dataesr/scientific-paragraphs-categorization huggingface dataset:
We thus measured the production of ROS by WT, DAP12deficient and CD11b-deficient microglia co-cultured with mesencephalic neurons challenged or not with MPP +. As expected, exposure of neuron/microglia co-cultures with MPP + induced a significant increase in the intensity of ethidium production by microglial cells (17. 2% ± 1. 3%, P = 0. 006, Dunn test) (Figure  1D ). Yet, the same increase was detected when DAP12-or CD11b-deficient microglia were co-cultured with WT neurons (DAP12 KI: 15. 1% ± 0. 9%, P = 0. 752; CD11b KO: 15. 0% ± 0. 7%, P = 0. 261 compared to WT microglia; Dunn test). This result shows that in contradiction with a previous in vitro study  [5] , the production of ROS following stimulation of microglia by MPP + -induced DN injury is not dependent on DAP12 or CD11b. Increased DAP12 and CD11b expression in the substantia nigra parallels DA neurons degeneration upon 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxication Our in vitro data show that DAP12 and CD11b contribute to the toxicity of microglia stimulated by MPP + -induced dopaminergic injury.
In control DAP12 +/+ mice, we found that MPTP injection induced a significant death of TH-positive neurons as well as the loss of striatal TH + -dopaminergic fibers when compared to saline-injected animals (Figure  4A ). Surprisingly however, alteration of TH-positive neurons and TH-positive fibers induced by MPTP injection in the DAP12 KI or in the CD11b -/-mutant mice, was the same as those observed in their WT littermates (Figure  4A  and B ). These results show that DAP12 and CD11b are not involved in the death of DN in the MPTP mouse model of PD using a subchronic mode of intoxication. These results seem in contradiction with our in vitro data and to a previous study showing that CD11b deficiency attenuates the DN death upon sub-chronic intoxication of mice by MPTP. Whether such discrepancy may be related to the mode of dopaminergic injury and intensity of microglial cell activation and neuroinflammation was then tested by applying an acute regimen of MPTP intoxication.
Acknowledgements We thank  C. Lobsiger ,  P. P. Michel  and  S. Guerreiro  for helpful discussions and technical advices. This work was funded in part by the  Institut National de la Santé et de la Recherche Médicale  ( K. Kinugawa ). The research leading to these results has received funding from the program " Investissements d'avenir "  ANR-10-IAIHU-06  and from the  7th Framework Program Moodinflame  ( 222963 ).
The average spectra of two species were considered different when the spectral angle was bigger than the inner species variability of the respective vector bundles. Statistics. All normally distributed data are expressed as mean Ϯ SD, and the t test was used for testing the significance of p values. Non-normally distributed data were compared using their median Ϯ absolute deviation and nonparametric tests (Kolmogorov-Smirnov). All statistics used MATLAB (MathWorks). *p Ͻ 0. 05; **p Ͻ 0. 01; ***p Ͻ 0. 001; n. s. , not significant.
Discussion Our data provide no evidence in favor of the expression of any of the three vesicular glutamate transporters (VGLUT1-3) by the gray matter protoplasmic astrocytes found in the primary somatosensory cortex and the thalamic VB nucleus, as well as the hippocampus and the cerebellum. We first used VGLUT1-3 KO mice, VGLUT1 Venus KI, immunostaining, and Western blots, and we could not detect the expression of VGLUT1-3 in cortical and thalamic astrocytes in culture (Figs. 1 2 3 4 5 ). Second, using immunostaining and confocal imaging of brain slices, we quantified the degree of overlap between VGLUT1-3 and neuronal or astrocytic markers with fluorescence line profiles, dual-color scatter plots, and Pearson's correlation coefficient analysis, again finding no evidence for colocalization between VGLUT1-3 and astrocytic markers.
Polymorphism Detection and Analysis Previous gene expression analyses  [17]  did not detect expression of TRPM1 in the skin and retina of LP/LP CSNB individuals, suggesting that transcription of this gene was disrupted. However, when comparing raw read counts, we identified novel expression within intron 1, having 85 reads in the skin and 460 reads in the retina of the LP/LP horse compared to 0 and 4 reads (in the skin and retina respectively) of the lp/lp horse (Figure  3 ). De novo assembly of this transcript followed by PCR and genomic DNA sequencing identified a 1378 bp insertion in intron 1 (ECA1g. 108,297,929_108,297,930 ins1378) of TRPM1. In order to characterize this insertion we performed a blast analysis using RepeatMasker  [27]  (Figure  S2 ). This insertion is a long terminal repeat (LTR) of an endogenous retrovirus (ERV) class II retroelement and is characterized by flanking regions of microhomology, indicative of non-homologous end joining double stranded break repair as the mechanism of insertion (Figure  4A  and Figure  S2 ).
ucsc. edu/cgi-bin/hgGateway? hgsid=2633482&clade=mammal&org=Horse&db=0). RNA-Seq data was submitted as studies to the Sequence Read Archive (SRA at the European Nucleotide Archive http://www. ebi. ac. uk/ ena/ and can be found at http://www. ebi. ac. uk/ena/data/view/ ERP001524 and http://www. ebi. ac. uk/ena/data/view/ ERP001525 (Accession numbers. ERP001524 and ERP001525).
Bioinformatics analysis of ORFs The transcript sequence from the LP/LP pigmented skin sample was translated using the Sequence Manipulation Suite  [66]. All identified ORFs were analyzed using BLASTP against the nr database at www. ncbi. nlm. nih. gov. These ORFs were further analyzed using the Protein Function Prediction server  [33]  available at http://kiharalab. org/web/pfp. php and the Extended Similarity Group server  [34]  available at http:// kiharalab. org/web/esg. php. Only probability scores greater than or equal to 60% were retained for the predicted molecular function and biological process.
5% glutaraldehyde, and processed for transmission electron microscopy. Ultrathin sections were observed and photographed using the Jeol 100 electron microscope (Tokyo, Japan) at the UW Electron Microscope Facility. Quantitative RT-PCR. Total RNA was isolated using RNeasy mini kit (Qiagen, Valencia, CA). Total RNA (1-3 µg) was reverse transcribed using the SuperScript III First-Strand Synthesis system for RT-PCR (Invitrogen). Primers for TRPM1 and β-actin were designed using PrimerExpress software (Applied Biosystems, Foster City, CA) and obtained from IDT Inc. (Coralville, IA). The primer sequences and the calculated amplicon length are represented in Table  S4. qPCR was performed in triplicate with SYBR Green PCR core reagents (Applied Biosystems), in 20 µl of reactions containing 50-150ng cDNA and 10µM each primer.
After washing with PBS, coverslips were mounted using a mounting medium containing anti-fade reagent (Molecular Probes, Invitrogen). Calcium imaging. Melanocytes plated on glass chamber slides were washed in buffer D (153mM NaCl, 5. 4mM KCl, 1. 8mM CaCl 2 , 10mM N-2-hydroxy ethylpiperazine-N'-2ethanesulfonic acid (HEPES), 25mM glucose, 0. 8mM MgSO 4 , 0. 9mM NaH 2 PO 4 and 2. 4mM NaHCO 3 , pH 7. 4), incubated in 2 µM Fura-2 (Invitrogen) in buffer D at 37°C for 60 minutes, washed three times with buffer D without calcium and deesterified for 30 minutes at 37°C. Cells were imaged and ratio of fluorescence emission was monitored using Nikon Ti fluorescence microscope and NIS-Elements software. In a 20x field with well separated cells (n=8-10), baseline was established in buffer D without Ca 2+ and change in F340/380 was monitored after addition of various reagents or Ca 2+ for a total of 15 minutes with no cell exposed to light for longer than 20 min.
Acknowledgements The authors wish to thank all of the horse owners who provided hair and skin samples for nucleic acid extraction and for melanocyte culture work. We would especially like to thank those owners who donated their horses for retinal research purposes. We are grateful to  Dr. Jay Clifford  and  Mr. Richard Grist  for their assistance with skin biopsy collections. We thank  Karla Brown ,  Cathryn Cuka ,  Taryn Cranford ,  Elizabeth Kowalski , and  Scott Lawson  for technical assistance as part of their  Independent Study Courses at the University of Tampa.
Physical Model for Current Propagation In order to map the spatial distribution of the electric field on the cortical surface, we built a physical model for current propagation using a three-step approach. First MR images were segmented. For this purpose we used T1 and Proton Density (PD) phantom images based on the Colin27 template (http://www. bic. mni. mcgill. ca/brainweb). Segmentation was performed using the BrainSuite software (http://www. loni. ucla. edu/Software/BrainSuite, [22] [23] [24] [25] ). White matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) were segmented from the T1 images whereas the skull and scalp were obtained from the PD images. The resulting masks were used to generate surface meshes representing the boundaries between the different tissues. The mesh of WM-GM interface had 189494 triangles and 94743 vertices (average area of triangles 1.
036 mm2, maximum 3. 832 mm2, minimum 0. 008 mm2) and is shown in figure  2B. Secondly, a volume mesh representing the whole head was generated from the surface meshes using MIMICS (http://www. materialise. com/). At this stage, virtual tDCS electrodes were also incorporated into the model. The anode and the cathode could be placed at any of the positions defined in the 10-10 International System. The resultant mesh comprised more than 1. 9610 6  tetrahedral second order Lagrange elements (Figure  2A ). Thirdly, the volume mesh was imported into a finite element program to calculate the electric field (Comsol 3. 5a, www. comsol. com). The upper surface of each electrode was set to uniform electrical potential and the potential difference between them was adjusted to reach the desired custom amplitude of injected current through the anode.
The position of the center of each eye in space was measured on-line using a LaserBird optical head tracker (Ascension Technology, Burlington, VT). The sensor (weight 40 g) was mounted on a light but tightfitting helmet, which the participants wore on their heads. The head tracker provides the 3D position and orientation of the sensor, at a sampling frequency of 240 Hz, in the reference frame of the LaserBird scanner. These data were converted to the reference frame of the monitor by means of a specially developed calibration procedure involving touching the sensor to the monitor surface. The position of the eyes relative to the sensor was measured for each participant using another specially developed procedure, in which the participants optically aligned each eye with two sets of two points on a planar object.
The initial orientation of the background was calculated in order to obtain orientations symmetrical about the frontoparallel at the beginning and the end of the trial. The two stimulus planes were projected onto the darkest possible background on our monitor. Participants wore sunglasses, inside the stereo shutter glasses, to further attenuate this background light, but the ''black'' background was nevertheless slightly visible (i. e. , participants could faintly perceive the monitor's edges). The duration of the stimulus was 800 ms. Each trial had fixed values of foreground object and background velocities (V o and V b , respectively). Velocity values within a block were determined using a factorial design with randomized order. In order to generate each eye's image, data from the motion tracker were polled immediately before each stereo pair was drawn (i.
Use of visual reference by an immobile observer In order to determine the role of the background as a visual reference, we first analyzed the data from the condition in which the subject was immobile and the background was present (rotating or stationary). ''Right'' responses are coded as þ1, ''Left'' as À1. An example of mean responses for one subject, as a function of object velocity V o , for two extreme values of background velocity V b , is shown in Figure  3a. Both object and background velocities are expressed in an earth-fixed reference frame. For each background velocity V b , we fit responses to a logistic function of V o : RðV o Þ ; r kðV o À uÞ ½ ; where r ¼ 2=ð1 þ e Àx Þ À 1 ð1Þ The regressions were computed using the maximumlikelihood model  (Wichmann & Hill, 2001). We used a prior distribution on the slopes k, in which we assumed that probability is approximately uniform for k , k max and then decreases, where k max is equal to the slope obtained by going from one extreme value of mean response to the other between two adjacent values of V o -this is the largest slope value that can be supported by the discrete nature of our independent variable.
Mobile condition Participants' movement: Before describing the results in the mobile condition, we first present data on participants' movement. Because the movement was  voluntary with only some control, details of the trajectories varied from subject to subject and trial to trial. In order to describe the trajectories, we defined the following axes for the earth-fixed reference frame: the x and y axes were parallel to the monitor and point rightwards and upwards from the subject's point of view, and the z axis was perpendicular to the monitor, pointing towards the subject. On each frame, we defined the subject's position as the midpoint between the eyes. First, we calculated the discrete path length of the subject's movement, the sum of absolute displacements in all three dimensions from frame to frame, while the stimulus was visible.
Moving observer and background We have already shown that both a visual reference (for a stationary observer) and self-motion (in the absence of visual reference) can influence motion perception. We next analyzed data from trials with both a visual reference and observer motion, to check for a possible interaction between these two factors. The regression formula is a generalization of the previous regression models, including both the V b and V s terms: RðV e ;V b ;V s Þ ; r kðV e À aV b þ bV s À uÞ ½ ð 4Þ The fitted values of the a and b parameters and their confidence intervals are shown in Table  3. As in the immobile condition, individual a values were signifi-cantly different from both 0 and 1 for every subject. A t test across subjects likewise showed that the mean value a ¼ 0. 43 was significantly different from both 0 and 1.
Results We analyzed the data using the same model as in the immobile condition of Experiment 1. We extracted the parameter of interest, a, the gain of background movement in subjects' motion judgments. For each subject, as in Experiment 1, we found that a values were significantly between 1 and 0 (see Table  5 ). Values of a above 0 mean that the object velocity was perceived relative to background velocity; a values below 1 indicate that the use of the background was partial. The mean value of a in Experiment 2 was slightly higher than in Experiment 1, but the difference was not significant.
Records of childhood infections and illnesses were obtained from formal examinations by a paediatrician at the end of the first, third and fifth years. During the school years, visits were made at least once a year to record height, weight and any health problems up to the age of 15 years in 1962. Additional data from GP and hospital consultations were provided to the study team. Infections from birth to 13 years, and considered in analyses, consisted of measles, mumps, whooping cough, scarlet fever, chicken pox, rubella, tuberculosis and ear infections. Respiratory infection during the first year of life included tonsillitis, bronchitis and pneumonia. Infection events, for all but ear infections, were collated for each individual and grouped into "ever had a specified infection" or "never had a specified infection".
Ear infections were not grouped due to the larger range of numbers of infections seen, so are included as counts. Hearing thresholds were assessed at age 14 years (1961-62) and measured for 147 study members using pure-tone audiometry at eight frequencies between 250 Hz and 8 kHz and recorded on Amplivox audiogram forms. In line with current British Society of Audiology guidelines, hearing thresholds better than 0 dB HL (i. e. negative values) were given a zero value. An intra individual average (IIA) hearing threshold was calculated as a weighted mean between the 'best' and 'worst' ear measurement in the ratio 4:1  [26]. Pure tone average (the average of 500 Hz, 1 kHz, 2 kHz and 4 kHz) in both ears was also calculated  [27]. Ethical approval for the study was obtained from the appropriate local research ethics committees, the lead of which was the Joint Newcastle Health Authority / University of Newcastle upon Tyne Ethics Committee (ref 94/146), for the analysis of the data and all participants and a parent or legal guardian gave their informed consent at the time of the original data collection.
Outlier analysis Residuals were checked in line with standard checks of linear regression assumptions. One study member had outlying data with high IIA hearing thresholds at all frequencies (range 32-47 dBHL) and a short gestation period (31 weeks). Looking at hearing thresholds separately for each ear at each frequency, the individual had significant unilateral hearing impairment and thus gave a high leverage point in regression diagnostics (shown in leverage versus residual squared plots). Further to the associations previously outlined when this study member was included, birth weight (standardised for sex and gestational age) was significantly and negatively associated with IIA hearing thresholds at frequencies 250 Hz, 500 Hz, 1 kHz, 3 kHz and 6 kHz. After adjustment for other significant associations standardised birth weight remained negatively associated with hearing thresholds at frequencies 250 Hz, 500 Hz, 1 kHz and 3 kHz, but again was limited to females.
However, this does not necessarily mean that associations found when this individual is included in analyses are invalid. The main strengths of this study are those of the dataset analysed, in particular the longitudinal nature, breadth of and completeness of data collated within the Newcastle Thousand Families study. Data were prospectively collected on early life experience, including gestational age, parity and socio-economic circumstances at birth, as well as other indicators of early life socio-economic, familial and nutritional status. Hearing thresholds at age 14 years throughout low to high frequencies were also assessed prospectively. This meant potential biases that may be introduced when using recalled information were eliminated. This study may also uniquely have assessed risk factors for non-noise induced hearing loss, as during the era in which these individuals were aged 0 to 14 years, it is likely that exposure to hazardous levels of noise would have been lower than for children today due to the inexistence of personal media devices and, probably for this age and era, much less exposure to heavily amplified music.
Briefly, a CASY cell counter (Scha ¨rfe systems) was used to measure the cell counts, 500 cells were plated on full media (YEPD) agar plates and CFUs were quantified after 2 days of growth using a Scanalyzer Colony Counter (LemnaTec). To measure the level of cellular oxidative stress, cultures were subjected to dihydroethidium (DHE) staining followed by quantification using a fluorescence reader after 24 h of a-synuclein expression as previously described  (Bu ¨ttner et al, 2007). DNA fragmentation was quantified after 36 h of a-synuclein expression using TUNEL staining as previously described  (Bu ¨ttner et al, 2007). For quantifications using flow cytometry (BD FACSAria), 30 000 cells were evaluated and analysed with the BD FACSDiva software. Same cells were visualized via epifluorescence microscopy with the use of a FITC filter (Zeiss) on a Zeiss Axioskop microscope.
The PCR products have a length of 1117 bp and 441 bp for the wild-type and the mutant alleles, respectively. Seven-day old animals were used for aSyn-induced neurodegeneration quantification. The four CEP dopaminergic neurons in the head of the worm were scored as described previously  (Qiao et al, 2008). Statistical analysis was performed using the GraphPad Prism software package (GraphPad Software Inc. ). For immunoblotting, worms were sonicated in lysis buffer (50 mM Tris-HCl (pH 7. 4), 1 mM EDTA, 1 mM PMSF, and protease inhibitor cocktail (Roche Diagnostics)) and centrifuged at 14 000 g for 20 min. Protein concentrations were determined by Bradford assay. Samples were boiled for 5 min in 3 Â sample loading buffer, resolved on 12% SDS polyacrylamide gel and transferred onto nitrocellulose membrane.
Image acquisition was performed with a confocal microscope (TCS SP5, Leica) using the LCS AF software (Leica). For immunoblot analysis, 20-30 fly heads were homogenized on ice in 50 ml 2% SDS with protease inhibitor cocktail (Roche Diagnostics). Equal volume of 2 Â La ¨mmli was added, samples were incubated at 951C for 5 min and then kept at RT for 5 min prior to centrifugation for 5 min at 13 000 g and subsequent SDS-PAGE analysis. Blots were probed with primary antibodies against a-tubulin (Abcam) and a-synuclein (Sigma) and respective secondary antibodies.
High-content analysis of a-synuclein aggregation and cell death We used the cell culture model described by  Gerard et al (2010)  to induce a-synuclein aggregation  (Gerard et al, 2010). Cells were plated in 96-well plates (1. 5 Â10 4 cells/well). The next day, cells were treated for 72 h with 100 mM H 2 O 2 and 5 mM freshly prepared FeCl 2 in DMEM complete and filtered through a 0. 20-mm filter (Corning Incorporated). After 3 days, cells were washed with PBS, fixed with 4% formaldehyde for 15 min and stored in PBS until analysis. Cells were incubated with 0. 05% Thioflavin S (Sigma-Aldrich) for 20 min and washed twice with 70% ethanol for 2 min. Next, the cells in the wells were incubated with DAPI (1:10 000 in PBS). To quantify a-synuclein aggregation and apoptosis in our synucleinopathy cell culture model, the IN Cell Analyzer 1000 and IN Cell Investigator software (GE Healthcare) was used as described before  (Gerard et al, 2010).
Acknowledgements This work was supported by the  Austrian Science Fund FWF  (grants  T414-B09  and  V235-B09  to SB,  S-9304-B05  to FM and DC-G, LIPOTOX,  P24381  and  P23490  to FM and DK-MCD to LH and FM), the  European Research Council (ERC , to NT), the  European Commission (Apo-Sys  to FM and TE), the research council of the KULeuven ( DBOF fellowship  to FM,  OT 08-052A ),  IWT-Vlaanderen (SBO NeuroTARGET  to JW and VB), and the  FWF  and the  Deutsche Forschungsgemeinschaft DFG  for grant  I2000  to FM and the  DFG, Excellence Initiative of the German Federal and State Governments  ( EXC 294  BIOSS; GSC-4 Spemann Graduate School to AAT). TE is recipient of an  APART fellowship  of the  Austrian Academy of Sciences  at the  Institute of Molecular Biosciences, University of Graz. In addition, this work is supported by grants to GK from the  Ligue Nationale contre le Cancer (Equipes labellisee) ,  Agence Nationale pour la Recherche (ANR) , the  Longevity Research Chair of the AXA Foundation ,  Association pour la Recherche sur le Cancer, European Commission (ArtForce) ,  European Research Council  ( Advanced Investigator Award ),  Fondation pour la Recherche Medicale, Institut National du Cancer, Canceropole Ilede-France ,  Fondation Bettencourt-Schueller , the  LabEx Onco-Immunology , and the  Paris Alliance of Cancer Research Institutes.