dataesr/scientific-paragraphs-categorization huggingface dataset:
Neurite was defined as a cell process Ͼ10 m. Real-time Polymerase Chain Reaction-Total RNA was isolated from PC12 cells using the Tri-Reagent (Sigma-Aldrich). Approximately 1 g of total RNA was reverse-transcribed using the ImProm-II TM Reverse Transcription System (Promega). One tenth of the reaction mixture was used to quantify RelA, c-Rel, p52, and p50 expression by real-time PCR. Genespecific forward and reverse primers were designed using the Primer Express software (Applied Biosystems) as follows: 5Ј-CTTCTGGGCCATATGTGGAGA-3Ј and 5Ј-TCGCACT-TGTAACGGAAACG-3Ј for the RelA gene, 5Ј-CTTCCTGAT-GAACATGGTAACTTCA-3Ј and 5Ј-GGGCACGGTTGTCG-TAAATC-3Ј for the c-Rel gene, 5Ј-AGCACCAAGACCGAA-GCAA-3Ј and 5Ј-TTATCCTGAAACCCCACATCCT-3Ј for the p50 gene, 5Ј-CCAAGGACATGACTGCTCAATTTA-3Ј and 5Ј-TGAATCATAATCTCCATCATGTTCTTC-3Ј for the p52 gene, and 5Ј-AACTCCCTCAAGATTGTCAGCAA-3Ј and 5Ј-TGGTCATGAGCCCTTCCA-3Ј for the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) used as a reference gene.
Immunodetection was revealed with FITC-conjugated goat anti-rabbit immunoglobulin G (1:300 dilution), and nuclei were visualized by DAPI staining (1 pg/ml; Sigma). After mounting, fluorescence was analyzed using a Leica TCS SP2 confocal microscope. For each staining analysis, three fields were selected. Before acquisition, we used a z stacking to select a z section containing the plain nucleus as visualized by DAPI staining. This method permits to avoid measurement of fluorescence of z sections located above or below the nucleus during analysis. For all images of the same experiment, the acquisition settings were unchanged except the z parameters. For each field, images of DAPI and NF-B subunit stainings were acquired with the confocal microscope. The two images obtained were used to create layer masks of nuclear and cytoplasmic NF-B staining thanks to the image treatment software GNU Image Manipulation Program (GIMP).
The DAPI staining layer mask was used to define the nuclear region of interest by eliminating all regions except nuclear staining in the NF-B staining layer mask. The DAPI layer mask was subtracted from the NF-B layer mask to create a staining mask defining the cytoplasmic region of interest. This technique adapted from a procedure described by Noursadeghi et al. (22)  was used to separate nuclear and cytoplasmic stainings within each image allowing thus to avoid measurement of fluorescence cross-contamination. The fluorescence of each region of interest was measured using the ImageJ software. Western Blot Analysis-Antibodies against phospho-ERK1/2 and Lamin-A were obtained, respectively, from Cell Signaling Technology and Sigma-Aldrich. For cell fractionation, cytoplasmic and nuclear fractions were prepared by using a NE-PER nuclear and cytoplasmic extraction kit (Thermo Scientific) according to the manufacturer's protocol.
The antigen-antibody complexes were visualized by the chemiluminescence ECL Western blotting analysis system (Amersham Biosciences) and exposure to Kodak X-OMAT films (Sigma-Aldrich). Signals were quantified using ImageJ software. siRNA Transfection-PC12 cells were transfected with siRNA (Qiagen) by using the Amaxa Nucleofector system and the Cell Line Nucleofector kit V electroporation method (Lonza, Switzerland) according to the manufacturer's protocol (program U-029). To assess the efficiency of siRNA-induced knockdown, mRNA levels of the target genes were determined by real-time quantitative PCR. Statistical Analysis-Results were expressed as means Ϯ S. E. Statistical significance was assessed through the nonparametric Mann-Whitney test and Student's t test. A probability level of p values Ͻ 0.
2B ). ABT inhibited 3-hydroxy-, 6hydroxy-and 7-hydroxycoumarin formation with IC50 values of 41, 52 and 19 mM, respectively. Ninety percent of metabolite formation was inhibited by 400 mM of ABT. However, coumarin metabolism was not affected by the addition of BNPP (data not shown). Metabolism of isoamyl acetate. Carboxylesterases hydrolyze volatile esters to their corresponding acids  [24]. Thus, we assessed the hydrolysis of isoamyl acetate by measuring acetic acid liberation in the reaction medium following incubation with olfactory or hepatic S9 fractions. Esterase activity was equivalent in both tissues (approximately 390 mmol acetic acid/mg protein/ min) (Fig. 4A ). Isoamyl acetate hydrolysis in the olfactory S9 fraction was inhibited in a dose-dependent manner by BNPP, a specific carboxylesterase inhibitor, with an IC50 value of 0.
Effects of XME Inhibitors on EOG Responses To investigate the functional role of the olfactory XMEs, we recorded odorant-induced EOG responses before and after applying two phase I enzyme inhibitors, ABT and BNPP. First, we confirmed that superfusion of OM with ABT or BNPP was sufficient to inhibit CYP and carboxylesterase activities, respectively. For this purpose, the in vitro metabolism of quinoline, coumarin and isoamyl acetate was measured. All steps were performed as described previously except that the microsomal or S9 fractions were prepared from OM that had been superfused with inhibitors for 20 min. Superfusion of the OM with 400 mM of ABT or BNPP decreased the metabolism of quinoline/coumarin or isoamyl acetate, respectively, by approximately 30 to 80% (Fig. S6 ). In addition, we verified that the magnitude of 3-isobutyl-1methylxanthine (IBMX)-induced EOG responses did not vary before and after inhibitor application to demonstrate that inhibitor treatment does not interfere with signal transduction in OSNs (data not shown).
Discussion The goal of this study was to determine whether odorant metabolism by olfactory tissue enzymes modulates the first step of olfactory perception. Because data on odorant biotransformation by the OM are scarce, we studied the phase I metabolism of several odorant molecules. Then, we evaluated the consequences of biotransformation on the stimulating properties of these odorants. We accomplished this step by comparing EOG responses to odorants and their derivatives and by measuring EOG responses following phase I enzyme inhibition. Collectively, these studies demonstrate that the OM can enzymatically modify odorant molecules and thus change their stimulating properties.
The recording electrode was an Ag/AgCl wire positioned in a disposable pipette tip filled with a conductive gel (WPI, Sarasota, USA). The reference electrode was an 8-mm diameter Ag/AgCl disk covered with conductive gel that was placed under the rat hemi-head. Electrical signals were amplified using an AC/DC differential amplifier (A-M Systems, model 3000, Phymep, Paris, France), run through a low-pass filter of 300 Hz, digitized at 100 Hz using a Digidata 1440A interface board (Axon Instruments, DIPSI Industrie, Chatillon, France) and acquired using Axoscope 10. 2 software (Axon Instruments). The data were analyzed using Clampfit software (Axon Instruments). The peak amplitudes of EOG responses were measured at the maximum negative voltage deflection from baseline. The data were normalized by dividing the peak amplitude by the maximum amplitude elicited by 100 mM of IBMX, a phosphodiesterase inhibitor that activates the transduction pathway bypassing the receptor step.
The protocol used to assess the effect of XME inhibitors (ABT or BNPP) on EOG responses is presented in Fig. 8. First, two series of odorant stimulations at 2-min intervals were performed with an 8-min recovery period between each series. Under control conditions, a 2-min interval is sufficient to recover normal response amplitude. Then, the inhibitor was diluted in the Ringer buffer (final concentration 400 mM) and applied to the olfactory turbinates at a rate of 2. 5 mL/min for 20 min using the Rheodyne injection valve. The preparation was rinsed for 5 min with the Ringer buffer and the epithelium was stimulated by applying odorant using the same procedures as described above. EOG responses were recorded on endoturbinate IIb. IBMX was applied at the end of each measurement series for data normalization as described above.
Acknowledgments Authors would like to thank  Claire Chabanet  ( Centre des Sciences du Gout et de l'Alimentation, Dijon, France ) for her statistical expertise and the staff of the animal facility for the handling and care of the rats. They kindly acknowledge the ChemoSens platform ( UMR-CSGA CNRS/INRA/ Burgundy University, Dijon, France ) for the technical support in LC-MS/MS.
This work was supported by grants from the  Agence Nationale de la Recherche  ( ANR-05-PNRA-1. E7-Aromalim ) and the  Burgundy Regional Council  and by fellowships from the  French Research Ministry  ( N. Thiebaud  and  S. Veloso Da Silva ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Background: Antidepressants are often considered to be mere placebos despite the fact that meta-analyses are able to rank them. It follows that it should also be possible to rank different placebos, which are all made of sucrose. To explore this issue, which is rather more epistemological than clinical, we designed an unusual meta-analysis to investigate whether the effects of placebo in one situation are different from the effects of placebo in another situation. Methods: Published and unpublished studies were searched for by three reviewers on Medline, the Cochrane Library, Embase, clinicaltrials. gov, Current Controlled Trial, in bibliographies, and by mailing key organizations. The following studies in first-line treatment for major depressive disorder were considered to construct an "evidence network": 1) randomized controlled trials (RCTs) versus placebo on fluoxetine, venlafaxine and 2) fluoxetine versus venlafaxine head-to-head RCTs.
Types of outcomes Response was chosen as the primary outcome. Remission was chosen as a secondary outcome. These outcomes are the most consistently reported estimates of acute-treatment efficacy. Response was defined as the proportion of patients who had a reduction of at least 50% from the baseline score on the Hamilton Depression Rating Scale (HDRS)  [8]  or the Montgomery-Åsberg Depression Rating Scale (MADRS)  [9]. Remission was defined as the proportion of patients who had a HDRS score ≤7 or a MADRS score ≤12. When trials reported results from both rating scales, we extracted data from the scale considered in the study as the primary outcome.
Search strategy We used the search strategy from an earlier paper  [10]  on venlafaxine and fluoxetine to conduct this metaanalysis on aggregated data. Eligible studies were identified from PubMed/Medline, the Cochrane library and Embase, including congress abstracts. A three-step search was used for each component of this review. In a first step, an initial search on Medline was carried out in order to refresh optimal search terms and include possible changes in the databases. The search terms used were double-checked before starting the main search. In a second step, all keywords identified were used to search all the abovementioned databases. A third search was undertaken by searching the reference lists of articles identified. Initial keywords used were: "Depressive Disorder NOT Depression, Postpartum NOT Seasonal Affective Disorder"; "Antidepressive Agents"; "Fluoxetine"; "Venlafaxine".
In addition, manual searches of articles were performed in previous meta-analyses. Unpublished studies were searched for by communication with key organizations such as the Food and Drug Administration (FDA) and the European Medicines Agency (EMEA), and key researchers in the area. A search on clinicaltrials. gov and Current Controlled Trial was performed. Authors of abstracts or meta-analysis were contacted for further information and were asked for references of the studies when needed. If no response was obtained to a first solicitation, they were then contacted a second time.
Study selection The search of Medline, Cochrane and Embase databases provided a total of 11,051 citations. An additional 66 studies were identified by manual search. After adjusting for duplicates, 4,615 remained. Of these, 4,063 studies were discarded because, after review of the abstracts, it appeared that these papers did not meet the criteria. A total of 114 studies were excluded because of the language (among which 97 were in Chinese). Of 33 unpublished relevant studies identified, only 3 were made available by pharmaceutical firms. Thirty-one studies were included in the quantitative review. A flow-chart detailing the study selection process is given in Figure  1.
Acknowledgments We thank all the authors of the different studies who cooperated,  Guillemette Utard  for her advice on bibliographic research,  Lionel Riou França ,  Hervé Maisonneuve  and  Nicolas Naudet  for their very interesting comments,  Claudine Naudet , and  Angela Swaine Verdier  for revising the English. ASM is funded by the  Conseil General d'Ile de France (PICRI). This paper was supported by the  Institut National de la Santé et de la Recherche Médicale (INSERM). The sponsor had no role concerning the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript.
Production of GST-fused Proteins cDNAs encoding the cytoplasmic C-tail of 14 GPCRs and 2 one-transmembrane receptors were cloned into the pGEX-2T prokaryotic expression vector downstream the GST sequence. The following pGEX constructs were engineered: pGEX-DOR encoding residues 314-372 of the d-opioid receptor (referring to Swiss-Prot accession number U10504), pGEX-MOR encoding residues 334-400 of the m-opioid receptor (L29301), pGEX-KOR encoding residues 326-380 of the k-opioid receptor (U17298), pGEX-ORL 1 encoding residues 315-370 of the opioid receptorlike 1 (X77130), pGEX-M 1 encoding residues 414-460 of the muscarinic M 1 acetylcholine receptor (X52068), pGEX-M 2 encoding residues 436-466 of the muscarinic M 2 acetylcholine receptor (M16404), pGEX-ADRB1 encoding residues 373-477 of the b 1 adrenergic receptor (J03019), pGEX-ADRB2 encoding residues 322-413 of the b 2 adrenergic receptor (P07550), pGEX-CALCR encoding residues 407-490 of the calcitonin receptor (L00587), pGEX-CNR2 encoding residues 295-360 of the cannabinoid type 2 receptor (P34972), pGEX-5HT 7 encoding residues 380-445 of the 5-hydroxytryptamine 7 receptor (L21195), pGEX-H 2 encoding residues 284-349 of the histamine 2 receptor (S57565), pGEX-TXA 2 encoding residues 304-343 of the a isoform of the thromboxane A 2 receptor (D38081), pGEX-FZ 4 encoding residues 493-537 of the frizzled 4 receptor (AB032417), pGEX-TGF b encoding residues 805-849 of the type III transforming growth factor b receptor (L07594), pGEX-IGF 1 encoding residues 1268-1367 of the insulin growth factor I receptor (X04434).
The high peptide concentrations resulted in large spikes at the beginning and end of each injection; these points were clearly artifacts and they were removed for presentation purposes. Endpoint responses were read 20 s after injection end. The double-referenced dose-response curves were fitted with Biacore X100 Evaluation Software 2. 0. 1 (GE Healthcare). The dissociation phases were first fitted separately to a one-to-one binding model to obtain the dissociation rate constants. The association and dissociation phases were then fitted simultaneously to a model with two parallel independent one-to-one reactions (heterogeneous ligand), with the dissociation rate constants fixed to the single value found by fitting of the dissociation phases separately. The mass transport contribution was negligible in both data sets.
As shown in Figure  3A , DOR, ADRB1 and M 1 C-tails interacted similarly with full-length GASP-1 and mutant 380-1395, indicating that the N-terminal portion of GASP-1 is not implicated in the interaction with GPCRs. Unexpectedly, the conserved C-terminal domain did not display detectable interactions with the ADRB1 or M 1 C-tails and interacted only weakly with DOR. Conversely, the central domain of GASP-1 retained around 70% of interaction with ADRB1 and M 1 C-tails and 30% with DOR. These data suggest that the central domain of GASP-1 is necessary and sufficient for the interaction with ADRB1 and M 1 receptors, while both the central and C-terminal domains of GASP-1 are important for the interaction with DOR. In order to delineate more precisely which regions of GASP-1 are important for the interaction with DOR, we evaluated the interaction of the DOR C-tail with four additional truncated mutants of GASP-1 (Figure  3B ).
A key issue will then be to define how the selectivity of interaction between GASPs and GPCRs is achieved in a cellular context. Among the receptor C-tails that we have tested, ADRB1 is the one that displays the highest level of interaction in vitro with GASP-1 and GASP-2. This result is in contrast with previous results showing a low interaction of GASP-1 with ADRB1 C-tail  [10]. This discrepancy is most likely due to the fact that we used fulllength GASPs to perform our experiments, while Heydorn and collaborators used a truncated form of GASP-1, corresponding to amino-acids 898 to 1395. When we performed GST-pull down experiments with a similar fragment of GASP-1 (corresponding to amino acids 924 to 1395), only 5% of the input was retained by the ADRB1 C-tail (data not shown), which is in agreement with the results of Heydorn et al.
Moreover, the interaction of GASP-7 with these different GPCRs was also blocked by a synthetic peptide containing a GASP motif (Figure  7 ). These data suggest that the two GASP subfamilies (with or without GASP motif) most likely interact with the same region within carboxyl-terminal domain of GPCRs but with a distinct mode of binding. Although the region within GASPs from subfamily 2 that promote the interaction with GPCRs remains to identify, we propose that the conserved carboxyl-terminal domain of the GASP family is involve in this interaction as it is in GASP-1 and DOR interaction (Figures  3A  and 3B ). The GASP motif is critical for the interaction of GASP-2 with GPCRs. A, GST-pull down experiments with two truncated mutants of GASP-2 and ADRB1, M 1 and CALCR C-tails. Grey boxes represent the 15 AA GASP motifs.
In vivo Electrophysiological Recording during Sleep and Data Analysis Mice were handled and habituated to the recording chamber and room for 48 hours prior to each monthly recording. Recordings were performed for at least 4 hours during the light cycle. We were able to obtain 5 monthly recording sessions (from 2 to 6 months) from 6 R6/1 and 4 WT mice. The remaining mice were recorded only at 2 (1 R6/1 and 1 WT), 3 (3 R6/1 and 2 WT), and 4 (1 WT) different age points due to transient technical failures in the recording system. These recordings, however, allowed us to reveal the time points when a mouse displayed both the b synchrony and the clasping phenotype. Hindlimb clasping, considered as a hallmark symptom of HD, was also examined monthly on recording days. Recordings were performed using Sciworks (Datawave Technologies, Loveland, CO).
An experimenter naive to age and experimental group performed this operation. The specific segments of LFP recordings attributed to different brain states were then processed for averaged power spectra using the Matlab platform with laboratory-built programs. Fast Fourier transforms were calculated on 4-s Gaussian windows with 50% overlap. Because of the possibility that the intensity of the spectra might differ between probes and between animals, intensities at different frequencies were normalized by the sum of the overall spectra before being averaged by genotype.
All samples were analysed in a random order and alternating injections of IgG from controls, obese and AN patients. For the affinity kinetic analysis, a multi-cycle method was run with five serial dilutions of each patient and control IgG: 0. 5, 0. 25, 0. 125, 0. 625 and 0. 03125 (mg ml À 1 ) including a duplicate of 0. 125 mg ml À 1 and a blank (buffer only). During each cycle, 60 ml were injected (KINJECT) into the flow conduit of the BIAcore instrument with flow speed of 30 ml min À 1 at 25 °C followed by 5 min of dissociation. Between injections of each sample, the binding surface was regenerated with 10 mM NaOH resulting in the return of the sensorgram to the same baseline. The affinity kinetic data were analysed using BiaEvaluation 4. 1. 1 programme (GE Healthcare). For fitting kinetic data, the Langmuir's 1:1 model was used and the sample values were corrected by subtracting the blank values resulting from the injection of HBS-EP buffer.
of either: (i) PBS, (ii) ghrelin alone, (iii) ghrelin with IgG extracted from lean C57Bl6 mice and (iv) ghrelin with IgG extracted from ob/ob mice. Mouse ghrelin (Peptide institute, Inc. ) was injected at the dose of 0. 1 nmol during the first 4 days and 1. 0 nmol for next ten days. Two IgG pools were prepared from IgG of six ob/ob and six lean mice characterized by low and high KD vales, respectively, as measured by the SPR and 1 nmol of IgG was given at each injection. Food (SERLAB, Montataire France) and drinking water were available ad libitum and body weight was measured daily. Feeding data were continuously monitored for 14 days and analysed using the BioDAQ data viewer 2. 3. 07 (Research Diets). For the meal pattern analysis, the inter-meal interval was set at 300 s. After 14 days of injections, body composition in mice was analysed by the EchoMRI.
Statistical analysis. Data were analysed and the graphs were plotted using the GraphPad Prism 5. 02 (GraphPad Software Inc. , San Diego, CA, USA). Normality was evaluated by the Kolmogorov-Smirnov test. Group differences were analysed by the analysis of variance (ANOVA) or the non-parametric Kruskal-Wallis test with the Tukey's or Dunn's post tests, according to the normality results. Where appropriate, individual groups were additionally compared using the Student's t-test or the Mann-Whitney test according to the normality results. Effects of absorptions were analysed using the paired t-test. Body weight gain in mice was analysed using the two-way repeated measurement ANOVA. Data are shown as means ± s. e. m. and for all tests, Po0. 05 was considered statistically significant.
Acknowledgements This work was supported by  Grants-in-Aid for Scientific Research  from the  Ministry of Education, Culture, Sports, Science and Technology of Japan. It also received supports from Fonds Franc¸ais Alimentation & Sante, from the  European Regional Development Fund (FEDER)  and from  EU   INTERREG IVA 2 Seas Programme  ( 7-003-FR_TC2N ). We are grateful to  Dr Emeric Gueneau ,  GE Healthcare , for the help with BIAcore instrumentation and affinity kinetics analysis.
While many software packages do incorporate a cell tracking module or plugins, the normalization of the calcium signal for each cell as well as the classification of calcium responses and any quantification generally have to be performed manually involving tedious excel datasheets  [31]. Here we have developed a complete approach named Methods for Automated and Accurate Analysis of Cell Signals (MAAACS) which enables the simultaneous tracking of a population of individual moving cells (multiple target tracking, MTT)  [32]  and the automatic extraction of robust statistics on pertinent observables. The MAAACS program has been conditioned to synchronize, normalize and assemble the recorded cell traces to provide an at a glance calcium barcoding of a heterogeneous cell population and facilitate the a posteriori data mining and interpretation.