dataesr/scientific-paragraphs-categorization huggingface dataset:
Since the above algorithm may lead to symbols that are at the same time input and output symbols, we introduced an additional Step 3, that, for each of these symbols (x), created a new input symbol x in and copied all rules involving x in the reactants or inhibitors lists replacing x by x in for all possible combinations of occurrences. We remark that this step can lead to an exponential blow-up of the number of reactions, so it is strongly suggested to manually identify input and output symbols. Then Step 4 was performed according to the algorithm described in Section 3. Step 5 is straightforward, as a sequential Boolean (switching) function/circuit in DNF can be directly translated to Verilog. As a result, two files were obtained: a synthesizable (in FPGA) Verilog module containing the code that simulates each step of the reaction system and a (non-synthesizable) test bench that contains the timed update of the input symbols using the provided context.
Finally, the compiler can optionally construct the Moore automaton of the obtained circuit (if "-g" command-line switch is provided). This automaton is iteratively constructed by varying all the inputs starting from the initial state given by the first context. By adding the command-line switch "-ga" all possible initial states are constructed. The result was yielded using the GraphViz format  [58]. Due to the combinatorial explosion, it was necessary to construct the automaton (the corresponding algorithm used standard enumeration techniques-so it was exponential), graph generation was limited to systems having less than 32 species. Another reason for this restriction was that bigger graphs were very difficult to analyze visually. The Verilog test bench obtained by RStoVerilog can be directly simulated in software using a Verilog compiler and simulator.
Since the result of our translation consists only of the circuit simulating each step of the reaction system (the test bench cannot be synthesized in hardware), we had to manually add the circuits allowing to enter the (input) context sequence as well as to save the output result. We used several test reaction systems (including those from Examples 2 and 3) as well as different input/output circuits. For small-size examples (up to 16 inputs and 16 outputs) we used switches and leds present on the board as input and output, allowing to verify the correctness of the simulation. In order to speed-up the computation we also considered input coming from the serial port at 115,200 bits/s. The tests have shown the correctness of the simulation. Finally, the last tests were performed using an autonomous execution of the system without output and using distributed read-only memory data storage for the input (or context-less models).
Data collection. GP practices were contacted one by one between March 15 and July 15, 2017, using the telephone directories available on Internet and asked by which means they preferred to receive the study questionnaire: fax, postal mail or email. The questionnaire consisted of 10 questions (see Supplementary figure). The demographic data collected for the GPs were: sex, start of practice (year), kind of practice, estimated total number of patients. Their general acceptance of vaccination was evaluated. GPs were asked to estimate the number of adult patients who received chemotherapy in 2016, the number who were given a prescription for immunization, and the number of chemotherapy patients who were actually immunized. They were also asked to assess the obstacles that hinder vaccination, their need for education on the vaccination of chemotherapy patients, and to propose potential solutions for improving the vaccination coverage of this at-risk patient population.
Maheswaran et al  [34]  demonstrated from the population-based case-crossover study in South London an association between an increased NO2 exposure with a higher risk of cerebrovascular small vessel disease, within the period 1995-2006. Contrasting with this positive association, Butland et al  [35]  did not find any association in 2017. It is a time-stratified case-cross over study, using data from the population-based study of South London from 2005 to 2012. They included 1 311 incident ischemic strokes and 256 haemorrhagic strokes. The authors found no evidence for an association between all strokes or ischemic strokes and same day exposure to PM2. 5, PM10, O3, NO2. For haemorrhagic strokes, they found a negative association with PM10 suggestive of a 14. 6 % fall in risk per 10 µg/m 3 increase of pollutant.
Autopilot and Acquisition System OVLI-TA flies by the 3DR Pixhawk autopilot that ensures stable navigation. The autopilot was composed of an independent data acquisition system with a GPS for measuring the absolute position. This was coupled with the ADIS16448 IMU including a triaxial digital gyroscope, a triaxial digital accelerometer, and a triaxial digital magnetometer, in order to measure the three components of the angular speed, the linear acceleration, and the magnetic field, respectively. In addition, it contained a digital barometer from which the fast altitude variations can be computed, and an embedded temperature sensor. All these parameters were delivered to the acquisition system at a rate of 100 Hz. The GPS data was updated with a frequency of 5 Hz. The Pixhawk telemetry system sent in-flight data to the ground station, and also recorded them on an SD card.
The first pressure sensor made it possible to measure the difference between the total pressure (from the center hole of the five-hole probe) and the static pressure (from the Pitot tube) in order to calculate the dynamic pressure and thus the airspeed, as a redundant system to the Pitot tube. The other sensors measured the differential pressure between the up and down (resp. left and right) holes in order to calculate the angle of attack  (resp. angle of sideslip ). These sensors need a calibration procedure (see below). The acquisition rate of pressure data was 100 Hz. The payload was installed at the front of OVLI-TA. The overall equipment is presented in Figure  5.
The relative contributions of local TF binding site turn over versus more global GRN rewiring between ascidian species also remains unknown. In this study, we first used ATAC-seq  (Buenrostro et al. , 2013)  to characterize the temporal patterns of chromatin accessibility in two distant phlebobranch species that diverged around 270 million years ago (Figure  1A )  (Delsuc et al. , 2018) , Phallusia mammillata and Ciona robusta. We then used this dataset to identify in both species the early embryonic cis-regulatory sequences controlling the expression of ten orthologous pairs of regulatory genes. These analyses brought to light a surprising level of conservation of chromatin accessibility landscapes and cis-regulatory logic between these species despite extreme sequence divergence.
ATAC-seq sequence pre-processing, alignment and peak calling Illumina adapters were trimmed with Cutadapt  (Martin, 2011). Alignment on the Phallusia mammillata and Ciona robusta genomes was performed with bowtie2, (very-sensitive parameter)  (Langmead and Salzberg, 2012). Although our Ciona dataset came for Ciona intestinalis animals, the very poor quality of the Ciona intestinalis genome assembly  (Brozovic et al. , 2016)  led us to align these sequences onto the closely related Ciona robusta genome. In both Phallusia and Ciona, only a minority of sequences aligned to the nuclear genome (Ciona ~30%; Phallusia ~17%). Significant Peaks were extracted with MACS2  (Zhang et al. , 2008)  with the following parameters for Phallusia mammillata: gsize=187138625 (genome size = genome mappable size excluding repeated sequences) --nomodel -f BAMPE -q 0.
01. For Ciona, peaks were extracted with MACS2 with the following parameters for Ciona: gsize= 99000000 -nomodel ---f BAMPE -q 0. 01. Ciona and Phallusia raw ATAC-seq sequences were submitted to the Short Read Archive (Bioproject IDs PRJNA474750 and PRJNA474983). Peaks and short read coverage normalized per million of aligned reads can be seen on the ANISEED WashU browser: https://www. aniseed. cnrs. fr/browser/ Construction of a reference peak dataset for each species. To compare chromatin accessibility between experimental conditions and developmental stages, we constructed a reference set of non-coding non-overlapping ATAC-seq peaks for each species. We started from MACS-called peaks for each biological sample and excluded peaks overlapping exonic sequences. A chromatin accessibility score for each reference peak was defined by allocating for each condition the sum of the depth of normalized ATAC-seq sequence coverage over all peak bases (all peak score values below 1 were considered unreliable and arbitrarily set to 1 to calculate fold changes).
Gateway cloning and electroporation of the regulatory sequences Constructs to test the activity of the regulatory sequences from both species were generated by Gateway cloning into pSP1. 72. RfB::NLS-LacZ destination vector  (Lamy et al. , 2006) , or in modified versions, in which the Foxa. a minimal promoter from Ciona robusta (ANISEED ID: REG00001035) was placed upstream of NLS-LacZ to generate pSP1. 72. RfB. pFoxa. a::NLS-LacZ, or into pSP1. 72. RfB. pFog::NLS-LacZ as indicated in Table  S1. The primers for each of the non-coding sequences, and their spatio-temporal patterns of activity and reference in the ANISEED database are listed in Table  S1. The genomic DNA used to amplify by PCR the genomic fragments from Ciona robusta was a kind gift from Dr. A. Spagnuolo (Naples). Phallusia mammillata genomic DNA was extracted from Roscoff animals.
Construction of a reference set of open chromatin regions during early ascidian embryogenesis. To assess the spatio-temporal dynamics of chromatin accessibility in Phallusia and Ciona, we extended our Phallusia dataset to encompass the 16-cell, 32-cell, 64-cell, 112-cell, mid-gastrula and mid-neurula stages. The Ciona dataset was also extended with mid-gastrula and mid-neurula stage samples. In addition, to estimate the impact of tissue specification on chromatin accessibility landscapes, we collected in both species ATAC-seq data from early gastrula embryos in which the GSK3 kinase was inhibited from the 8-cell stage, a treatment known to activate the canonical Wnt/ß-catenin signalling pathway, thereby converting most embryonic cells into endoderm  (Imai et al. , 2000). To compare the chromatin accessibility landscapes more quantitatively across conditions and species, and to relate them to patterns of gene expression, we compiled a reference set of around 15000 noncoding, non-overlapping peaks for each species including all peak regions called across all conditions (see methods).
We then associated to each peak its closest coding gene, its position with respect to this gene and the expression pattern of this gene at the 64-cell, early gastrula, mid-neurula and mid tailbud stages (see Tables  S1  and Table S2  for Ciona and Phallusia, respectively). All ATAC-seq datasets generated in the frame of this project can be explored through public hubs in the ANISEED Ciona robusta and Phallusia mammillata WashU browsers (https://www. aniseed. cnrs. fr/browser). Raw reads were also deposited in the NCBI Short Read Archive (Bioprojects PRJNA474750 and PRJNA474983). Temporal dynamics of chromatin accessibility in Phallusia mammillata and its relationship to gene expression. Starting from this dataset, we first analysed the temporal dynamics of chromatin accessibility between the 64 and neurula stages and its relationship to gene expression.
, 2006 (Imai et al. , , 2004)). To more generally assess the correlation between tissue-specific gene expression and chromatin accessibility, we mined the ANISEED in situ hybridization data for Ciona genes expressed mostly in either epidermal or endodermal precursors during early embryogenesis. This search returned 26 and 23 genes, respectively. Figure  3G  illustrates that endodermal genes were predominantly associated to ATAC-seq peaks with increased chromatin accessibility upon CHIR treatment, while conversely epidermal genes were primarily associated to ATAC-seq peaks of decreased accessibility upon GSK3 inhibition. This analysis suggests that fate specification and the dynamics of chromatin accessibility also seem to be strongly correlated during ascidian early embryogenesis.
Conservation of early regulatory gene expression between Ciona robusta and Phallusia mammillata up to the early gastrula stage While extensive expression datasets are available for Ciona robusta, much fewer data are available for Phallusia mammillata. Using the ANISEED orthology section, we identified the Phallusia mammillata orthologues of the 49 Ciona robusta epidermal and endodermal genes studied in the previous section. The Ciona endodermal and epidermal gene sets had each 20 1-to-1 orthologs in Phallusia mammillata. Interestingly, chromatin accessibility landscapes around Phallusia orthologs genes matched the behaviour seen for the Ciona orthologs, suggesting a conservation of chromatin accessibility landscapes despite extensive sequence divergence. The similarity of the chromatin accessibility profiles in WT and CHIR-treated embryos suggests a conservation of the expression pattern of Phallusia orthologues of Ciona genes.
Future work based on single-cell RNA seq in ascidians  (Horie et al. , 2018; Sharma et al. , 2018; Treen et al. , 2018; Wang et al. , 2017 ) may be required to discriminate technical issues from bona fide evolutionary changes. In the following sections, we used our extensive ATAC-seq dataset to identify the cis-regulatory sequences driving the conserved expression of these genes and to compare their activity in both species.
Most open chromatin regions have embryonic cis-regulatory activity To confirm the helpfulness of our ATAC-seq dataset to identify the cis-regulatory sequences driving the expression of the ten ortholog pairs in both species, we first surveyed the chromatin state of known Ciona elements controlling the expression of four of these genes. For each of our test genes, we selected 2 to 7 candidate cis-regulatory regions ranging from 209bp to 1316bp (average 525bp) and located up to 4kb upstream from the transcription start site of the gene, within the 5' UTR, in introns, or immediately downstream of the transcription start site (Figure  6 ). In most cases, selected regions corresponded to a single ATAC-seq peak called at this stage. Candidate cisregulatory sequences were cloned upstream of a minimal promoter (Table  S3 ) driving NLS-LacZ, to test for enhancer activity.
CONCLUSIONS In this study, we addressed how Ciona and Phallusia species, despite their extremely divergent genomes can undergo almost identical early developments. We established ATAC-seq in both species and showed that open chromatin landscapes obey similar rules as in other metazoa (Figures  1, 2 ): Non-coding open chromatin regions are enriched in GC, highly conserved within each genus, cluster around developmental regulatory genes, mostly transcriptional regulators, and are highly enriched in cisregulatory sequences. Our analysis further suggested that the spatio-temporal dynamics of chromatin accessibility in both species correlates with transcription control of the immediate flanking gene with closest 5' end (Figure  3 ). This publicly-accessible ATAC-seq dataset will be of general interest to the ascidian community.
To go beyond a global analysis of regulatory landscapes, we selected ten early Ciona robusta regulatory genes with early endodermal expression. We identified the Phallusia orthologs and showed that their expression profiles up to the gastrula stages were highly consistent with the Ciona data (Figure  4 ). We identified 39 cis-regulatory sequences for these genes, including 17 with activity by the gastrula stage  (Figures 5, 6). Thanks to this dataset, we could reveal features of ascidian transcriptional regulation and its evolution. First, in half of the genes we studied, we found 2 or more enhancers with overlapping spatial activity (Figure  7 ). This suggests that ascidians make frequent use of shadow enhancers with partially overlapping activity. Given the proposed function of shadow enhancers in ensuring developmental robustness to environmental and genetic stress  (Frankel et al.
AUTHORS CONTRIBUTION: PL and JLG-S initiated the project. MSM and AM performed the ATAC-seq experiments, which were computationally processed and analysed by CD and PL. AM performed most in situ hybridizations, with contributions from UMF. AM, SH and DG performed all cloning and electroporation experiments. LG participated to the analysis of the data and to the construction the figures. AM and PL wrote the manuscript. All authors commented on the manuscript. around predominantly endodermal (N=23) and epidermal (N=26) genes Ciona genes and their Phallusia 1-to-1orthologs (N=20 for each category) (genes listed in the "Comments" column of Tables  S1  and S2 )      REG00000321 and REG00001175, Fanelli et al. , 2003; Doglio et al. , 2013)  and Otx (ANISEED REG00000010,  Bertrand et al. , 2003).
ACKNOWLEDGEMENTS: We thank Dr. A Spagnuolo (Stazione Zoologica Anton Dohrn, Naples, Italy) for the kind gift of Ciona robusta genomic DNA, Marc Plays and Philippe Richard for excellent animal husbandry, members of our groups for many discussions and suggestions. PL's lab was supported by grants from the Agence Nationale pour la Recherche (TED project, ANR-13-BSV2-0011). JLG-S's lab was funded by.
GPS data processing methods and theories are under continuous refinement in the past 30 years. Using the latest products is supposed to provide more stable and reliable geocenter estimates. In this paper, geocenter estimates from deformation inversion approach with new observations of IGS second data reprocessing campaign (IG2) are investigated. Results indicate that our IG2-derived geocenter motion estimates agree well with solutions from network approach for SLR. The truncated degree 5 exhibits the highest consistency between GPS-inverted geocenter estimates and the SLR results in both annual amplitudes and phases. Then, the GPS-derived geocenter motions are compared with results from other different approaches. We find that except for a discrepancy in the annual phase estimates of Z component, geocenter motions predicted with the IG2 data are in line with those based on other techniques.
In addition, the effects of the translational parameters and the comparison with the IGS first data reprocessing campaign (IG1)-estimated geocenter motions are investigated, and results demonstrate that the translation parameters should be estimated when inversing the geocenter motion with the newly IG2 solutions and the advantage of the IG2 data reprocessing over the previous IG1 efforts. Finally, we address the impacts of post-seismic effects and the missing ocean data on the IG2-derived solutions. After removing the stations affected by large earthquakes, the amplitudes of Y component become higher, but the annual phases of the Y component become far away from the SLR solutions. Comparisons of the equivalent water height from the IG2-estimated coefficients and the solutions from the estimation of the circulation and climate of the ocean indicate that the differences between the two types of solutions vary with different truncated degrees, and the consistency is getting worse and worse with the truncated degree grows.
2012 Rietbroek et al. , 2014;; Wu et al. 2015 Wu et al. , 2017)). GNSS data processing methods and theories have been under continuous refinement in the past 30 years. Until now, the newest products come from the second data reprocessing campaign implemented by the International GNSS service (IGS). Hereafter, we call it the IG2 products. Using the latest models and methodology, the IG2 products come out of the reanalysis of the full history of GPS data  (Altamimi et al. 2016; Rebischung et al. 2016). As the accuracies of the tracking systems are increasing, more uniform and denser network geometry is required to provide more stable and reliable geocenter estimates. Considering that the IG2 data processing strategies and models will be implemented in the GNSS data processing in the next few years, it is favorable to apply these newest solutions to the estimates of the geocenter motions, and assess its quality to see whether it has advantage or not compared with previous solutions.
One of the potential sources of errors is the approximation that we make use of the motion of the CF to replace the motion of the CN when estimating the geocenter motion with the surface load theory, and the translation parameters are mainly used to reduce the errors when replacing the CF frame with the CN frame. The differences between CF and CN are related to the network distribution, data quality, etc. , and whether the translational parameters should be ignored in the inversion process or not is also one of the questions that would be discussed. In this paper, we detail the characteristics of the geocenter motions using the degree-1 deformation approach with the newest IG2 products. Firstly, the inversion model and GPS observations from IG2 products are described in detail. Then the GPS-inversed geocenter motions under different truncated degrees are compared with SLR results in terms of the correlation coefficients.
Moreover, both the seasonal and non-seasonal signals of the GPS-derived geocenter time series are analyzed quantitatively and qualitatively. Finally, investigations are done on the effects of the translational parameters and the improvements compared to the IGS first data reprocessing campaign (IG1). Analyses of this paper can help readers get a thorough understanding of the ability of GPS to produce geocenter motions. It would also provide numerical support for interpreting and making use of the IGS products.
Correlations of the GPS geocenter estimates with SLR results To assess the quality of the IG2-inverted geocenter motion, we compare our results with SLR to investigate the correlations of the geocenter estimates obtained from two different space geodesy technologies. We adopt the UT/CSR monthly geocenter time series from the analysis of SLR data based on five geodetic satellites (LAGEOS-1, LAGEOS-2, Starlette, Stella and Ajisai) as reference (ftp://ftp. csr. utexa s. edu/pub/slr/geoce nter/ GCN_RL06_2018_11. txt). Although the SLR ground stations are very sparse and unevenly distributed with only 20 active stations on average, there is also correlated noise existing in the SLR time series, and SLR results still appear to exhibit the most reliable sensitivity to CM due to simpler orbit dynamics and have offered the first competitive geocenter motion result and adopted to estimate the ITRF origin  (Altamimi et al.
However, for truncated degrees from degree 7, the correlation coefficients of all the three components exhibit obvious decreasing behavior, especially for the X and Z components, implying that the more truncated degrees estimated, the more significant the impact of the aliasing errors of higher degrees in the GPS geocenter motions. UT/CSR geocenter vector is consistent with IERS conventions, approximating the vector from the origin of the TRF to the instantaneous mass center of the Earth (ftp:// ftp. csr. utexa s. edu/pub/slr/geoce nter/READM E_RL06). That is to say, the SLR time series reflects the motion of the CN with respect to the CM, which is not the same as the CM-CF estimates as obtained from the GPS estimates. To investigate the effects of the differences in SLR CN-CM data and SLR CF-CM data, we also select the GCN_L1_L2_30d_CN-CM (CN-CM reflects the correction required to best center the SLR network on the geocenter in the absence of modeling any local site loading) and GCN_L1_L2_30d_CF-CM (CF-CM is intended to reflect the true degree-1 mass variations without being affected by the higher-degree site loading effects (particularly at the annual frequency)) as references.