dataesr/scientific-paragraphs-categorization huggingface dataset:
Various reports were also produced and made available on a quasi-daily basis (this includes meteorology and dust over the basin, regional and local oceanographic conditions, ship trajectory). The complete series of reports is available at http://poc. sedoo. fr/source/indexGarde. php?current= 20170602&nav=Reports (last access: 22 September 2020). Concerning the oceanic conditions, several remote sensing datasets were exploited using the SPASSO (Software Package for an Adaptive Satellite-based Sampling for Ocean campaigns https://spasso. mio. osupytheas. fr/; last access: 22 September 2020) in order to guide the cruise through a Lagrangian adaptive sampling strategy with the aim of avoiding regions of complex circulation and dynamics (fronts, small-scale eddies). The idea behind this approach was to aim at a situation where the air-sea exchanges dominate and lateral advection and diffusion can be neglected.
Such an approach was already successfully adopted during several previous cruises such as LATEX  (Nencioli et al. , 2011; Doglioli et al. , 2013; Petrenko et al. , 2017) , KEOPS2 (d  'Ovidio et al. , 2015) , OUTPACE  (Moutin et al. , 2017; de Verneil et al. , 2018)  and OSCAHR  (Rousselet et al. , 2019). During PEACETIME, we used the following datasets: (1) near-real-time altimetry data from the AVISO Mediterranean regional product (now distributed by CMEMS, https://resources. marine. copernicus. eu/?option= com_csw&view=details&product_id=SEALEVEL_MED_ PHY_L4_NRT_OBSERVATIONS_008_050, last access: 11 November 2020), where the altimetry-derived currents were then processed by SPASSO to derive Eulerian and Lagrangian diagnostics of ocean circulation: Okubo-Weiss parameter, particle retention time and advection, finite-size Lyapunov exponent (e.
Conclusion The PEACETIME oceanographic expedition conducted in spring 2017 cruised over a 20 • longitudinal gradient across the western and central Mediterranean Sea during the season characterized by strong stratification, low productivity and high probability of wet dust deposition. Those conditions were required in order to fulfill the objectives of the project aiming at quantifying the biogeochemical processes at play after atmospheric deposition and its impact on ecosystem functioning. Different atmospheric situations were encountered during the cruise. In particular, luckily, three contrasted https://doi. org/10. 5194/bg-17-5563-2020 Biogeosciences, 17, 5563-5585, 2020 situations in terms of atmospheric deposition characterized the long-duration stations, allowing the acquisition of a large dataset under different dynamical and biogeochemical in situ conditions to explore the chemical and ecosystem response to deposition.
Statistics All statistical analyses were performed using R version 3. 5. 3 [31]  and packages reshape  [32] , ggplot2  [32] , rstatix  [33] , ade4  [34] , factoextra  [35]  and cowplot  [36]  for data processing and visualisation. Raw GC-FID text file data together with in-house R script for data processing, univariate and multivariate statistics as well as figures are available at github repository: https: //github. com/Hubas-prog/Paradendryphiella_traject.
The students are invited to use phone apps as EqInfo 7 , which allow them to track in real time seismic detections in the network stations (Figure  2B ). The research team will support the centers most committed to the project with guidance and appropriate software tools so that students can locate earthquakes and study the propagation of seismic waves. The degree of involvement of each school will vary depending on their respective pedagogical plans. For example, the installation of the seismic network can be used to implement transversal educational projects that involve not only the natural sciences, but also physics, technology, and even social sciences. Seismometers can be used to study the pendulum laws, electromagnetic induction, elastic wave propagation or frequency analyses. The network can also be a motivation to develop technological projects with the objective of designing in-house seismometers based in existent and affordable elements and to develop programing exercises for processing the recorded data.
(C) Entrainment region, for the same multiciliated cell, in the frequency and flow velocity domain; each marker here is the result of a separate recording. Markers are dark (solid circles) when the average CBF of the cell matches the frequency of the external flow. The entrainment strength, (v EX ), is the range of frequencies spanned horizontally by the black dots. The entrainment region is highlighted here as the area between the red dashed lines; lines are a guide to the eye. (D) The entrainment strength (v EX ) increases proportionally to the applied external flow, but decreases with the number of cilia per cell, Nc. Each line is the average of this trend over a group of cells with similar number of cilia. Error bars represent the SD. Complete datasets are shown in SI Appendix, Fig. S9.
A B Fig. 2. The frequency and phase of each cilium, and the number of cilia per cell, are extracted from high frame rate video microscopy recordings. (A) Dynamics of the phase difference ∆(t) when an external flow of v EX = 0. 6 mm/s is applied on a cell with 13 cilia. (B) Data for a single cilium when an external flow of v EX = 0. 2 mm/s is applied. The phase difference is constant (phase locking) when the cilium is entrained by the external flow. The interrogation windows used are marked in red, over the SD maps. For the phase of the external flow, we used φ EX (t) = 2πf EX t + φ 0 , where φ 0 is set such ∆(t = 0) = 0. synchronization will be used to indicate when many individual cilia coordinate their beating to a coherent collective beat pattern  (35). The entrainment regimes for a multiciliated cell in the frequency and flow domain are shown in Fig.
For this geometrical rower model, an analytic solution for the entrainment strength of the rower with the external oscillatory force has been found in ref. 36 , highlighting a linear dependence of entrainment on the ratio of the driving and external forces. See SI Appendix, section 1 for more details. The entrainment strength is thus (N ) = 2(CBF0)F i EX F dr. [2] Entrainment Strength on Multiciliated Regions Can Be Explained as an Effect of Hydrodynamic Screening. We now compare data with the consideration on screening from above. The CBF0 is the BF of the cilium in the absence of external forces. In the cell cultures, the CBF of isolated cilia were measured to be CBF0 15 Hz (Fig. 3C ). The force applied by the external flow on a cilium is given by Eq. 1, F i EX = γe (N )vEX /N , with vEX as the average magnitude speed of the oscillatory fluid flow.
Inspired by the work of ref. 32 , we consider internal friction forces to be proportional to the hydrodynamic drag experienced by the cilium while beating. The total driving force can then be written as F dr = F h dr /ηc, where ηc < 1 is the chemomechanical efficiency of the ciliary beat. More details can be found in SI Appendix, section 1. Finally, for the cilium i, in a bundle of other N cilia arranged in a hydrodynamically impenetrable cylindrical rod of radius re (N ) and length L, we have (N ) vEX = 2 CBF0 (F h dr /ηc) 4πηL N [log (L/re (N )) -1/2]. [3] We can fit this model to our data using the effective radius re found previously from experimental data, with the beating efficiency ηc as a single fit parameter. Results are provided in Fig. 3D. We find the driving force F dr = F h dr /ηc = 60 ± 3 pN, with R-squared=0.
At each image, a running average of 60 frames was subtracted. To define entrainment events, CBF is measured as the highest peak of the first harmonic of the average periodogram, P S (f) = px∈S | Ĩ px (f)| 2 , as in refs. 37, 38, and 63, with Ĩ px (f) as the FFT over time of the pixel intensity Ipx, and S as the ensemble of pixels in a subimage thresholded for ciliary motion. The subimage was defined to include all of the pixels for which the SD of the intensity over time is larger than a threshold value (this is found with Matlab function using Otsu's method) (Fig. 6 ). Entrainment with the external flow is identified when the frequency of the signal highest peak pk 1 coincides with the frequency of the external flow within a certain error σf. For our acquisition rate σ = 0. 25 Hz, the requirement is half of our frequency resolution.
This area is small, such that only one or, at most, two cilia can be detected per time. When a cilium passes through this area, the pixel intensity I A spikes (Fig. 6 ). The time of the spike is an indication that the cilium completed a cycle, and the phase of the cilium φ cilium increases by 2π. The number of cilia per cell was counted by inspection of movies at 500 fps, after median filtering (window of 3 × 3 pixels) and contrast correction. All of the analyses were performed in Matlab. Simulations. The simulation scheme builds on previous work  (36, 49, 50)  but implements external flow on an array of active phase-free oscillators. Rowers are driven by repulsive harmonic traps, with the potential U(xr) = kx The rowers are coupled through the Blake tensor H. The tensor is implemented in a plane at a constant height above the no-slip boundary, h = 7 µm (49).
The greater variability in the number of entrained rowers likely stems from coexistence of two stable states, entrained and not entrained, during the transition from a chain that can be phase-locked to one too strongly coupled to do so. Instead, in these cases, the sum of phase-locked cases is multiplied by the resolution of the frequency sampling 0. 017f 0 to give an estimate of. The measurement for across each case is repeated for the 10 simulations sets, and the average is plotted in Fig. 5. Further details regarding the steps to measure are described in SI Appendix, section 2. Data Availability. A frequency scan dataset for a cell is available as a Zenodo repository, https://doi. org/10. 5281/zenodo. 3604352, and the complete set of movie files supporting this paper is available on request to the authors.
ACKNOWLEDGMENTS. We thank  B. Friedrich ,  E. Lauga ,  D. Das , and  C. Maggi  for stimulating discussions. N. P. and P. C. were supported by the  European Union   Horizon 2020 research and innovation program  under  Marie Sklodowska-Curie Grant   641639 ITN BioPol ; P. C. and J. K. were also supported by  European Research Council (ERC)  CoG HydroSync; and E. H. was supported by Cambridge Trusts. M. F. , N. D. , and N. S. were supported by  INSERM ,  CNRS ,  École Normale Sup érieure , and  ERC CoG  Grant  647466.
Default parameters were used for all software and tools except BLAST-X and PromoterHunter. A total of 394,491 reads were obtained, and the genome of XaF13 was assembled into a single contig with a median coverage of 33,597ϫ. The genome is composed of a single-stranded DNA molecule, as shown by the DNase I, RNase A and S1 nuclease results, with a length of 7,045 bases and a GϩC content of 60. 3%. Bioinformatic analysis revealed 14 open reading frames (ORFs), 12 in the positive strand and 2 in the negative strand (replicative form); no tRNAs or rRNAs were found. Seven ORFs were annotated as hypothetical proteins, and 7 were annotated as having virus-related functions, namely, ORF-2 (membrane protein), ORF-3 (major capsid protein), ORF-4 (minor capsid protein), ORF-6 (ZOT-like protein), ORF-8 (TrbP conjugational protein), ORF-13 (replication protein A), and ORF-14 (DNA polymerase III).
, 2016). The identification of the comammox bacteria overturned "a century-old dogma of nitrification research"  (Koch et al. , 2019). Metabolism of the members of Nitrospira genus is not limited to nitrite oxidation or comammox, but also comprise other functionalities beyond the N cycle, either under aerobic conditions (growth on formate and hydrogen) and anoxic conditions (reduction of nitrate to nitrite)  (Koch et al. , 2019). The growing interest in the role of Nitrospira in WWTPs is reflected by the number of scientific papers published annually and focused specifically on that microorganism. In the Scopus database, the number of papers with the keywords "Nitrospira" and "wastewater" has continuously been increasing over the last decade from 6 (2010) to 89  (2019). Despite those numerous studies, there are still a lot of open questions concerning the importance and actual role of Nitrospira in nitrogen removal systems, effective methods of suppression, especially in deammonification systems, comparison of the kinetic parameters of these bacteria and Nitrobacter, coexistence of canonical and comammox Nitrospira, etc.
e. presence of the regions characterized by both significant degrees of conservation and high variation in the nucleotide composition. Other method that allows for bacteria species detection on site without the need of prior isolation is Fluorescence in Situ Hybridization (FISH). This semi-quantitative technique is used for specific detection of particular bacteria by hybridization of fluorescently labelled probes to complementary target rRNA sequences within intact cells. After hybridization, samples are analysed by the fluorescence microscopy  (Wang et al. , 2008). This technique, combined with flow cytometry, allows to enumerate the labelled cells  (Lenaerts et al. , 2007). Currently, extensive databases containing 16S rRNA geneo sequences from almost all microorganisms known so far are widely available (e.
g. SILVA database https://www. arb-silva. de, Genomicbased 16S ribosomal RNA Database -GRD https://metasystems. riken. jp/grd, Ribosomal Database Project -RDP https://rdp. cme. msu. edu) to conduct a comparative analysis to determine the phylogenetic position of isolates derived from the tested environmental samples  (Tsukuda et al. , 2017). Although the most commonly used gene for examination of microbial populations is the 16S rRNA, its use in the microbial ecology has some drawbacks. The main disadvantage is that it may not be related to the physiology of the target organisms  (Kowalchuk and Stephen, 2001). Moreover, since comammox bacteria do not form a unique clade within Nitrospira lineage II, comammox and canonical Nitrospira NOB cannot be individually detected by 16S rRNA-based methods  (Pjevac et al.
, 2011; Li et al. , 2011; Miao et al. , 2016). During the SBR operation with intermittent aeration and low DO concentration (0. 2-1. 0 mg O 2 /L), the Nitrospira abundance observed in 16S rRNA sequencing datasets increased from 3. 1% (day 3) to 53% (day 407)  (Roots et al. , 2018 ). An appropriate configuration of the intermittent aeration system is challenging, and the recent discovery of the comammox Nitrospira might bring additionally challenges in implementation of that aeration mode.
Meta-analysis of the literature data The Response Surface Methodology (RSM) is a method to investigate a relationship between one or more responses with multiple variables (factors). The RSM is useful where statistical data play a key role, and the effect of specific individual variables and their combined interaction on each response can be determined  (Anwar et al. , 2015). In this study, a standard RSM model, implemented in Minitab (19. 1) and DX (10. 1) software (Stat-Ease, USA), was applied to determine the effects and interactions of four process variables (factors) influencing the Nitrospira abundance (response) in nitrogen removal systems. Based on the results of previous studies, four process parameters were used as input independent variables, including DO concentration, influent NH 4 -N concentration, pH, and temperature.
However, genetic reports on A. nidulans are also included because of the capacity of this fungus to produce sterigmatocystin, the penultimate stable metabolite during AFB1 production. The aim of this review is to provide a general overview of the AFB1 enzymatic biosynthesis pathway and its link with the genes belonging to the AFB1 cluster. It also aims to illustrate the role of global environmental factors on aflatoxin production and the recent data that demonstrate an interconnection between genes regulated by these environmental signals and aflatoxin biosynthetic pathway.
As one of the most hazardous mycotoxins, there are many reviews concerning different aspects of aflatoxin biosynthesis  [29, [32] [33] [34] [35] [36] [37]. Thus, the present review is timely and provides an overview of the different factors interacting with the AFB1 gene cluster and hence with toxin production. However, an effort to link these factors in order to synthesize the global network regulating aflatoxin production is proposed. Data on Aspergillus flavus and A. parasiticus, the two main producers of aflatoxins in crops, are presented. Studies of A. nidulans linked with sterigmatocystin production are included since this mycotoxin is the penultimate stable intermediate in the AFB1 synthesis cascade and its cluster shares 25 homologous genes with the AF cluster  [24]. After reminding the AFB1 biosynthetic pathway and its internal gene regulation, we describe other genes found to interact with AFB1 synthesis according to their role in fungal metabolism.
The aflS Transcription Enhancer aflS (previously named aflJ) was characterized by Meyers and co-workers  [87]  and was shown to be required for aflatoxin synthesis. In A. parasiticus, this gene encodes a 438-amino acid protein that has no important homology with any other proteins found in databases  [22]. The aflS gene is located adjacent to aflR in the AF biosynthetic cluster, and aflS was also shown to be regulated by aflR  [24]. Both genes share a 737-bp intergenic region from their translational starting sites  [22]. In A. flavus and A. parasiticus, it was also demonstrated that aflS interacts with aflR but not with the biosynthetic enzymes, revealing the co-active function of aflS  [25, 88]. Disruption of aflS in A. parasiticus resulted in mutants with a 5-to 20-fold reduction in the expression of some AFB1 genes, such as aflC, aflD, aflM and aflP, and a subsequent loss in the ability to synthesize AF intermediates  [25].
Acknowledgments: The authors would like to thank the  Consejo Nacional de Ciencia y Tecnología (CONACYT) México funding Isaura Caceres , as well as the  Agence Nationale de la Recherche (ANR) , the  Research Council of Saint-Joseph University (Lebanon)  and the  National Veterinary School of Toulouse funding Rhoda El Khoury and Anthony Al Khoury. This work has benefited to the  International Cooperation Program CAPES/COFECUB  ( Sv 947/19 ).
A search on two scientific databases, Web of Sciences and Science Direct, shows that the scope of these writings is limited. Two keywords "food safety" AND "Vietnam" returned 141 results in the Web of Science, and 835 in Science Direct, including conference papers. Regarding abstracts, the inventory provided only 10 and 11 relevant publications in the two databases, respectively. The papers focused on safety controls in different sub-sectors of the food system, for example Fisheries and Aquaculture, Meat, and Fruits & Vegetables. They also discussed the attitude and behavior of the food chain's stakeholders toward public regulation and standard promotion. Other keywords such as "food control" and "food protection policy" also returned similar results, but with a more modest scope. The latter are mostly included in the results from the two terms, "food safety" AND "Vietnam" as mentioned above.
Here we take the first step towards developing the ODP Site 865 MECO sequence as a palaeoceanographic reference by adding new datasets that allow development of a composite splice and a detailed chronostratigraphy for the site. This involves integration of high-resolution X-ray fluorescence (XRF) core scanning, benthic foraminiferal stable isotope (δ 13 C and δ 18 O), and planktic foraminiferal and calcareous nannofossil biostratigraphic data across the MECO interval at the site. These data are combined with published calcareous nannofossil datums  (Bralower and Mutterlose, 1995)  to (1) generate the first composite sedimentary section across the middle Eocene interval of Site 865, (2) identify and constrain the isotopic character of the MECO in the Pacific Ocean, and (3) determine the position of key biostratigraphic datums relative to the MECO event.
X-Ray fluorescence (XRF) scanning XRF data are routinely employed for stratigraphic correlation and the construction of high-resolution composite depth scales because of their higher signal-to-noise ratio and more consistent hole-to-hole character than shipboard physical property measurements  (Röhl and Abrams, 2000). Prior to XRF analysis, the top ∼ 0. 5 cm of the split section surface of the archive halves was scraped off with a glass slide. This revealed bioturbation structures, indicating that this interval did not have significant coring disturbance (Fig. S1  in the Supplement), as might be expected from the foraminiferaooze lithologies and the massive appearance of the unprepared cores. Using an Avaatech XRF scanner with a Canberra X-PIPS SDD, Model SXD-150-500 X-ray detector, a suite of elemental (including Fe, Ca, Sr, and Ba) intensity data were collected every 2 cm down-core with a constant spot size (cross-core slot = 12 mm; down-core slit = 10 mm) using a 6 or 10 s count time at 30 and 50 kV, respectively, on the split surface of the archive half of each section using the TAMU ODASES XRF scanner at the Interna-tional Ocean Discovery Program (IODP) Gulf Coast Core Repository.
We measured the elemental composition of sediments that encompass planktic foraminiferal Zone E12 from ODP Cores  865B-4H and -5H (27. 52-44. 58 metres below seafloor, m b. s. f. ) and Sections 865C-4H-1 to  6H-2 (22. 30-42. 80 m b. s. f. ) in order to capture overlapping sections and construct a composite splice. We primarily used Sr/Ca and Ba/Sr ratios determined from the 50 kV scans for splicing purposes. These are unconventional ratios for hole-to-hole correlation, but the low detrital component of the Site 865 sediments necessitated the use of high-intensity elements associated with the carbonate and biogenic barite fractions (Ca, Sr, and Ba) for detailed correlation. All XRF elemental data are reported in Table  S1  in the Supplement.
Cyclostratigraphy To investigate if astronomical forcing drove patterns in the elemental data records, the Fe intensity data, measured at 30 kV, and the natural logarithm of the Sr/Ca ratio, ln(Sr/Ca), measured at 50 kV, were subjected to time series analyses. The Fe intensity data were selected to allow comparison with published datasets  (Westerhold and Röhl, 2013) , and the ln(Sr/Ca) record was selected for its low signal-to-noise ratio (see Sect. 3. 1). The records were evenly sampled and periodicities larger than 7 m were removed in the program AnalySeries  (Paillard et al. , 1996). Spectral analyses were performed with Redfit 3. 8  (Schulz and Mudelsee, 2002)  using a Welch window. The behaviour of periodicities over the length of the dataset was investigated by evolutive harmonic analysis with the astrochron package in R  (Meyers, 2014) , using window lengths of 5.
5 m for ln(Sr/Ca) and 6 m for Fe intensity. The Fe record displays a stronger imprint of short-term (< 1 m) variability than the ln(Sr/Ca) record. To test whether the observed cycle hierarchy in the Fe record can be confidently linked to an orbital origin, the interval with most persistent periodicities as identified in the evolutive spectrum, between 32. 5 and 44. 5 "adjusted" metres composite depth (amcd; see below), was investigated with the average spectral misfit (ASM) method in astrochron  (Meyers, 2014). Bandpass filters were applied to the datasets centred at periodicities of 1. 9 and 50 cm with broad bandwidths of 1/3 of the centre frequency. The ln(Sr/Ca) record displays a stronger imprint of longer (> 1 m) periodicities than the Fe record, with minima in the 1. 9 m bandpass filter of ln(Sr/Ca) generally coinciding with maxima in the 1.