the clinical-functional and radiographic data were compared based on patients' demographic parameters (age, gender, BMI, and smoking) and the number of osteotomies. 2. 9. Clinical Functional Outcome Measures. The clinical preoperative evaluation included a complete clinical history of the patients, their main characteristics (age, gender, BMI, dominant side, smoking, occupation, and anesthesia ASA class), and physical examination of the foot for preoperative planning, as well as the percutaneous procedures to perform (number of metatarsals to treat). To evaluate clinical outcomes at the preoperative period and last follow-up (FU), the following and most used questionnaires for forefoot assessment were used according to our study protocol: (i) The 100-point AOFAS hallux metatarsophalangealinterphalangeal scale  [35, 36]  was the only questionnaire used to assess clinical outcomes at the different FU points (preoperatively, 3-, 6-, and 12-month FU), and the difference of median values (Δ) between preoperative and the last evaluation was calculated; (ii) The Foot Functional Index (17-FFI)  [35, 37]  to measure the persistence of pain, disability, and restriction of activity with 17 number rating scales from 0 to 10; (iii) The Manchester-Oxford Foot Questionnaire (MOXFQ)  [35]  to establish how frequent the restrictions in specific situations were, including 16 questions divided into three basic domains: pain (five), walking/standing (seven), and social interaction (four); (iv) The Short Form 36 (SF-36) to identify the overall health reported by the subjects; (v) The Visual Analog Scale (VAS) to quantify patient satisfaction with a score from 0 to 10.
Radiographic Outcome Measures. Routine standing anteroposterior and lateral X-ray views were obtained before surgery, at discharge, at one-month after surgery, and at different FUs (3-, 6-, 12-month, and last FU), according to our study protocol (Figures  5  and 6 ), respecting the Maestro method (weight-bearing, 15 ∘ -30 ∘ inclination of the X-ray beam, 1 m distance from the foot to the X-ray source). They were analyzed at our institution in a standardized manner using electronically computer-assisted Maestro measurements for weight-bearing radiographs provided by our MedStation program (the X-ray database of our hospital). This software allows the retrieval of electronically computerassisted measurements from weight-bearing radiographs to minimize investigator bias. Our sample was classified radiographically according to Maestro and Besse criteria  [9] , adding to this classification one more group to include those feet that did not reflect any morphotype as defined by Maestro parameters (Table  1 ).
Pharmacological inhibition of Irak4 normalises metabolism. Since the Irak4 -/- mice lack the whole protein, we compared the knock-out phenotype with the phenotype of PF06650833, a recently discovered chemical inhibitor of the human IRAK4. CC-BY-NC-ND 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted March 7, 2018. ; https://doi. org/10. 1101/277434 doi: bioRxiv preprint protein 38 currently being assessed in a clinical trial (NCT02996500). Treatment with PF06650833 improved BW in LC-HFD mice (Suppl. Fig. 6b ). This inhibitor also yielded significant improvements in plasma glycemia at the latter time-points of the GTT and ITT and in cumulative glycemia (Fig.
64 , we sampled each system. CC-BY-NC-ND 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted March 7, 2018. ; https://doi. org/10. 1101/277434 doi: bioRxiv preprint 2 0 without restraints for 100 ns using the GPU implementation of pmemd 58. Analyses of simulation data were performed using ptraj and cpptraj from AmberTools 65. After performing standard stability checks for energy and overall structure, hydrogen bonding between protein and ligands was counted using cpptraj's default criteria. All protein-ligand contacts within a distance cutoff of 5Å were considered for contact analysis. Grid-based analyses of TMA positions were performed on a grid capturing the entire simulation box with a spacing of 0.
Statistics. Potential outliers were identified by a Grubbs test. For statistical comparisons between study groups, normality was tested using D'agostino-Pearson omnibus normality test, then one-way ANOVA was used, followed by Tukey's post hoc testing when data were normally distributed, otherwise groups were compared using the two-tailed Mann-Whitney test (P < 0. 05 considered to be statistically significant). Data are displayed as mean ± s. e. m in all figures. All cell culture experiments included at least three biological replicates (as indicated in figure legends). All animal cohorts included at least five animals in each study group (as indicated in figure legends) and animals were randomized to treatment groups. CC-BY-NC-ND 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
IRAK- 4 in mice 40. 440 is the first regulatory checkpoint after MyD88, the adapter protein connecting IRAK-4 to at least six TLRs sensing bacterial compounds 39. IRAK-4 deficiency is associated with bacterial infections in humans 35 and Consistent with the involvement of the TLR signalling pathway at the crossroads between gut microbiota and dietary lipids 41,42 , IRAK-4 deletion and its inhibition by TMA and PF06650833 38 rescued HFD-induced low-grade inflammation and IR 4,43,44.
Patients This retrospective study was carried out from November 2015 to April 2016 in Libreville, Gabon. HCV antibody detection was performed on 500 blood samples taken from PLHA who came to the laboratory as part of their virological and immunological follow-up (HIV viral load and CD4+ T cells count). For 9 of them, the data were insufficient and were excluded from the study. For 491 patients, the data on gender, age and antiretroviral treatment were provided by clinicians. The study was approved by the Ethics Committee of Gabon (N˚0021/ 2013/SG/CNE). Written informed consent was obtained from each patient.
Similarly, fragments of 384 bp of the gene region encoding the Core protein were amplified with Cor-eOS/CoreOAS primer pairs for RT-PCR, and with CoreIS/CoreIA for the nested PCR as described previously in Njouom et al  [20]. Sequencing was performed by Macrogen Europe (Amsterdam, the Netherlands). Pairwise alignments were performed using MEGA 6. 06 software  [24]  that generated neighbour-joining trees using a Kimura two-parameters model  [25]. The reference sequences representing all HCV genotypes were retrieved from the GenBank (https://www. ncbi. nlm. nih. gov/nucleotide/) and from Hepatitis C Virus (HCV) Database Project (https://hcv. lanl. gov/content/index). The.
Acknowledgments We are indebted to all patients who participated to this study. We also especially thank the clinicians. We thank  Mrs. Leonie NGOUANGA  for blood sampling. We thank  Dr Katharine Abernethy  for reading the manuscript. The  Centre International de Recherches Medicales de Franceville (CIRMF) ,  Gabon , is funded by the  Gabonese Government, Total Gabon  and the  French Foreign Ministry.
The capillary voltage was 2 kV, the sampling cone voltage 20 V and the source offset 20 V. Lock mass corrections using [M-H] -at m/z 554. 2615 of a leucine-enkephalin solution (1 ng/µL in 50:50 acetonitrile/water + 0. 1% formic acid) were applied for accurate mass measurements and elemental composition determination. The mass range in full-scan mode was 50-2000 Da and spectra were recorded at 0. 2 s/scan in the profile mode at a resolution of 25,000 (FWHM). For MS/MS experiments, argon was used as collision gas and the collision energy was optimized to 33 eV for [M-H] -precursor ion at m/z 719. Data acquisition and processing were performed with MassLynx 4. 1 software.
NMR Analysis For nuclear magnetic resonance (NMR) analysis, compounds were dissolved in 0. 75 mL of DMSO-d 6 containing 0. 03% of tetramethylsilane (TMS). NMR analysis protocols were adapted from previous works  [15]. Briefly, 1 H-NMR spectra were obtained using a classic proton sequence (90 • proton pulse), 12,019 Hz spectral widths and 2 s relaxation delay. Each spectrum consisted of 4 dummy scans and 512 scans of 128 K data points. The NMR signal was multiplied by an exponential weighing function corresponding to a line broadening of 0. 3 Hz prior to Fourier transformation. The DEPTQ spectra were acquired using 8 dummy scans and 24 K scans of 64 K data points, using spectral widths of 37,878 Hz. A 2 s relaxation delay was employed. To obtain a better 13 C sensitivity in particular to enhance the intensity of quaternary carbons, UDEFT experiment has been performed using a 5 mm BBFO probe.
The UDEFT spectra were acquired using 4 dummy scans and 24 K scans of 32 K data points, using spectral widths of 37,878 Hz. A 2s relaxation delay was employed. The FID was multiplied by an exponential weighing function corresponding to a line broadening of 2 Hz prior to Fourier transformation. The 2D COSY spectra were acquired using 8 scans per 256 increments that were collected into 2 K data points, using spectral widths of 12,019 Hz in both dimensions. A 2 s relaxation delay was employed. The 2D TOCSY spectra were acquired using 8 scans per 256 increments that were collected into 2 K data points, using spectral widths of 12,019 Hz in both dimensions. A 2. 0 s relaxation delay and a mixing time of 100 ms were employed. The 2D HSQC spectra were acquired with 2 s relaxation delay using 8 scans per 256 increments that were collected into 4K data points, using spectral widths of 12,019 Hz in F2 and 26,412 Hz in F1.
The 2D HMBC spectra were acquired with 2 s relaxation delay using 16 scans per 256 increments that were collected into 4K data points, using spectral widths of 12,019 Hz in F2 and 37,732 Hz in F1. All non-zero filled obtained spectra were manually phased and baseline-corrected, calibrated at 0. 0 ppm to TMS.
Funding: This research was supported by  Cosmetosciences , a non-profit global training and research program dedicated to the cosmetic industry (grant number  LBL1307-MariLine ). Located in the heart of the  Cosmetic Valley , this program led by  University of Orleans  is funded by the  Region Centre-Val de Loire. This research was also supported by the  Conseil Departemental d'Eure et Loir.
Western blot Total protein lysates were extracted with lysis buffer (1% Triton, 50 nM Tris, 15 mM NaCl) supplemented with protease inhibitors (Sigma-Aldrich, St. Louise, MO, USA). The following primary antibodies were used: rabbit anti-human IgG antibodies against pHER3 (21D3, #4791), pAKT (D9E, #4060), AKT (#9272) (Cell Signaling, Danvers, MA, USA), HER3 (C-17, sc-285) (Santa Cruz, Dallas, Texas, USA); Vinculin (V9131); mouse horseradish peroxidase-conjugated anti-human IgG anti-β actin (A3854) (Sigma-Aldrich, St. Louise, MO, USA). Proteins were visualized by enhanced chemiluminescence detection system (Sigma-Aldrich, St. Louise, MO, USA). Quantification was performed by Quantity One 4. 6. 6 software (Bio-Rad, Hercules, CA, USA).
Cell cycle analysis SKBr3 were transfected with 100 nM hsa-miR-205 Pre-miR™ miRNA Precursor (Thermo Fisher, Waltham, MA, USA) or Pre-miR™ Negative Control #1 (Thermo Fisher, Waltham, MA, USA) for 24 h and treated with 2 µg Trastuzumab for additional 48 h. Cells were then trypsinized, washed in PBS and fixed in 70% ethanol for 2 h at -20° C. After fixation, cells were washed in PBS and centrifuged for 5 min at 1200 rpm. Cells were resuspended in PBS containing 10 mg/ml propidium iodide (Roche, Basel, Switzerland) and incubated for 20 min at 37° C. Cells were analyzed using FACS-Calibur flow cytometer and the results were further analyzed with the ModFit software, v3. 2 (Verity Software House).
3D colony assay SKBr3 were transfected with 100 nM hsa-miR-205 Pre-miR™ miRNA Precursor (Thermo Fisher, Waltham, MA, USA) or Pre-miR™ Negative Control #1 (Thermo Fisher, Waltham, MA, USA) and 50 nM siRNA HER3 or siRNA negative control. Following 24 h of transfection, cells were seeded in 96 wells coated with matrigel (Corning, New York, NY, USA) at a density of 5 × 10 3 cells/well and treated or not with 1 µg and 10 µg trastuzumab for 5 days. Images of colony formation were acquired using a EVOS inverted light microscope, and quantified by a macro made with the Image-Pro Plus 7. 0 software. The mean ± S. D. of three replicates is reported.
Statistics Data are expressed as mean ± s. d. Statistical comparisons were tested by Student's t-test using Graphpad Prism software. P < 0. 05 was considered statistically significant. To evaluate the association of miR-205 expression with outcome in BC patients, human samples were divided in tertiles according to the miRNA expression, as assessed by qRT-PCR. by a START UP AIRC Grant (11699). Alessandra Cataldo is supported by a fellowship from Fondazione Umberto Veronesi.
The reaction conditions used were: one cycle (93 C for 2 min), 30 cycles (92 C for 30 s, 55 C for 30 s, and 72 C for 1 min), with a final extension of 5 min at 72 C. PCR products were then purified and sequenced by Institut für Klinische Molekularbiologie (IKMB), Kiel University, and submitted to BLAST for the phylogenetic affiliation. The strain identified as Aequorivita sp. was selected for further studies and the 16S rRNA gene sequence was deposited in GenBank (accession number MH012204). MEGA7 software  [17]  was used to align the sequences and to construct the phylogenetic tree. The evolutionary history was inferred using the Neighbor-Joining method.
For each sample, remaining processed reads were assembled and scaffolded with SPAdes  [22]. Genomes were analyzed using the anti-SMASH 3. 0 web server (http://antismash. secondarymetabolites. org) and the biosynthetic gene clusters were identified. The newly isolated Aequorivita sp. strain was deposited in the Collection of Institut Pasteur (CIP), France, under accession number CIP 111184. Moreover, the three genomes were deposited in European Nucleotide Archive (ENA) with codes: Aequorivita sp. GCA_900489465. 1, A. lipolytica GCA_900489485. 1 and A. antarctica GCA_900489835. 1.
Acknowledgements FP thanks  German Academic Exchange Service  ( DAAD ) for enabling research stay (fellowship) at  GEOMAR Centre for Marine Biotechnology, Kiel, Germany. CI thanks  BE-Foundation  (NL) for supporting culture chip development. DT and FP thank to  Institut für Klinische Molekularbiologie (IKMB), Kiel University  for 16S rRNA sequencing. We thank  Ms Arlette Wenzel-Storjohann  ( GEOMAR ) for her assistance in antimicrobial assays.
1  Expression of 14 Tuber genes related to programmed cell death in various stages (III-VI) of fruit body development. Heatmap of log2 arbitrary expression values. Relative expression indexes (REI) were calculated for the dataset. For each gene, a mean expression level was calculated from the four samples, and the REI corresponds to the ratio between the expression level measured for a given sample and the mean reference. Log2 transformed data were subjected to MeV software for visualization. Each gene is represented by a row of colored boxes (corresponding to REI values) and a single column represents each stage all of the nuclei and so evaluate the extension of the cell death. Stage 1 ("hyphal stage") and 2 ("peridial stage") FBs did not exhibit any significant positivity to the TUNEL reaction (not shown).