dataesr/scientific-paragraphs-categorization huggingface dataset:
These projects take advantage of the most recent 1000 genomes reference panel (www. 1000genomes. org) that enables more reliable imputation (statistical inference) of genotypes for millions of genetic variants that have not been genotyped. Availability of newer reference panels like the Haplotype Reference Consortium panel (http://www. haplotype-referenceconsortium. org) that enable imputation of low frequency variants also provide an exciting opportunity. Efforts are now being made to expand genetic studies to non-European ethnic groups, an essential step to enhance the discovery of stroke risk loci, as was shown for other conditions  [77]. In parallel data on rare variants obtained through exome chip genotyping, whole exome and whole genome sequencing is being accrued. In addition to uncovering new risk loci, sequencing will likely help fine-map genetic risk loci discovered by genome-wide association studies and facilitate the identification of the underlying causal variant and gene.
In this regard, we studied the effect of a nanoliposome treatment on the network formation of primary cortical cells. We quantified the connectivity of neuronal networks in two-dimensional cultures based on the statistical density of neurites (see Supporting Information). The cultures were treated with F22 for three days at the same concentration that was used for the Sholl analysis, followed by the same protocol for fixation and staining. The results showed an increase in the network formation rate and its complexity for treated cells compared to the control (Fig. 2c, d ). This finding corresponded with data obtained from the Sholl analysis, indicating the positive role of F22 in promoting dendritic and axonal arborization as well as increasing the complexity of the formed neuronal network.
Liposome size measurement by dynamic light scattering (DLS). A Malvern Zetasizer Nano ZS (Malvern instruments, UK) was used to estimate nanoliposome size distribution. The solutions were mixed with ultra-filtrate distilled water (ratio of 1:400) and were placed in cylindrical cells (10 mm diameter). The scattering intensity was measured at an angle of 173° relative to the source at 25 °C. Intensity autocorrelation functions were analyzed by a general purposed algorithm (integrated by the Malvern Zetasizer software). An average of five different measurements are reported as the size of nanoliposomes.
Hoechst (33342, 2. 5 mg/ml, Sigma) was added to stain cell nuclei. The primary antibodies used here include polyclonal anti-neuronal class III β -tubulin (#T2200, Sigma), monoclonal anti-glial fibrillary acidic protein (GFAP) IgG (#G3893, Sigma). Fluorescent-conjugated secondary antibodies were obtained from Molecular Probes (Invitrogen) and used for staining. An upright Leica TCS SP5 AOBS TANDEM confocal microscope was used for image acquisition from regular and MEA cultures. Images were further processed by using ImageJ and Adobe Photoshop CS3 software.
Morphological analysis of cortical neurons. To analyze the neurite growth and branching, cells were treated with 100 μ g/ml F22 for 3 days and were then fixed and stained with anti-β -III tubulin antibodies. Neurites were identified using the NeuronJ plugin of the ImageJ software. The Sholl plugin for ImageJ was used to perform Sholl analysis with the starting radius 10 μ m, radius step size 5 μ m, and ending radius 500 μ m. Details of image analysis of neural network formation is provided in the Supplementary Information. Multielectrode array (MEA) spike analysis. Cortical neurons were cultured on MEAs as described above. Network activity was recorded using the commercially available 60-channels MEA filter-amplifier system (0,1 Hz-25 kHz, 1200× amplification, MEA1060-upright-standard, MCS) with an A/D conversion card (64-channels, 25 kHz sampling frequency/channel, PCIbus) and software interface (MC_Rack, MCS).
Multiplex cytokine assay Freshly excised hippocampi from P14 and P75 rats (24 h after ventral hippocampal injection) were homogenized and total protein was extracted in PBS supplemented with protease inhibitors (Roche Diagnostics, Meylan, France). After a 12500-rpm centrifugation for 30 min, supernatants were collected. IL-1β, interleukin 6 (IL-6), tumor necrosis factor α (TNFα), and interleukin 10 (IL-10) levels were measured in microglia supernatants and hippocampal protein  extracts using a Bio-plex 200 and a 96-well magnetic plate assay according to the manufacturer's instructions (Biorad Laboratories, Marnes la Coquette, France). All samples were run in duplicate, and data were analyzed using Bio-Plex Manager software. For hippocampal measurements, cytokine levels were expressed relative to total protein levels (pg of cytokine/mg of total protein).
Electroencephalograms (EEGs) were acquired using the MP100/EEG100B acquisition system and AcqKnowledge software (BIOPAC, Santa Barbara, CA, U. S. A. ). The electrical stimulus used for the assessment of the ictogenesis parameters and the kindling protocol was a square wave biphasic electrical stimulus with the following characteristics: 10-second train duration, 20 Hz, 1-ms pulse duration, delivered every 5 min. At 24 and 48 h post-injection, afterdischarge threshold (ADT) and afterdischarge duration (ADD) were assessed using 0. 1 mA incremental currents delivered every 5 min. An AD was defined as paroxysmal epileptiform activity lasting at least 5 s with peak-to-peak amplitude of at least twice the baseline background EEG observed after the end of the hippocampal electrical stimulation. The kindling protocol consisted of 60 trains delivered every 5 min with a current of 0.
Apparatus A DLP video-projector (ACER H5360, 1280 Â 720 pixels) displayed the stimuli on a projection screen (170 Â 150 cm, ORAY). The participants wore 120 Hz active shutter glasses (NVIDIA 3D Vision Pro) to fuse the left and right views. The framerate was 60 Hz per view. The black level was 1. 91 cd m À2 on the screen and was reduced to 0. 02 cd m À2 when measured through the glasses, using a spectroradiometer (Minolta CS1000). The crosstalk percentage measured as x ¼ leakageÀblack level signalÀblack level  (Woods, 2012)  was less than 0. 1% in the two eyes. To simulate distortions in the horizontal and vertical disparity fields created by a specific cameras configuration, we used virtual cameras. Stimuli were designed using OpenGL and were displayed using the PsychToolbox extension for MATLAB  (Brainard, 1997; Pelli, 1997).
Correlation Analysis: Distance Versus Depth To further study how cameras configuration can affect distance and depth perception together, we compared data on perceived depth and data on perceived reachable distance (Figure  9 ). A correlational analysis was indeed justified by the fact that perceived depth from disparity depends on an estimate of distance. First, we analyzed the depth ratios observed in Experiment 4 and the distance ratios (perceived reachable distance over actual reachable distance) computed from Experiment 2. We performed the correlation over individual data so as to study how the depth-distance relationship fluctuates with changes in the cues to distance. We found a positive correlation between the depth ratios and the distance ratios (Pearson's coefficient R ¼. 38, p <.
3. Patch-clamp recordings in vivo were performed blindly, and the positions of recorded neurons were identified during post hoc reconstruction of the DiI trace of the recording pipette on 100-m-thick coronal brain sections. During recordings from brain slices in vitro, patchclamp recordings were performed 100 -200 m below the slice surface to avoid sampling of neurons within the damaged zone  (Dzhala et al. , 2012). The signals were digitized at 10 kHz using a Digidata 1440 analogto-digital converter (Molecular Devices). To monitor the excitatory/inhibitory effects of GABA under various experimental conditions in wild-type mice in vitro, we examined the responses evoked by local puff application of GABA in visually identified L5/6 neocortical cells recorded in loose cell-attached mode with ACSF in the pipette solution.
All reagents were purchased from Sigma-Aldrich and Tocris Bioscience. Data analysis. pCLAMP 10. 1 (Molecular Devices), Mini Analysis 6. 0. 7 (Synaptosoft), Origin 7. 0 (Microcal Software), and custom-written functions in Matlab (MathWorks) were used for data acquisition and analysis. The response time window was calculated individually for each recorded neuron. The onset and the end of responses were determined as time points corresponding to the maximum and minimum of the curve obtained after subtraction of the cumulative peristimulus time histogram from the diagonal reflecting constant event frequency  (Mitrukhina et al. , 2015). Nonoverlapping unitary glutamatergic EPSCs (Glu-EPSCs) were manually selected for the EPSCs' amplitude measurements. The statistical significance of differences between groups of data was assessed using the Wilcoxon signed-rank test and Mann-Whitney test.
(d) Generalization-gradient modelling We analysed the behavioural responses by fitting a simple model of Gaussian excitatory and inhibitory generalization gradients for the CSþ and the CS2, respectively. To this end, we fitted for each experiment a Gaussian function G s with maximal amplitude 100, standard deviation s and centred on the CSþ, to the response percentages obtained after absolute conditioning. Simultaneously, we fitted the product G s Â (1 2 G s 0 ) to the data obtained after differential conditioning, with G s 0 being centred on the CS2. This constituted a two-parameter fit (of s and s 0 ) to eight data points (four from absolute conditioning and four from differential conditioning). The fit was performed as a least-mean-squares fit with the lsqnonlin function in MATLAB (Natick, MA, USA).
However, when we measured sperm methylation of this downstream region, it was not correlated with paternal age (data not shown). We first developed genotyping pyrosequencing assays for bisulfite-treated DNA which can determine the SNP sequence and at the same time quantify methylation of several individual CpGs in the target region. Both the FOXK1 and the KCNA7 assay showed significant correlation between FCB methylation and paternal age (data not shown). For FOXK1, we identified 21 informative duos which were heterozygous for rs9791644 in the offspring (FCB) and homozygous in the father (sperm). For KCNA7 (rs117676231), only nine such sperm-FCB duos were found. DBS  Sequencing primers were specific for rs9791644 (G/A) with one containing an A and the other a G at the 3' end (Supplementary Material, Table  S8 ).
Bisulfite pyrosequencing The PyroMark Assay Design 2. 0 software (Qiagen, Hilden, Germany) was used for primer design (Supplementary Tables  S2  and S3 ). Assays were established using standard DNAs with 0, 25, 50, 75, and 100% methylation. PCR was performed in 25 ml reactions consisting of 2. 5 ml 10x PCR buffer with MgCl 2 , 0. 5 ml dNTPs, 1. 25 ml (10 pmol/ml) of each forward and reverse primer, 0. 2 ml FastStart Taq DNA polymerase (Roche Diagnostics, Mannheim, Germany), and 1 ml ($25 ng) bisulfite converted DNA. Pyrosequencing was performed on a PyroMark Q96 MD system using the PyroMark Gold Q96 CDT reagent kit and Pyro Q-CpG software (Qiagen, Hilden, Germany). In our experience, the average methylation difference between technical replicates (including bisulfite conversion, PCR, and pyrosequencing) is approximately 1-2 percentage points.
DNA quality was checked on the Bioanalyzer with the DNA 7500 LabChip kit. Amplicons were quantified using the NanoDrop 2000c spectrophotometer, pooled, and diluted to 1x 10 9 molecules/ll. The bisulfite amplicon libraries (generated by emulsion PCR) were sequenced on a Roche/454 GS Junior system following the manufacturer's protocol. The sequence reads were processed using the Roche Genome Sequencer software and SFF files were further analysed using the Amplikyzer software  (58). Target regions included a single nucleotide polymorphism (SNP) to distinguish between parental alleles. Each DBS run included DNA standards with 0, 50 and 100% methylation. Processing of standard flowgram files (SFF) has been performed using the Amplikyzer pipeline which directly aligns the intensity sequences from SFF files to amplicon reference sequences and provides a detailed nucleotide-level analysis including the calculation of CpG methylation rates.
Analogously, bisulfite pyrosequencing data of autism patients have been analysed using a linear model including age (as categorical variable with three age classes, 2-5, 5-10 and 10-20 years). To control for varying variance across observations a heteroscedasticity-corrected covariance matrix ('hc3') has been used as described in Long and Ervin  (61)  and implemented in the car package  (62). For DBS, processing of standard flowgram files (SFF) has been performed using the Amplikyzer pipeline (58) which directly aligns the intensity sequences from SFF files to amplicon reference sequences and provides a detailed nucleotide-level analysis including the calculation of CpG methylation rates. The direct use of SFF information, without prior conversion to FASTQ format avoids information loss by rounding flow intensities.
Acknowledgements The authors thank  Dr. Michael Rehli  for providing the pCpGL vector,  Dr. Douglas Carrell  and  Dr. Timothy Jenkins  for unpublished information on sperm DMRs, and  Professor Almut Schulze  for SH-SY5Y cells. We sincerely thank all IVF/ICSI couples who participated in this study. R. P. was supported by a grant of the  German Excellence Initiative  to the  Graduate School of Life Sciences, University of Wu ¨rzburg.
The stimulus screen consisted of a fixation point, one circular gray disk with a 3D-shape stimulus and another with a random-lines stimulus (with randomized positions on the left and right of fixation for every trial). One disk had a fixed contrast level and the other a variable contrast value around that level (randomly assigned on every trial). Subjects were instructed to compare the luminance of the two disks. No feedback was given after the response. (B) Comparison of the grand average psychometric functions (when pooling data over all subjects). Each curve represents the selection probability of the variable disk when this disk contained the 3D-shape (green) or the random-lines stimulus (red). Error bars represent standard error of the mean (SEM) across subjects (C) Psychometric shift for each subject and mean across subjects.
(C) Comparison of psychometric shift for the same subjects in the main experiment and during the attention bias control, either including all trials, or only those in which the counting task was performed correctly. Similar psychometric shift was obtained for all conditions, indicating that attention bias is unlikely to explain our findings. Error bars represent SEM. We found that the effect was not reversed by the change of contrast polarity (Fig. 3 ). The psychometric shift for this control experiment was 3. 23% ± 4. 44% (average ± standard deviation across subjects; N= 10 including 4 participants from the main experiment); the grand average psychometric shift (when the psychometric functions were computed from the grand-average data across participants) was 3. 1%. A one-sample Student's t-test showed that this effect was incompatible with a full reversal (null hypothesis of a psychometric shift of -8.
Data analysis The trials were classified into two categories: either the 3D-shape disk had a variable luminance value, or the random-lines disk had a variable luminance value. For all experiments except the same/different luminance experiment, for each trial type, the selection probability of the disk with the variable luminance value was computed, separately for each variable luminance value. Two psychometric functions were generated, one for each trial type, expressing the selection probability as a function of the variable luminance value, and fitted using normal cumulative distribution functions (each pair of psychometric functions was fitted with Gaussian cumulative functions with six parameters: mean and standard deviation separately for each psychometric function, and a common guess rate and lapse rate for both functions; the guess rate was set in the range of [0,1] and the lapse rate was set in the range of [0, 1-guess rate], which limited the maximum and minimum values of the psychometric functions to 1 and 0, respectively).
We used the following marker proteins: clathrin  57  and caveolin  58  as markers for endocytic structures; EEA1 (ref. 59), Rab4 and Rab5 (refs 60,61) for early endosomes; Rab11 for recycling endosomes  62  ; Rab7 for late endosomes  63  ; LAMP1 for lysosomes  31  ; the secretory pathway Ca 2 þ -ATPase (SPCA1) for Golgi  64  ; the sarco/endoplasmic reticulum Ca 2 þ -ATPase (SERCA2) for endoplasmic reticulum  65  ; and vesicular stomatitis virus G-protein, a widely studied marker for the secretory pathway  66. SPCA1 and SERCA2 contained GFP coupled to their N termini, while all other marker proteins had GFP coupled to their C termini. Analysis fluorescence intensity and of the speed of moving structures was performed with AxioVision 4. 8 digital image processing software (Zeiss). Quantification of particle size and number was performed with Imaris software (Bitplane).
Measurement of intracellular Ca 2 þ concentration ([Ca 2 þ ] i ). Changes in [Ca 2 þ ] i in HEK293 cells and TGN were monitored using ratiometric Fura-2-based fluorimetry. Cells were loaded with 2 mM Fura-2AM-ester (Alexis Biochemicals) for 30 min. Fluorescence was measured during repetitive illumination at 340 and 380 nm using the filter-based MT-10 illumination system and xcellence pro software (Olympus). Absolute calcium concentrations were calculated from the ratio of the fluorescence signal at both wavelengths was calculated  67. Whole-cell patch-clamp recordings. After 16 h of transfection, currents in HEK293 cells were recorded in the whole-cell configuration of the patch-clamp technique using an EPC-9 amplifier and Patchmaster software (HEKA Elektronik). Data were sampled at 5 kHz and digitally filtered off-line at 2 kHz.
Acknowledgements We acknowledge all members of the  Laboratory of Ion Channel Research  for helpful discussions. We thank  Hoaxing Xu  and  Peter Vangheluwe  for providing us cDNA clones for various marker proteins. This work was supported by grants from the  Belgian Federal Government  ( IUAP P7/13 ), the  Hercules Foundation  ( AKUL-029 ), the  Research Foundation-Flanders  ( G. 0565. 07 )and the  Research Council of the KU Leuven (PF-TRPLe ).
fMRI analysis Preprocessing used the fMRI Expert Analysis Tool version 5. 98 software, part of the FMRIB Software Library, version 4. 1 (www. fmrib. ox. ac. uk/fsl), as described  (4, 28). The average (median) BOLD signal for the contrast highenergy food greater than object and low-energy food greater than object were calculated for each subject at each visit in these functional regions of interest (fROIs): amygdala, nucleus accumbens, anterior insula, and caudate nucleus  (4, 28). The fROIs were determined from a separate cohort of 24 overweight/obese subjects who underwent an identical protocol after fasting overnight, without administration of octreotide/Insulin, for the food (high energy or low energy) greater than object contrast at voxelwise false discovery rate corrected P Ͻ. 05, as previously described (4) (and see Supplemental Methods).
Acknowledgments We thank  Mr Ahmed Ahmed  and  Mr Torsten Olbers  (consultant bariatric surgeons) and other staff of  Imperial Weight Centre ; the staff of  Sir John McMichael Centre  ( Imperial College Healthcare National Health Service Trust, London ); and  Professor Alan C. Spector  and  Drs Mat Arimin ,  Aftab Khattak ,  Gadintshware Gaoatswe , and  Adam Waldman  for their assistance with the studies. Address all correspondence and requests for reprints to:  Dr Tony Goldstone, MRCP, PhD ,  Centre for Neuropsychopharmacology ,  Room E313 , 3rd Floor,  Burlington Danes Building, Division of Brain Sciences, Imperial College London ,  Hammersmith Hospital ,  Du Cane Road , London  W12 0NN , United Kingdom. E-mail: tony. goldstone@imperial. ac. uk. The views expressed are those of the authors and are not necessarily those of the supporting institutions, the  National Health Service , the  National Institute for Health Research , or the  Department of Health.
Acknowledgements This work was supported by the  Institute National de la Santé et de la Recherche Médicale, le Centre National pour la Recherche Scientifique, University of Poitiers, Mission Interministérielle de la Lutte contre les Drogues et la Toxicomanie  ( MILDT-INSERM-INCA 2007-2009 ) and the  Contrat de Projet Etat Région (CPER)  no. 5.
Materials and Methods In order to thoroughly explore the role of the cannabinoid system in the retina, a search for relevant articles was conducted in the PubMed, ScienceDirect, and Google Scholar databases using the following keywords: ("cannabinoid system" or "endocannabinoids" or "cannabinoids" or "cannabinoid ligands" or "cannabinoid receptors" or "cannabinoid enzymes") and ("neurotransmission" or "neuroplasticity" or "neuroprotection") and ("retina" or "retinal"). All results up to June 1, 2015, were examined for the selection process. Relevant publications were chosen through an individual independent selection of titles by the following authors: Thomas Schwitzer, Raymund Schwan, Anne Giersch, and Vincent Laprevote. The articles selected had to be written in English and be related to the topic of the review.
Acknowledgments The authors thank the company  Metrovision (Pérenchies, France)  for its collaboration, the  French National Research Agency  (Grant  ANR-12-SAMA-0016-01 ) and the  French Mission Interministérielle de Lutte contre les Drogues et les Conduites Addictives (MILDECA)  for their support, and  Coline Jeantet  for her contribution to this work.
Statistics Statistical analysis was carried out using IBM SPSS software version 23. The validity effect was investigated with a threeway mixed factorial ANOVA with Group (adults, children) as a between-subjects factor and Cue type (space, time) and Validity (valid, invalid) as within-subjects factors. The validity effect was calculated using data from the 500 ms FP trials only to avoid confounding the temporal validity effect with Variable FP effects. In cued RT paradigms, the probability of target appearance increases with the length of the FP -the "Hazard Function"  (Luce, 1986 ) -which leads to faster RTs at longer FPs  (Woodrow, 1914)  -the "Variable FP effect"  (Niemi and Näätänen, 1981). In temporal orienting paradigms, the RT benefits of the Hazard Function render the RT benefits of the temporally valid cue negligible at long FPs  (Coull and Nobre, 1998; Coull et al.
Statistics Statistical analysis was carried out using IBM SPSS software version 23. The validity effect was investigated with a threeway mixed factorial ANOVA with Group (adults, children) as a between-subjects factor, and Cue type (Space, Time) and Validity (valid, invalid) as within-subjects factors. As in Study 1, only the 500 ms FP trials were analysed. Please refer to Table  2  for the 1100 ms data. The FP and sequential effects were investigated with a three-way mixed factorial ANOVA involving Group (adults, children), FP of the current trial, i. e. , FP(n) (500, 1100 ms), and FP of the previous trial, i. e. , FP(n -1) (500 and, 1100 ms), on the neutral trials only. The alpha level was set at 0. 05 and Bonferroni-adjustments were made for pair-wise comparisons.
Acknowledgments We express our thanks to  Corey Butler  for discussions and corrections of the manuscript. This work was supported by the  ANR NanoDom, Labex BRAIN , and  ANR-10-INBS-04   FranceBioImaging ,  Centre National de la Recherche Scientifique ,  ERC  Grant  ADOS 339541  to D. C. and a fellowship from the  MESR  to B. C. The authors have no relevant financial interests in this paper and no other potential conflicts of interest to disclose.