dataesr/scientific-paragraphs-categorization huggingface dataset:
The proportion of probe sets designated as "present" by the Affymetrix software was 52. 1±1. 2%, 52. 2±2. 2% and 56. 2±1. 2% for GK11-and MK801-treated rats and controls, respectively. To increase the accuracy of the analysis, we introduced two filtering steps. First, 10,192 probes detected as "Absent" in all 12 arrays were removed. Second 17,276 ESTs (genes for which no further information exists besides the tag) were removed. After these two filtering steps, 3,631 probes were left. All further analyses were performed with this "edited' list of probes.
Microarray data analysis We essentially followed the data analysis procedure described in detail by Nesic et al. [27]. We performed: (1) cluster analysis of the overall expression profiles in order to establish similarities among arrays; (2) cluster analysis of gene expression levels in order to classify similar groups of genes; (3) identification of genes whose expression levels were significantly changed statistically (p-value<0. 05) in each treated group compared to the control group; and (4) a pathway analysis to identify the relevant physiological networks. Clustering of arrays. The clustering of arrays is done in order to detect significant differences among the arrays belonging to the same experimental group. We compared the overall expression profiles of all arrays by hierarchical cluster analysis, using SPSS software®.
The clustering method used Average Linkage and Manhattan distance measures between the expression vectors. Statistical significance. In order to compare the effects of MK801 and GK11 treatments, we calculated the ratio of mRNA expression values between each treated group versus the control group. We then introduced a cut-off and selected only the probes with a ratio higher than 1. 5 for upregulated genes and lower than 0. 66 for downregulated genes  [28]. To identify the transcripts with different expression levels, we used the statistical analysis microarray software (SAM), developed at the Stanford University by Tusher et al. [29]  (http://wwwstat. stanford. edu/~tibs/SAM/, September 2012). At this stage, genes not detected as "present" in at least 3 out of the 4 arrays of a same experimental group were removed from the list of selected genes.
We thus identified: (1) genes with statistically significant changes in expression levels (for consistently expressed genes; SAM analysis) and (2) genes that have different absolute calls (i. e. Absent/Present) between the compared groups. The changes from "Absent" to "Present" (or vice versa) indicated a consistent increase (or decrease) in mRNA levels in a treated group compared to the controls. In those cases, expression ratios were not calculated, and up-or downregulation is indicated by arrows (Table  S1 ). Pathway analysis. Results were further analyzed using the Ingenuity Pathway Analysis software (IPA). After examination of the published literature, genes were classified according to their most relevant biological function.
Validation studies qPCR. Total RNA from the cingulate and retrosplenial cortex was extracted as described earlier and used as a template in RT-qPCR. The quality of the total RNA was checked using the Agilent 2100 Bioanalyzer. All RNAs used in the present studies had RNA integrity numbers above 9. 20. Total RNA (1 µg) was reverse transcribed using oligo dT 12-18 primers and Superscript III (Invitrogen). The RT product was then diluted 5 times with H 2 O and stored at -20°C until use. Real-time PCR was performed in 96-well plates in a final volume of 10 µl using SYBR Green dye detection on the LightCycler480 system (Roche-Diagnostic). Cq for individual determination were calculated using the 2 nd Derivative Max tool of the LightCycler®480 software. Primers were designed with Primer 3 input software or were commercially available (Table  1 ).
Their specificity was checked by examining the melting curve performed at the end of the qPCR run. Their efficiency was calculated by performing a standard curve by serial dilution of cDNA. The relative ratios of specifically amplified cDNAs were calculated using the ΔΔCq method  [30]. The syntenin gene (NM_031986) was used as a reference gene, as its expression was found to be very stable among the 12 DNA chips (data not shown). The results are expressed as foldchanges compared to expression levels in control rats, and are shown as the mean ± SEM. Statistical analyses were performed using one-way non-parametric ANOVA analysis followed by Dunn's post-tests, with p<0. 05 considered significant. Immunohistochemistry & quantitative analysis. Tissue blocks containing the cingulate cortex were cut into 50 µm sections using a Vibratome (Microm) and processed for immunostaining.
GK11. The number of genes significantly altered by GK11 or MK801 treatment is presented in a Venn diagram (Figure  2B  and Table  S1 ): MK801 and GK11 treatment affected the mRNA levels of 205 genes and 134 genes respectively, with 80 genes common to the two groups. However, the direction of mRNA expression changes and the fold-change (FC) values for those 80 genes differed depending on the treatment. For example, we found that Hsp70 mRNA expression was upregulated by 18-fold in MK801treated rats and only by 6-fold in GK11-treated rats, consistent with MK801 eliciting a robust HSP70 protein expression (Figure  1E ). qPCR validation of the microarray data (Figures  2C-E ). qPCR validation of the microarray results was performed on independent groups of animals that underwent the same type of treatments as animals used in the DNA microarray study.
In the qPCR experiments we also included samples from animals treated with 50 mg/kg Memantine to compare the effects of the three treatments at the transcriptional level. Figure  2E  shows that both Memantine and MK801 treatments had significant effects on the expression levels of the selected genes. On the other hand, GK11 treatment elicited markedly lower transcriptional effects. Pro-Inflammatory pathways are triggered by MK801, and less by GK11 (Fig. 3 ) Ingenuity Pathways Analysis (IPA) software and analysis of the literature were used to classify the differentially expressed genes (DEGs) according to their biological functions (Table  S1  and Figure  3 ). Figure  3  shows that after either MK801 or GK11 treatment, the DEGs had a similar distribution among the different biological functions.
The lists of DEGs were also used to map the canonical pathways contained in the IPA database. Up to 29 pathways were found to be significantly altered (p-value<0. 01) after MK801 treatment, but only 6 after GK11 (Table  2 ). Interestingly, none of the 5 pathways that were the most significantly altered in MK801-treated animals were affected by GK11. In agreement with the results shown in Figure  2  and Table  S1 , which show lower transcriptional effects after GK11 treatment, the proportion of DEGs representing transcription factors was much smaller in GK11-treated rats than in MK801treated rats (10% in GK11-treated animals vs. 17% after MK801 treatment). Interestingly, the largest number of genes differentially affected by both antagonists belonged to the immune response and inflammatory processes (15 to 19% of the DEGs for GK11 and MK801).
Most notably MK801 affected a large number of genes involved in inflammation regulation, whereas the effects of GK11 were much weaker. Among the 5 top pathways specifically affected by MK801 treatment but not by GK11, we found Corticotropin Releasing Hormone and Acute-phase Response signalling and RAR activation, all recognized as playing important roles in response to stressful conditions (see IPA software, http:// http:// www. ingenuity. com, for the description of these biofunctions). Biofunctions associated with altered gene expressions after the two treatments were also differentially affected: the apoptosisrelated "Cell Death/Compromise" biofunction was more altered in MK801 samples (99 DEGs compared to 51 in GK11 samples). Additionally, the main biofunction affected after GK11 treatment is "Lipid Metabolism" (39 genes), but with 48 DEGs associated with this specific biofunction, MK801 has a greater impact on it.
In situ hybridization on inner ear cryosections was performed as described  (19). Pictures were taken for (ii) by a confocal laserscanning microscope (LSM510; Zeiss), analyzed off-line with ZEN 2009 light edition software (Zeiss), and assembled using Adobe Photoshop (Adobe Systems). Pictures for (iii) were taken with a Zeiss Axiophot or Zeiss Stemi-2000-c microscope. Electrophysiology-Whole cell recordings were done on HCs from acutely dissected utricles that were perfused at 0. 5 ml/min with oxygenated solution containing 137 mM NaCl, 5 mM KCl, 2 mM CaCl 2 , 1 mM MgCl 2 , 10 mM HEPES, 11 mM glucose, pH 7. 4. The epithelium was cut transversally and anchored to the chamber floor with two pieces of glass, exposing the basolateral membrane of hair cells. Central and peripheral hair cells could not be easily distinguished in this semi-intact preparation.
After cancellation of capacitive transients, R s was compensated up to 85%. The resting potential was measured as the zero current voltage in the current clamp mode. Data analysis used pClamp 10 software (Molecular Devices) and Origin 7. 5 (OriginLab). Data were sampled at 10 kHz and filtered at 2 kHz. The voltage clamp protocol started from a holding potential of Ϫ70 (for type II HCs) or Ϫ90 mV (for type I HCs), followed by a 50-ms pulse to Ϫ110 mV for type I HCs and Ϫ100 mV for type II HCs followed by test pulses of 200 ms between Ϫ110 and ϩ40 mV for type I HC and Ϫ100 to ϩ50 mV in type II HC in steps of 10 mV, and a constant step to Ϫ30 mV for tail currents. In statistical analysis, the number of cells is given by n, and number of animals by N. Expression in Xenopus Oocytes and Two-electrode Voltage Clamping-Xenopus oocytes were obtained and injected as described  (15).
A final amount of 20 ng of cRNA/oocyte was injected for each condition. Oocytes were incubated 3-4 days at 17 °C and then examined by two-electrode voltage clamping using a Turbo Tec03 (NPI Electronics) amplifier and pClamp 8. 0 software (Molecular Devices). The protocol consisted of 5-s steps from Ϫ110 to ϩ50 mV in 10-mV increments from a holding potential of Ϫ80 mV. Vestibulo-ocular Reflexes-The vestibulo-ocular reflex (VOR) was tested in four groups of adult mice including wildtype (WT, n ϭ 15), Kcnq4 Ϫ/Ϫ (n ϭ 13), Kcnq5 dn/dn (n ϭ 17), and Kcnq4 Ϫ/Ϫ /Kcnq5 dn/dn (n ϭ 13). In each experimental group about half of the mice were male. Mice were prepared for chronic head-restrained experiments, as described  (21). The experimental protocol was approved by the Animal Experimentation Committee (DEC) of the Royal Dutch Academy of Sciences (KNAW).
During the experiment the mouse was placed head-fixed in a holder tube on a vestibular motion platform (R2000 Rotopod; Parallel Robotic Systems Corporation). Left eye orientation was measured using video pupil tracking with a table fixed CCD camera (Pulnix TM-6710CL, 120 frames/s) and IR illumination (850-nm LED, 6. 5-cm distance from the eye). Pilocarpine (2%) eye drops were applied before the experiment to limit pupil dilatation in darkness. Online image analysis was performed to extract the location of pupil edges and corneal light reflections using custom built software for Labview (National Instruments, Austin, TX). Angular eye velocity was computed offline using custom software written for Matlab (The Mathworks Inc. , Natick, MA) using the algorithm outlined elsewhere  (22, 23). Saccadic eye movements and nystagmus fast phases were removed using a 50°/s velocity threshold and 200-ms margins at each threshold crossing.
Each mouse was accustomed to the setup and experimental paradigm in a period of up to 3 training days before the experimental data were collected. The horizontal VOR was characterized in darkness and in the light using sinusoidal rotation about the yaw axis, using frequencies ranging between 1/16 and 4 Hz, presented in a sequence of increasing order. Peak velocity was held constant at 25°/s. The number of cycles ranged between 5 (at 1/16 Hz) and 60 at 4 Hz. Eye velocity amplitude and phase shift relative to head movement were calculated using multiple linear regression of eye velocity to in-phase and quadrature components of the stimulus velocity. Gain of the eye movement response was defined as the ratio between the eye velocity amplitude and the stimulus velocity amplitude. Phase shift is expressed in degrees; positive phase shifts indicate phase lead.
ACKNOWLEDGMENTS I. Charo ,  B. Engelhardt  and  J. V. Stein , and  R. Alon  kindly provided Ccr2 À/À , Icam1 À/À and Icam2 À/À , and Igal À/À mice, respectively. The authors are also indebted to  G. Burn  and  A. Fischer  for helpful discussions, to  C. Trouillet  for the management of the Geissmann lab, and to  A. McGuigan  and her colleagues from the  Biological Service Unit at King's College London, Guy's Campus , for support with mouse husbandry. E. G. S. is supported by a PhD fellowship from the  Oliver Bird Rheumatism Programme ,  Nuffield Foundation, UK. Work was supported by grants to F. G. from the  Medical Research Council, UK  ( MRCG0900867 ), the  European Research Council  ( ERC-2010-StG-261299 MPS2010 ), and the  European Science Foundation  ( ERC EURYI  Award).
This effect was dose dependent, as it was ineffective at low concentration (1/10 9 v/v octanal in mineral oil) and most effective at 1/10 5 (1. 69 ± 0. 28 vs. 1 ± 0. 2, respectively). In order to further test the specificity of the octanal effect on rI7-expressing OSN population in a pro-apoptotic context, we evaluated the modulation of other ORs mRNA level in the same conditions. To our knowledge; apart from rI7, U131 (Olr748), activated by low chain fatty acids  (Murrell and Hunter, 1999; Glatz and Bailey, 2010) , is the only deorphanized OR in rats. We quantified the level of mRNA coding for U131 and 5 other putative ORs genes (Olr363, Olr1576, Olr1306, Olr1195, and Olr448, accession numbers in Additional file 2) sharing high homology (92-94%) with mouse deorphanized ORs (putative ligands for those ORs in Additional file 2).
To prevent variable accumulations of the odorant in the pipette, an air flush was applied to the Pasteur pipette before it was placed in the glass tube. EOG voltage signals were recorded using an XtraCell 2 channels amplifier (DIPSI, Chatillon, FRANCE) used in a DC currentclamp configuration (I = 0), low-pass bessel filtered at 1 KHz and digitized at a rate of 2 kHz using an Digidata 1322a A/D converter (Axon Instruments, Molecular Devices, Union City, CA, USA) interfaced to a Pentium PC and Pclamp 9. 2 software (Axon Instruments). A reference Ag/AgCl electrode was placed on the frontal bone overlaying the olfactory bulb. Recordings were made with glass micropipettes of 4-5 M filled with a saline solution. EOG were recorded from the center of turbinates IIb and III. These positions gave robust, reproducible and long-lasting EOG recordings ranging from 7 to 14 mV when stimulated with the mixture of odorants at 10 -3 M.
Images of each turbinate were taken by an operator blinded to the treatment under X40 magnification on a DMBR Leica microscope equipped with an Olympus DP-50 CCD camera using CellF software (Olympus Soft Imaging Solutions GmbH, OSIS, Münster, Germany). rI7 OSN were counted using ImageJ software (Rasband, W. S. , ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http://imagej. nih. gov/ij/, 1997-2012). qPCR Total RNA was extracted using the Trizol method from frozen olfactory epithelia. OligodT first strand cDNA were synthesized from 2 μg total RNA by the Superscript II reverse transcriptase (Invitrogen) following the manufacturer recommendations then treated with DNase I. For quantitative PCR, 5 μl of 125 fold diluted cDNA templates were added to the 15 μl-reaction mixture containing 300 nM primers (sequences in Additional file 2, melting curves in Additional file 3) and SYBR Green GoTaq® qPCR Master Mix (Promega, Charbonnieres, France).
ACKNOWLEDGMENTS This work was funded by the  Institut National de la Recherche Agronomique (INRA). We would like to thank  Vincent Bombail  for his help for improving the manuscript and data analysis,  Birte Nielsen  for her help for improving the manuscript,  Xavier Grosmaitre ,  Roman Vidaltamayo  and all lab members for fruitful discussions, the  UEIERP (INRA, Jouy-en Josas)  for animal care and treatments,  Marie Annick Persuy ,  Stephan Bouet  and  Emmanuelle Duthoit  for technical help.
Introduction The goal of the present study is to describe accurately the effect of support inclination on the ants Lasius niger's motion in terms of their behavioral decisions, namely how the directional information given by the graviception continuously affects their decision process about where to go. To address this question, we have gathered high-quality movement data by tracking the spontaneous motion of 345 ants walking on a 0. 560. 5 m plane canvas, which was tilted with various inclinations c by (0,p=9,p=6,p=4,p=3) rad. This study fits in a series of works devoted to the modeling of collective building processes in social insects  [1, 2]. Such processes require that individuals (ants, termites) transport tiny loads of material from one place to another. In such a description, an individual picks up a load of material at some place, walks for a while, and ends up dropping its load some distance away from the picking site.
Data set For experiments, a 0:5|0:5 m virgin painting canvas was set up under HD video camera recording (1920|1080 pixels), and tilted with various inclinations c by (0,p=9,p=6,p=4,p=3) rad. Since we know that ant motion can be greatly affected by temperature  [31, 32] , the experiments were performed within a climatic room in order to control precisely the temperature (26 0 C) and relative humidity (50%). For each inclination and each of 3 colonies, 23 ants were collected from their housing container and placed within a Fluon-coated bowl, with a tuft of cotton soaked with sugar water. Then, each ant was gently picked up in turn using a small pig hair paintbrush, and the brush head was lowered to touch the canvas at the center point, where the ant could spontaneously walk down from the brush onto the canvas (see Movie S1 illustrating such an event).
To avoid taking into account the very first moments of ants experiencing a new surface, we have discarded the early part of the trajectory up to the time when the ant had walked at least 1 cm away from its dropping site. To avoid the geometrical bias due to the square shape of the canvas, we defined the end of a trajectory as the point where the ant exited the 0. 2 m radius circle centered on the starting position. Overall, we obtained 69 trajectories for each inclination c, yielding a total of 345 trajectories, representing 845263 data points (Min = 127, Median = 1798, Max = 14434 data points per trajectory). We believe that this experimental data set benefits from being well controlled for factors affecting the ants' motion (temperature, humidity, stress), and uses high tracking precision to determine ants' positions.
Computer tracking procedure The tracking program was written from scratch using the Core Image infrastructure of Mac OSX (Objective-C+GPU-based Image manipulation), starting from the CIColorTracking example (  [54] ). Each movie frame was successively applied with the filters CIGammaAdjust (with inputPower 0. 3), CICrop (with inputRectangle set as a 40640 pixels square centered around the latest detected location), CIColorControls (with inputContrast as 3. 5), and the CIColorTracking ad hoc filter MaskFromColor (with inputThreshold 0. 27083 and inputColor defined by the user clicking on the background color in the first frame). This yielded a binary representation of the 40640 pixels area containing ONpixels corresponding to the ant and noisy speckle from background, from which the centroid of the largest spot was computed, using a partition algorithm where two adjacent ONpixels were considered to belong to the same spot.
Data availability The whole set of data is made available as supplementary information. The data are given as supplemental data files (zip archives) : c~0 : Dataset S1; c~p=9 : Dataset S2 ; c~p=6 : Dataset S3 ; c~p=4 : Dataset S4 ; c~p=3 : Dataset S5. Each archive file contains a series of 69 files, one file per ant. Each file contains the data of a trajectory in a tab-delimited text format with 9 columns, corresponding in order to the inclination index, the colony index, the temperature, the humidity, the recording date, the individual index, the rank of the video frame, the corresponding time in second, and the x and y coordinates in meters. Each file starts with a header line labeling this information.
Circular Statistics In order to conduct heading statistics analysis, we used circular statistics, taking heading distribution as the input. Linear statistical measures cannot be used because angles on a unit circle have modulus 2p (0~2p~4p etc), and the fact that {p and p correspond to the same direction  [66]. Given the shape of the distribution (with a combined skew towards upward and downward directions), we used a test for uniformity that is capable of dealing with bimodal data: the Hodges-Ajne test. This test is reputed to work well for bimodal or multimodal distributions. It was written with R  [55]  using code written for a MATLAB toolbox providing a useful approximation for large data sets, allowing us to avoid factorial calculations  [39, 40]. The null hypothesis is that the population is uniformly distributed (isotropic).
In order to measure the dispersion, Batschelet proposes the mean angular deviation: s 2 ~½2(1{r 2 ) 1=2 ð9Þ The final angular deviation value of our bimodal samples is: s 1 ~s2 =2 ð10Þ The function to compute the P-value for the test of uniformity was adapted for R from circ_otest of Circular Statistics MATLAB toolbox  [39, 67].
To this end, we have used the eight sector-based experimental distributions of mean free path and heading deviations shown in Fig. 6  and 7. Since we used eight sectors a s , the resolution of the extended BW model is an approximation regarding angular dependence, but otherwise keeps the structure of the algorithm 2. These simulations were performed in the R environment  [55]. In order to program the random sampling function for each sector, and each parameter, the empirical cumulative distribution was first estimated from the corresponding data set, using ecdf. Then, this estimated function was sampled over an abscissa interval discretized in 100 bins, using approx. For instance, let's denote F(a) as the discretized cumulated function of heading deviations for a given sector and a given inclination, with a i , i~1::100 spanning ½{p,p.
Briefly, cells (4 ϫ 10 4 cells/well) in poly-L-lysine-coated 96-well plates (Corning) were rinsed twice with PBS and incubated in the presence or absence of the different effectors in DMEM (50 l) at 37 °C in 5% CO 2 atmosphere. Cells were then homogenized in 50 l of Homogeneous Caspase-3/7 Buffer containing the caspase-3 substrate Z-DEVD-rhodamine 110, and the fluorescence intensity (excitation at 498 nm and emission at 521 nm) was measured in cell lysates during 3 h, using a Flexstation II spectrofluorophotometer. Neurite Outgrowth Measurement-PC12 cells cultured in 6-well culture plates were observed under a macroconfocal Leica TCS LSI microscope. Neurite analysis was performed using ImageJ software (National Institutes of Health). Neurite outgrowth was evaluated by calculating the number of processes per cell and measuring neurite length.