dataesr/scientific-paragraphs-categorization huggingface dataset:
Upstream regulatory candidates A web tool (KeyRegulatorFinder. genouest. org/) that has been recently developed  [62] , was used to propose upstream transcriptional regulators that may have participated to the molecular flexibility in response to diet within each AT. This methodology aimed to provide a reasonable number of upstream regulatory candidates for the transcriptomic changes, by an automatic confrontation of the DEP dataset with the academic information on regulations and reactions in mammalian signal transduction included in Transpath® database. A causality graph was built across the different molecules, so that genes and(or) gene complexes being able to regulate a significant number of DEP from the input list could be considered as candidates for an upstream regulatory role. The algorithm can also predict whether the upstream candidates were activated or inhibited by the conditions under study.
Quantitative real-time PCR (qPCR) Finally, a graph-driven hypothesis qPCR validation was performed on a subset of the upstream regulatory candidates in PRAT and in SCAT of the 48 pigs. For qPCR, first-strand cDNA synthesis was performed with 1 μg of total RNA previously used in microarray analysis, using High Capacity RNA to cDNA Kit (Applied Biosystems, Foster City, USA). Primers were designed from porcine sequences available in Ensembl or NCBI databases using Primer Express® v3. 0 software (Applied Biosystems). Detailed information for each primer pair including gene name, gene symbol, primer sequences (forward and reverse) and amplicon size are provided in Additional file 7: Table  S7. A StepOnePlus™ real-time PCR system (Applied Biosystems) was used for qPCR. Amplification reactions and disassociation curves were realized as described previously  [63].
The TOP2B gene was the most stable reference gene stated by GenNorm algorithm among 3 other tested reference genes, and was used for normalization. For each sample, the normalized expression level was calculated using the formula E target -ΔCq (sample -calibrator) / E TOP2B -ΔCq (sample -calibrator) where E is the efficiency calculated from the slope of calibration curve, Cq is the quantification cycle and the calibrator is a pool of all samples. Then, ANOVA was used to determine significant effects of diet, line and the interaction between diet and line, using the R software. Both fold-change in gene expression levels and p-value were represented.
Acknowledgments This project was funded by the  French National Agency of Research  ( FatInteger  project,  ANR-11-SVS7 ). Microarray annotations were managed by  SIGENAE (Système d'Information des GENomes des Animaux d'Elevage  (http://www. sigenae. org). We would like to acknowledge  Hélène Gilbert  ( GenPhySE, INRA, Toulouse, Fr ) for line selection.
Availability of supporting data The molecular datasets supporting the conclusions of this article are available in Gene Expression Omnibus repository (GEO, http://www. ncbi. nlm. nih. gov/geo/) through the accession number GSE70836 for subcutaneous adipose tissue (SCAT) and GSE70837 for perirenal adipose tissue (PRAT). Microarray data are MIAME compliant. Other datasets are included within the article and its additional files.
The signals were amplified with an Axoclamp 2B amplifier in current-clamp mode. The intracellular and extracellular signals were digitized at 10 kHz with a 12 bit, 16-channel analog-to-digital converter (Digidata 1200A, Molecular Devices), and monitored and saved to a PC with AxoScope (Molecular Devices). Data analysis. Records were analyzed with Clampfit 10 software and scripts written in Matlab (2015a). Simulations. Single-neuron and neural-network simulations were performed in Matlab (2015a) using the direct Euler method of integration, with a time step of 0. 05 ms. We checked that smaller time steps provided substantially similar results. Bifurcation analysis was performed in XPPAUT 7. 0 and the Auto package. In all simulations, initial conditions were systematically varied to check stability of numerical results.
The model code is available on Model DB (https://senselab. med. yale. edu/ modeldb/). Neuron intrinsic properties. Single-neuron activity was modeled using the conductances derived from previous studies  (Mainen and Sejnowski, 1996; Krishnan and Bazhenov, 2011). The intrinsic currents selected represent the major currents needed to reproduce the firing patterns of subicular PYs  (Staff et al. , 2000; Jung et al. , 2001). We used a model of a regular-spiking neuron for the PYs and a fast-spiking neuron for the INs  (Mainen and Sejnowski, 1996; Bazhenov et al. , 2004). To take into account the activation of bursting properties of PYs due to increased extracellular potassium  (Jensen et al. , 1994) , the intrinsic potassium currents were modulated by its concentration in a manner similar to that reported by  Fro ¨hlich et al.
This work was supported by the following grants:  ANR-10-LABX-0087   IEC ,  ANR-10-IDEX-0001-02 PSL, ERC-322721 ,  FRM FDT20140930942. B. S. G. acknowledges partial support from  Research Program 5-100  at the  National Research University Higher School of Economics. The contribution of  Anton Chizhov  was supported by the  Russian Foundation for Basic Research  with the Research Projects.
Hardware The autopilot system uses the low-cost MBED microprocessor (NXP LPC1768) as its main processor, which has an execution speed of 96MHz and a 32-bit architecture, as well as 32KB of RAM and 512KB of FLASH memory. The processor is powered using a 5V USB or using an external supply (4. 5 to 9V) applied to the VIN pin, and includes a built-in USB programming interface, which is as simple to use as a USB Flash Drive. The processor comes in a module along with a wide variety of devices, such as an integrate USB bus, three serial ports, one CAN bus, one Ethernet port, six PWM outputs, general purpose ports, and six analogue input channels. In addition, the modules are small in size and are supplied in a 40-pin DIP package (54x26mm). The MBED microprocessor is programmed using a C-language development system, using a website lightweight online compiler for developers.
in a module with a wide variety of devices such as an integrate USB bus, three serial ports, one CAN bus, one Ethernet ports, six PWM outputs, general purpose ports, and six analog input channels. In addition the modules have a small size and are supplied in a 40-pin DIP package (54x26mm). MBED microprocessor is programmed using a C-language development system, with a Developer Website Lightweight Online Compiler. The figure  2  shows the autopilot architecture block diagram. The autopilot system use a microcontroller, that directly determines the position and angular velocity from the inertial unit MTI Xsens and receives the remote control commands or set point through the Wireless modem by serial port. The modem used is the Xbee-pro which is very stable if the distance is less of 100 meters.
This distance is enough for an indoor test bed platform. The microcontroller calculates the control law to send the correction through the IIC port to each motor driver. Through analog channels, the position data (x, y, z) is obtained, using the ultrasonic sensor LV-EZ1, with the purpose to control linear position (not used in this work). The set-point also can be received by a serial port directly from the PC using a wireless modem. In the second phase the main loop takes place, which is dedicated to calculate the control law, reading the IMU and Remote control by serial channels using interrupt.
Another activity that is executed periodically is linking with the ground station; this can be done using a wireless modem, or using the USB programming port in debug mode. module with a wide variety of devices such as an rate USB bus, three serial ports, one CAN bus, one rnet ports, six PWM outputs, general purpose ports, six analog input channels. In addition the modules a small size and are supplied in a 40-pin DIP package 26mm). MBED microprocessor is programmed using -language development system, with a Developer site Lightweight Online Compiler. The figure  2  shows autopilot architecture block diagram. The autopilot m use a microcontroller, that directly determines the tion and angular velocity from the inertial unit MTI s and receives the remote control commands or set t through the Wireless modem by serial port.
The em used is the Xbee-pro which is very stable if the nce is less of 100 meters. This distance is enough for door test bed platform. The microcontroller calculates control law to send the correction through the IIC to each motor driver. Through analog channels, osition data (x, y, z) is obtained, using the ultrasonic or LV-EZ1, with the purpose to control linear position used in this work). The set-point also can be received serial port directly from the PC using a wireless em. le with a wide variety of devices such as an SB bus, three serial ports, one CAN bus, one rts, six PWM outputs, general purpose ports, log input channels. In addition the modules ll size and are supplied in a 40-pin DIP package. MBED microprocessor is programmed using ge development system, with a Developer htweight Online Compiler.
The figure  2  shows ot architecture block diagram. The autopilot a microcontroller, that directly determines the d angular velocity from the inertial unit MTI receives the remote control commands or set gh the Wireless modem by serial port. The ed is the Xbee-pro which is very stable if the less of 100 meters. This distance is enough for st bed platform. The microcontroller calculates law to send the correction through the IIC h motor driver. Through analog channels, data (x, y, z) is obtained, using the ultrasonic Z1, with the purpose to control linear position this work). The set-point also can be received port directly from the PC using a wireless ur-rotor electronic onboard schema.
Numeric Simulation Before implementing the control algorithm in the experimental platform, a numerical simulation was conducted using MATLAB Simulink. A simplified block diagram of the closed-loop system simulation is shown in Figure  5 , in which the control law algorithm can be found on the block labelled "multi-model state feedback". The quadrotor nonlinear model block has as its input the vector u(t) = w 1 w 2 w 3 w 4 w 1 2 w 2 2 w 3 2 w 4 2 T , and as its output, the vector y(t) = x(t) = ϕ θ ψ ϕ ˙θ ˙ψ ˙T. In order to determine the parameters, an experimental identification was performed to obtain the thrust and drag coefficients, K t and K d , using as data the force and angular velocities of the rotors. Other parameters were taken from the bibliography  [8] , in order that both vehicles would have similar dimensions.
4m, and z < 1. 2m. This means that the mechanism serves to validate attitude stabilization and position, which imitates the vehicle's ordinary flight. The link between the platform and the ground station computer was established using the microprocessor's USB programming port, in order to send data bidirectionally; this data can be both visualized in real time and stored for later visualization. fficients, K t and K d , having as data the force and ular velocities of the rotors. Other parameters was en from the bibliography  [8]  due that both vehicles e similar dimensions. Table  1  summarizes main ameters. Simulation results of the T-S Fuzzy state back controller are shown in figure  6. The source e of this scheme can be found in Matlab Central, to http://www. mathworks. com/matlabcentral/fileexchange 11-x4-multimodel-control.
ACKNOWLEDGMENT Authors wish to thank to the Universite de Picardie Jules Verne France, the Autonomous University of Tamaulipas Mexico and the Mexican Council of Science and Technology (CONACYT) for the support in this work. Figure  10  shows the angular velocity response, which always converges to the values (θ ˙= ϕ ˙= ψ ˙= 0 °/ s). From Figures  8  and 10 , we can see that, if we move the helicopter manually from its stable position (this was done simultaneously for the three angles), the control algorithm takes a minimal time to arrive at stability with zero value for all the states. The execution time shown in the figure is only 16 seconds, but the experimental tests were run for a much longer period. Note that disturbance was applied by manually moving the helicopter, but this disturbance can be quantified by adding a mechanism for angle measurement for this purpose.
Mosaic organisation of chromosome ends The two ends of each chromosome (Σ) of E. cuniculi were designated as Σα and Σβ, referring to the 5' and 3' ends of the Watson strand of the sequence deposited in the database, respectively. Sequence comparison between the different chromosome ends was first performed with Miropeat software to identify gap free repeats (Additional file 1: Figures  S1  and S2A ) and confirmed by BLAST as previously described  [32]. Our analysis revealed that the available sequence of the subtelomeric regions is incomplete for the following three reasons: (i) the rDNAcontaining repeat is only found on both ends of chromosome I and on IVα extremity whereas previously reported physical mapping data indicated that each subtelomere includes the rDNA unit  [6] ; (ii) no genes belonging to gene families known to associate with chromosome ends were detected on IIIβ and IXα, and (iii) short duplicated sequences at far extremities are due to artificial truncations of subtelomeric specific repeats (Additional file 1: Figure  S2B ).
To determine chromosome ends organization in E. cuniculi in GB-M1 isolate, long PCR reactions were performed to amplify the chromosome extremities between the rDNA region and the sequences available in the Genbank database (Additional file 1: Figure  S3 ). Overall, we obtained about 26 kbp of new sequence data, which are accessible under accession numbers HG380753, HG967526, HG967527 and HG967528. The genome of E. cuniculi is diploid and the GB-M1 genome contains two chromosome III homologues differing by a single indel  [6]. We isolated and sequenced the two different chromosome IIIβ extremities from PCR products (Additional file 1: Figure  S4 ). Sequencing effort further revealed uncharacterized sequences at chromosome IIα and IXα extremities. The new DNA sequence characterized on chromosome IIα was also found to be present at chromosome IVβ extremity.
3 ). This organisation was determined based on long-read assembly from subclones obtained from a long-PCR product and it was confirmed using data from the genome project. The IIIβ1 consensus shows a genomic organization that is close to the VIβ extremity with repeats order SUB/EXT3-1/EXT4-1/EXT2-2. The EXT-to-core transition is made by a new EXT block (EXT10) encompassing the NewECU03 gene characterized at transcriptional These sites are often hot spots of sequence rearrangement and were identified by their telomere-associated distal sequence which was conserved after genetic events. The two IIIβ variants originate from a homologous recombination event that involving two R09 sites, that was conservative of the proximal block (EXT10). The distal sequence of these sites is highly conserved over about 1000 bp (98 % identity without gap) between EXT2-2 (R09a) and EXT3-2 (R09b) level by Dia et al.
1  and 2 ). R06 recombination site is at EXT3-EXT4 transition; the R07 site is associated with the EXT5-EXT2 transition; the R13 recombination hot spot is responsible for a rare translocation event at VIβ and IIIβ1 extremities. Consequently, the R09 site is located in two different EXT Fig. 3  Sequence features justifying Chromosome Length Polymorphism (CLP) for two chromosome III homologues in E. cuniculi GB-M1. CDSs are represented by boxes with arrows indicating transcription direction and are ordered from telomere (left) to chromosome core (right). Grey colour is applied to the members of three multigenic families: interB, interC or interD. Name and/or Uniprot accession number are given for CDSs characterized by the genome project. The telomere-associated distal parts of the two extremities are identical up to R06 recombination site.
Overall, we found 19 interAE, 30 interB, 23 interC and 78 interD related CDS in the E. cuniculi genome (details in Additional file 1: Figure  S5 ). The Pfam database identified four protein domains of unknown function among the proteins encoded by these genes: 1) DUF1609 domain was identified because of the high level of sequence similarities that exist at the amino acid level between the C-terminus part of InterAE (encoded by inter-regions A of interAE genes) and InterB proteins; 2) DUF3654 domain corresponds to the N-terminal part of the proteins encoded by full interAE and interB genes; 3) DUF1686 is found in interC genes encoded polypeptides; and 4) DUF2463 is found in InterD proteins. More divergent sequences were found in the Uncharacterized Protein Family entries of UNI-PROT Knowledgebase: UPF0328 (interD), UPF0329 (interAE and interB).
Two alternatives approaches have been used to evaluate in more details the base composition at chromosome ends. We first used the GeneFizz software implementing a helix-coil transition model to search for local variations in DNA melting properties (i. e. the transition between the close and open state corresponding respectively to the double stranded and the single stranded form of the DNA molecule  [37, 38] ). The state of the DNA molecule was measured at different temperatures along the whole chromosome with a sliding window of 20 bp  [37]. Curves calculated at different temperatures were superimposed to identify regions where the transition between closed and open states requires an increase of the temperature by several degrees (Fig. 6  and Additional file 1: Figure  S8 ). The GC rich regions of the genome such as chromosome ends are in closed state at 74 or 75 °C.
cuniculi chromosomes is apparently higher than thus observed in a random sequence (bottom right curve). Horizontal and vertical discontinuous lines indicate the zero position on the ordinate and abscise respectively. The two lines get cross at the first base in 5-prime of the consensus sequence deposited in the database and structure of chromosome coding core region  [34] [35] [36]. MicrosporidiaDB database confirmed the presence of the four gene families in E. intestinalis, E. hellem and E. romaleae genome. Other telomere-associated gene families were also described in these species  [35]. The EXT region remains much less extended in the genome of E. intestinalis  [34]. Protein features (Additional file 1: Figure  S9 ) strongly suggest the products of these gene families could interact between each other.
Pair ends DNA sequencing (Sanger method) was performed by Cogenics (Beckman Coulter). Sequence assembly was performed using DNABaser software (Heracle BioSoft SRL). Lr05debrev/ Lr02r1-2 and Lr05debrev/Lr13dir3 sequencing provide missing information at SUB-EXT2 transition (Acc N°H G967527). LK09a/Lr02r1-2 and LK09a3/Lr02r1-2 sequences give IXα organization (Acc N°HG967528). Sequencing and assembly of LK03b5/Lr02r1-2 subclones provide two consensus sequences, a short version (Acc N°H G380753), and a longer one including EXT4-1 region (Acc N°HG967526). All final consensuses were used as bait, using reads from the genome project as prey to confirm new sequence organizations. Sequencing of Lr08rev/Lr02r1-2 was used to study diversity in the EXT4-rDNA transition.
Bioinformatics analysis Miropeat software  [81]  was compiled on UNIX Solaris and LINUX operating system. The source code is available at http://genome. wustl. edu/pub/software/miropeats. Known E. cuniculi chromosome consensus sequences were compared to each other through the use of three-sequence combinations (Additional file 1: Figure  S1 ). Blastall program  [82]  was downloaded from NCBI ftp server or used through the web portal (www. ncbi. nlm. nih. gov/blast). GeneFizz server was used for analysing base skews along DNA strands (web site no longer available)  [37]. The DNA walk algorithm was an automaton reading the sequence from 5' to 3'  [39]  and was implemented with a movement going from the (0. 0) coordinate toward up, down, left and right for G, C, A and T bases, respectively. Graphic representation was accomplished using GNUPlot software or IDL data analysis and visualization software (Exelis).
Miropeat analysis The Encephalitozoon cuniculi genome analysis using Miropeat software detected large gap-free repeats at the end of the chromosomes (Additional file 1: Figure. S1 ). Overlapping distal repeats were separated in fifteen types of repetition units (r01 to r15, Additional file 1: Figure  S2 ). Five segments of unique type (be1 to be5) extend between some repeats on three chromosomes, the largest one (be3, 9 kbp) being intercalated between r02 and r09 on chromosome VIII. The two ends of every individual chromosome (Σ) were designated as Σα and Σβ, referring to the 5' and 3' ends of the Watson strand of the sequence deposited in the database, respectively. The EXT and "r" repeats are generally present once per extremity (Additional file 1: Figure  S1 ). Three chromosomes have large symmetrical organisation of their extremities: EXT1, r01-r02-r03-r04-r15 on chromosome I (37 kbp of internal repetition), EXT3-EXT4, r10-r07-r08 on chromosome VI (7 kbp of internal repetition) and EXT1, r02 on chromosome VIII (about 4 kbp of internal repetition).
Small vertical arrows at the bottom indicate the position that was taken into consideration to calculate the distance between open-to-closed transition and recombination site. C. Recombination sites R10 and R11 are associated with close regions. Corresponding colours, from 69 to 73 °C, are red, yellow, dark blue, light blue and violet. GC content curve is coloured in green. The R11 site is associated with a closed region in the proximal region. Figure  S9. Description and putative structure of InterAE, InterB, InterC and InterD proteins. Protein description was recovered from Pfam database. We use one entry per multigene family product which was considered to be the most representative. We recovered both graphical representation of the protein and feature table. A schematic representation can be deduced from each Pfam description.
We consider the distribution of positively charged amino acids (+) around the first transmembrane domain to assess the orientation of the InterC and InterD protein in the plasma membrane as they have no ER-targeting signal peptide. Figure  S10. MicrosporidiaDB resources presenting genomic distribution of interAE, interB, interC and interD genes in Encephalitozoon cuniculi genome. Data were recovered of the GB-M1 strain that was used in the present study. They were also recovered for two other isolates EC1 and EC3. A. The interAE and interB genes were selected from the database based on their conserved Interpro domain IPR011667-UPF0329. Some truncated genes and pseudogenes were not detected. B. The interC genes were selected from the database based on their conserved Pfam domain DUF1686. B.
g. EXT1-1, a sub-block of EXT1, is bounded by R02 and R03 sites). CDSs surrounded by dotted line are in the coding core sequence. CDSs with plain lines are EXT and SUB CDSs. Arrows without number are extrapolated from the present study. A. EXT1. B. EXT2. The thick horizontal bare indicate the region covered by corresponding Genbank accession number. C. EXT3. The thick horizontal bare indicate the region covered by corresponding EMBL/ Genbank accession number. D. EXT4. E. EXT5. The thick horizontal bare indicate the region covered by corresponding Genbank accession number. F. EXT6. G. EXT7. Figure S6. Gradient complexity of EXT repeats from R01 recombination to EXT-to-core transition. Recombination have place in a tree-like structure respecting their relative distance to R01 recombination site.