dataesr/scientific-paragraphs-categorization huggingface dataset:
However, a quantitative analysis of the database used by FVE, while confirming a strong hierarchical order, showed that, due to the absence of a distance measure, the FVE model of the visual cortex is indeterminate, with 150,000 equally plausible solutions  (Hilgetag et al. , 1996 (Hilgetag et al. , , 2000)). One possible method of constraining a model of the cortical hierarchy is to use quantitative data on connectivity, which has been shown to provide a measure of hierarchical distance  (Barone et al. , 2000). The structural regularities underlying the FVE hierarchy are thought to have a physiological underpinning. Many workers in the field subscribe to the notion that FF signals generate receptive field properties, while FB streams have a modulatory role  (Hup e et al. , 1998; Ekstrom et al.
Cortical counterstreams The Journal of Comparative Neurology | Research in Systems Neuroscience source and target areas, a model for all of the data can be specified in matrix form as gðEðY ÞÞ ¼ Xb; (2) where Y is a vector of length n containing the SLN values for each projection in the dataset (including possibly replicates of projections to the same area), b is a vector of length p containing the hierarchical levels to be estimated, and X is the n 3 p incidence matrix of the cortical graph revealed by the injections. An incidence matrix of a graph has one row for each edge and one column for each node of the graph. For the present dataset, it is constructed so that each row corresponds to a projection between two areas (e. g. , V2 ! V1, V4 ! V1, etc. ) and each column to an area (V1, V2, V3, etc.
The log likelihood of the model over the dataset is defined as: 'ðb; /; k; nÞ ¼ X i log fðl; /; k i ; n i Þ (5) Then, the hierarchical levels in the vector b and the dispersion u can be estimated using an optimization routine that minimizes the negative of '. Standard errors for each parameter are obtained from inverting the Hessian matrix, the second derivative of ' with respect to all pairs of the estimated parameters, evaluated at the maximum likelihood solution, and taking the square roots of its diagonal elements. In practice, we fitted the beta-binomial model to our data using the function betabin from a version of the aod package  (Lesnoff and Lancelot, 2012)  in the Open-Source software R  (R_Core_Team, 2012)  that we had modified so that it could use a probit link for the function g.
ACKNOWLEDGMENTS We thank  Delphine Autran ,  Souhila Zouaoui , and  Jennifer Beneyton  for data acquisition and histology;  Maud Kennedy-Brittain  and  Veronique Vezoli  for grant management and Administration;  Marco Valdebenito  and  Veronique Cortay  for animal husbandry; and  Louis Jan Pilaz  for computer software.
For the tests trials (D5 and D12), the escape box was removed and mice were allowed to explore the maze for 90 s. The number of visits (when a mouse dipped its head into a hole) into the target hole and the two direct adjacent holes were measured. CD3 ϩ/ϩ , CD3 ϩ/Ϫ , and CD3 Ϫ/Ϫ naive and grafted (42 d after graft) mice at 12 weeks of age were used for this study. Analyses were performed on 8 -11 animals per group. Data are presented as mean Ϯ SEM. Data analysis was performed using Excel and GraphPad Prism 5 software and statistical analyses were performed using two-way ANOVA with Bonferroni post hoc test. Object location memory task. The experimental apparatus used in this study was a square box made of opaque white plastic (50 cm ϫ 50 cm). The mice were first habituated to the box for 15 min and were then placed for 10 min in the box with four different plastic objects positioned in a defined spatial orientation (training).
Twenty-four hours later, the mice were placed in the same box with the same four objects, but two of them had switched locations (test). The time spent exploring the objects in novel and old (familiar) locations was measured for 10 min. Exploration of an object was assumed when the mouse approached an object and touched it with its vibrissae, snout, or forepaws. The object location preference was calculated as the exploration time of the old or novel location objects/total exploration time. Analyses were performed on 12week-old CD3 ϩ/ϩ (n ϭ 6), CD3 ϩ/Ϫ (n ϭ 4), and CD3 Ϫ/Ϫ (n ϭ 5) mice. Data analyses were performed using Excel and GraphPad Prism 5 software and statistical analyses were performed using two-way ANOVA with Bonferroni post hoc test.
Flow cytometry analysis Two, 6, and 8 weeks after BMT, grafted CD3 ϩ/ϩ (n ϭ 11) and grafted CD3 Ϫ/Ϫ (n ϭ 10) mice were anesthetized with 4% isoflurane (Forene) with 0. 8 L/min of O 2 and 300 l of blood was collected from the maxillary vein with a 20-gauge needle in an Eppendorf with 20 l of heparin. The same procedure was performed with 12-week-old naive CD3 ϩ/ϩ (n ϭ 7) and CD3 Ϫ/Ϫ (n ϭ 9) mice. After red cell lysis, peripheral blood cells were suspended in FACS buffer (10 g/L BSA and 0. 1% azide in PBS) and stained for 30 min for extracellular markers with antibodies for CD45. 2 conjugated to fluorescein isothiocyanate (FITC, 1 g/ml; BD Biosciences), and CD3 (2 g/ml; BD Biosciences) or TCR␤ (1 g/ml; BD Biosciences) conjugated with phycoerythrin. Labeled cells were analyzed with a FACS LSR II (BD Biosciences) and FlowJo software (TreeStar).
Image analyses and quantification Images were acquired with 63ϫ, numerical aperture (NA) 1. 4 oilimmersion objective using a digital camera (AxioCam HRC; Zeiss) driven by AxioVision Release 4. 2 software. For 3D reconstruction, highresolution confocal image stacks were acquired using a Leica SP1 laser scanning microscope equipped with argon 488 nm, DPSS 561 nm, and He-Ne 594 nm lasers and a 63ϫ, NA 1. 4 oil-immersion objective. In each sample, the two fluorophores (Alexa Fluor 488 paired with Alexa Fluor 594) were imaged separately using sequential scanning to eliminate the possibility of overlapping emission. The step size of the z-stack was 0. 25 m. The 3D reconstruction was performed using Amira 3D V4. 1 Software (Visualization Sciences Group). The quantification was performed using ImageJ software.
The number of CaMKIIimmunoreactive spines was counted in two dendrites of each selected neurons. A total of 30 -40 neurons were analyzed for each experimental condition from three to four independent cultures. Data analysis was performed using GraphPad Prism 5. 0 software. Values indicate mean Ϯ SEM. Group comparison was made by Student's t test or by two-way ANOVA with Bonferroni post hoc test as indicated.
For phosphorylation analysis, signal intensity of the phosphoprotein was divided by the signal of the total protein and normalized to control values. The statistical analysis was performed using two-way ANOVA with Bonferroni post hoc test. For co-IP quantification, signal intensity of the co-IP protein was normalized to the signal intensity of the protein in the input sample and then divided by the signal intensity of the immunoprecipitated protein. All statistical analyses were performed using GraphPad Prism 5 software.
E, Quantification of the expression of NMDAR subunits in the total membrane fraction and synaptosome-enriched fraction of CD3 ϩ/ϩ and CD3 Ϫ/Ϫ mouse brains normalized to GAPDH. Data are mean Ϯ SEM (n ϭ 4 for each group). **p Ͻ 0. 01, Mann-Whitney test. F, GluN2A, but not GluA1, is co-immunoprecipitated with CD3 from CD3 ϩ/ϩ mice brain lysate. Mice brain membrane homogenates solubilized in 1% Triton X-100 were immunoprecipitated with CD3 antibody. The immunoprecipitates were resolved by SDS-PAGE and probed with GluN2A or GluA1 antibodies. GluN2A is not detected in protein complex immunoprecipitated from CD3 Ϫ/Ϫ mice brain lysate. Input lanes contain 5% of extract used for IP. G, Disruption of GluN2A-PSD95 interaction in CD3 Ϫ/Ϫ mice. CD3 ϩ/ϩ and CD3 Ϫ/Ϫ mice brain membrane homogenates solubilized in 1% Triton X-100 were immunoprecipitated with GluN2A antibody and immunoblotted with a PSD95 antibody.
01 M phosphoric acid up to 80% in 5. 5 min, to 90% at 7. 5 min, and returning to 20% at 7. 6 min with a total run length of 10 min. The flow rate of the eluent was maintained at 6 mL/min. Befloxatone was eluted with a retention time of 6 min. Data acquisition and analysis were carried out using Winflow software (version 1. 21, JMBS Developments, Grenoble, France).
For each subject, regional V T values obtained with 2TCM at the regional level were considered as the gold standard. Comparisons to the V T calculated with Logan voi , MA1 voi , SA voi , Logan voxel , MA1 voxel , and SA voxel were performed with a repeated measures analysis of variance (ANOVA) for V T values in the various regions. Statistical analyses were performed with SPSS (version 17 for Windows; SPSS Inc. , Chicago, IL, USA).
The use of SA has long been hampered by the complexity of its implementation. However, new user-friendly software, such as SAKE or Pmod 3. 4, may encourage its use for clinical protocols where statistical parametric mapping analyses are performed. Autoradiography and immunohistochemistry data have demonstrated that MAO-A is widespread in the brain  [27, 28]. Moreover, studies of nonhuman primates found that [ 11 C]befloxatone binding was displaceable in all brain regions  [12]. These data suggest that a reference region may not exist to quantify [ 11 C]befloxatone binding. Without a reference region, quantification can only be achieved by using an arterial plasma input function, which is an invasive procedure. In addition, measuring the arterial input function usually requires labor-intensive HPLC analyses.
Methods The study procedures of this randomized, double-blind, parallel-group, dose-optimized, placebo-controlled, phase III trial have been described previously  [24]. Study SPD489-325 (ClinicalTrials. gov identifier: NCT00763971) was conducted in accordance with current applicable regulations, the International Conference on Harmonisation of Good Clinical Practice, local ethical and legal requirements, and the Declaration of Helsinki (including its amendments). The study protocol was approved by an independent ethics committee/institutional review board and regulatory agency in each centre (as appropriate) before study initiation. Each patient's parent or legal guardian provided written, informed consent, and assent was obtained from each participant (as applicable) before commencing study-related procedures.
Effect sizes were calculated as the difference in LS means between each active drug and placebo, divided by the rootmean-square error. Conventionally, effect sizes of 0. 2, 0. 5 and 0. 8 calculated by this method are operationally defined as small, medium and large, respectively  [32]. Results were analysed using SAS Ò Version 9. 1. 3 or higher (SAS Institute Inc. , Cary, NC, USA).
Acknowledgments This study was supported by funding from  Shire Pharmaceuticals. Shire develops  and markets drugs to treat psychiatric disorders, including ADHD. T. Banaschewski ,  D. Coghill ,  M. Johnson ,  M. Lecendreux ,  C. Soutullo  and  A. Zuddas  were principal investigators in this clinical study. P. Hodgkins  and  L. Squires  contributed to the study design. B. Adeyi was responsible for the statistical analysis. All authors were involved in discussion and interpretation of the data, critically revised the article and approved the manuscript before submission. Drs E. Southam  and  M. Cottingham  of Oxford PharmaGenesis TM Ltd were funded by  Shire  to provide writing support, including editorial assistance, collation of the authors' comments and editing of the manuscript for submission.
Quantitative Reverse-Transcription Polymerase Chain Reaction Cultured cells were lysed with Trizol (Invitrogen, Carlsbad, CA) and total RNA was extracted as described by the manufacturer. 2μg of RNA were reverse transcribed to cDNA using random primers and oligodT and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). Relative mRNA levels were assessed by quantitative reverse-transcription polymerase chain reaction with SyBR Green master mix (Applied Biosystems, Foster City, CA) in triplicates using an ABI Prism 7700 (Applied Biosystems, Foster City, CA). Primers for CD100, GAPDH, IL-1 β and STAT-1 (see below) were designed using primerexpress software and purchased from Invitrogen (Carlsbad, CA). Results were normalized using GAPDH. Primers: CD100(F): 5' CGAGAAGCAGCATGAGGTGTATTG 3' CD100(R): 5' CGGATGTAGTTGAGGCACTCTGTC 3' STAT1(F): 5' CAAGGTGGCAGGATGTCTCAG 3' STAT1(R): 5' TTCCATGGGAAAACTGTCATCAT 3' GAPDH(F): 5' TGGTCTCCTCTGACTTCAACA 3' GAPDH(R): 5' AGCCAAATTCGTTGTCATACC 3'.
Phage display and plexin B1 phage After two cycles of pre-clearing (subtraction) in normal carotids and selection (panning) in atherosclerotic plaques, we randomly selected and sequenced 100 phages among the ones that bound to the plaques. All 100 phages were different and alignment using ClustalW did not show important common sequences or domains. Comparison to public databases using BLASTp indicated that one of the phages (phage B6, and only this phage) presented four consecutive amino acids (ELGC) in nine (CGFSGELGC) identical to plexin B1, rendering an alignment score of 16. 3. Since plexin B1 is a high affinity receptor for CD100, we aimed to validate this finding by analyzing CD100 expression in atherosclerotic plaques.
The reverse transcriptase reaction was performed at 42uC for 60 min in a final volume of 20 ml. The real-time PCR was performed using the LightCycler 480 system with a 96-well format (Roche Diagnostics) in a final volume of 20 ml, containing 16LightCycler 480 SYBR Green I Master solution, 0. 5 mM of each primer and 6 ml of cDNA. The forward and reverse primer sequences for CRABP-I and Ppib that was used as a house-keeping gene are given in Table  1. The following program started with an initial denaturation step for 10 min at 95uC, then an amplification for 40 cycles (10 s denaturation at 95uC, 6 s annealing at 62uC, and 10 s extension at 72uC), finally a melting curve analysis was run. In order to verify the specificity and the identity of the amplified products : (1) the melting curve analysis showed a single melting peak after amplification, and (2) amplified products for each gene were verified by sequencing with the Big Dye Terminator v1.
1. (Applied Biosystems) and analyzed on a ABI3130 sequencer (Applied Biosystems). The peptidylprolyl isomerase B (Ppib) housekeeping gene was used as the reference gene for relative quantification as its expression level was unaffected by our experimental conditions. Quantification data were analyzed using the LightCycler 480 Relative Quantification software (version 1. 5). In order to compensate for differences in target and reference gene amplification efficiency, either within or between experiments, this software provides a calibrator-normalized relative quantification including a PCR efficiency correction. Therefore, the results are expressed as the target/reference ratio divided by the target/ reference ratio of the calibrator. In our case, the calibrator was chosen among the young rats.
Statistical Analysis Spatial learning and swim speed data were analyzed using a 2way ANOVA (3 groups) followed by a post-hoc Bonferroni test. Probe test, immunohistochemical (Ki-67 and DCX only) and PCR data were analyzed using a 1-way ANOVA followed by a post-hoc Bonferroni test. Two pairwise comparisons were performed between young and aged rats (age effect) but also between aged and enriched-aged rats (supplementation effect) using Bonferroni adjusted significance levels of 0. 025. Probe test comparisons to chance level (25%) were performed in each group using one sample test. Results are expressed as mean and standard error of the mean, and they were considered significant when p,0. 025 for ANOVAs and Bonferroni tests or p,0. 05 for one sample test.
ELECTROPHYSIOLOGY To record astrocytes in situ, individual hippocampal slice was transferred to the recording chamber with constant perfusion of oxygenated aCSF (2. 0 ml/min). The recording chamber is mounted on an Olympus BX51WI microscope and an infrared differential interference contrast (IR-DIC) video camera was used to identify astrocytes located in the CA1 region with the aid of a 40 × water-immersion objective. Whole cell patch-clamp recordings were performed using a MultiClamp 700A amplifier and pClamp 9. 2 software (Molecular Devices, Sunnyvale, CA). Borosilicate glass pipettes (outer diameter: 1. 5 mm, Warner Instrument) were pulled from a Flaming/Brown Micropipette Puller (Model P-87, Sutter Instrument). The pipettes had a resistance of 5-7 M when filled with gluconate-based pipette solution.
Blots were scanned and quantified by Quantity One software (Bio-Rad, Hercules, CA, USA). After detecting TWIK-1 immunoreactivity, the original membranes were stripped with stripping buffer (0. 4 M Glycine, 0. 2% SDS and 2% Tween 20, pH 2. 0) and re-probed with the following primary antibodies sequentially to determine the quality of protein fractionation: anti-caveolin-1 (CAV-1) (1:250; Abgent, San Diego, CA), anti-Na + /K + ATPase alpha 2(+) polypeptide (ATP1α2) (1:1000; Abgent, San Diego, CA), anti-K ir 4. 1 (1:600, Alomone Labs, Jerusalem, Israel), anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (1:8000, Sigma-Aldrich, St. Louis, MO), or anti-glial fibrillary acidic protein (GFAP) (1:500, DAKO, Carpinteria, CA).
DATA ANALYSIS Rectification index (RI) was used to determine the selective impact of TWIK-1 gene deletion on astrocyte passive conductance. RI was calculated by dividing the current amplitudes induced by +20 mV (y1) over -180 mV (y2) (Figure  3 ). RI = y1/y2 = I 20 mV /I -180 mV (1) The relative Cs + to K + permeability (P Cs /P K ) was determined by the relative shift in reversal potentials when K + in the bath solution was replaced by equimolar Cs + and calculated according to the following equation: P Cs P K = exp[(E Cs -E K )/(RT/zF)] (2) E K and E Cs were the equilibrium reversal potential of K + and Cs + , respectively. The patch clamp recording data were analyzed by Clampfit 9. 0 (Molecular Devices, Sunnyvale, CA) and Origin 8. 0 (OriginLab Corporation, MA). Data are presented as means ± SEM.
ACKNOWLEDGMENTS This study was supported by  NIH  grant  RO1NS062784  and a start-up fund from The  Ohio State University School of Medicine  (to Min Zhou),  NIH   DC01919  (to  Leonard K. Kaczmarek ), and  French Agence Nationale pour la Recherche (ANR) LabEx Ion channel Science and Therapeutics  grant  ANR-11-LABX-0015-01 (to  Florian Lesage  and  Jacques Barhanin ).
Subsequently, we isolated a ΔKMO-394 (deleted in residues 394 to 460) version of the enzyme engineered by site-directed mutagenesis (Supplementary Methods) to define the cleavage point prior to crystallization (Figure  S1 ; Table  S1 ). The ΔKMO-394 enzyme was active (Figure  S2 , S3), generated authentic 3HK in HPLC-based assays (Figure  1b ) and was inhibited by UPF 648 (K i 74 nM) with potency similar to that with human KMO (Figure  1b ). The structure of the proteolysed form of yeast KMO (ΔKMO-396Prot) was determined using selenomethionine single anomalous diffraction (PDB codes 4J2W and 4J31). We also solved structures of ΔKMO-394 to 1. 85 Α ̊ resolution. The final model contains residues 1-97 and 101-390 and the bound FAD cofactor. Both crystal forms contain a putative KMO dimer in the asymmetric unit (Figure  2a ).
We were unable to obtain a KMO complex with kynurenine but succeeded in cocrystallising with UPF 648 (Table  S3 , PDB code 4J36). The asymmetric unit contains a putative KMO dimer with one monomer containing UPF 648 bound in the active site, adjacent to the FAD re-face (Figure  2b , Figure  3 ). The UPF 648 carboxylate is bound by conserved residues R83 and Y97 while the aromatic dichlorobenzene moiety is flanked by several hydrophobic residues (L221, M230, I232, L234, F246, P321, and F322), which are conserved in many KMO enzymes. UPF 648 binding induced structural changes in the enzyme, notably reorientation of the 321-325 loop flanking the re-side of the FAD. A minor reorientation in the position of the six-stranded antiparallel β-sheet domain with respect to the flavin binding domain is also evident.
Crystallization and diffraction data collection Crystals of Saccharomyes cerevisiae KMO were obtained using the sitting-drop vapour diffusion technique. Details describing the crystallogenesis can be found in Supplementary Methods. Diffraction data from Saccharomyes cerevisiae KMO crystals were collected from single cryofrozen samples at the Diamond Light Source, Harwell, UK. A single-wavelength anomalous dispersion (SAD) data set at the selenium edge was used for initial phase determination. Data collection and refinement statistics are present in Table  S3.
Cloning, expression and purification of Saccharomyces cerevisiae kynurenine 3monooxygenase A synthetic gene (BNA4 UniProtKB accession number P38169) encoding Saccharomyces cerevisiae kynurenine 3-monooxygenase was 'codon optimised' for overexpression in E. coli (Genescript, Piscataway, NJ, USA). The gene was sub-cloned into pET15b and pET24b (Merck, Whitehouse Station, NJ, USA) as a Nde I -Xba I fragment for over-expression in E. coli strain BL21(DE3). A deletion variant of kynurenine 3-monooxygenase (Δ394BNA4) and single amino acid variants of this deletion (Δ394BNA4-R83A and Δ394BNA4-R83M) were generated by site-directed mutagenesis (Quikchange, Strategene, Agilent Technologies, USA). Sense and anti-sense primers are shown in Table  S1. Amplification conditions were: denaturation at 95 °C for 30 s, followed by 16 cycles of amplification at 95 °C (30 s), 55 °C (60 s), 68 °C (7 min).
Assays at each reaction condition were performed in triplicate. Apparent Michaelis constants, K m , for Lkynurenine and NADPH were determined by varying the concentration of the first substrate at a constant concentration of the second substrate and vice versa. Reaction data were fitted to the standard Michaelis-Menten equation using Origin Software (OriginLab, Northampton, MA). KMO inhibition by UPF 648 was measured by following formation of the product 3 hydroxykynurenine by C 18 reversed-phase HPLC. Enzyme (100 nM) was incubated at 37 °C in 1 mL reaction buffer (20 mM potassium phosphate buffer, pH 8. 5, 7 mM 2mercaptoethanol) with 2 mM NADPH, 500 μM L-kynurenine and different concentrations (0 -2 μM) of UPF 468. The reaction was stopped with 8 % trifluoracetic acid added at different time points during the assay.
Precipitated protein was removed by centrifugation, and the supernatant was analysed by C 18 reversed-phase HPLC equilibrated with 50 mM ammonium acetate, pH 3. 0, containing 1% methanol and 0. 1% heptanesulfonic acid; elution from the column was with 50 mM ammonium acetate, pH 4. 5, containing 5% methanol and 0. 5% heptanesulfonic acid, and monitored at 229 nm. 3-hydroxykynurenine was quantified by comparison with a 3-hydroxykynurenine calibration curve. Each experiment was performed in triplicate. Data were fitted to the Morrison equation (Equation  1 ): (1)   where ʋ 0 is the enzyme activity without inhibitor, ʋ i is the enzyme activity at ligand concentration I, [E] is the enzyme concentration, [I] is the inhibitor concentration and K i is the inhibition constant.
Ligand binding assays Fluorescence emission measurements were performed using a Cary Eclipse Fluorimeter (Agilent Technologies) to determine enzyme-ligand dissociation constants (K d ) for KMO ligands, exploiting ligand perturbation of flavin (enzyme-bound FAD) fluorescence. Excitation light was provided from a xenon light source and excitation and emission slit widths were 5 nm. The perturbation in FAD fluorescence emission was followed at 520 nm using an excitation wavelength of 450 nm and excitation spectra were recorded from 470 to 700 nm. L-kyn and UPF 648 were titrated into a 5 μM solution of KMO (20 mM potassium phosphate buffer, pH 8, 50 mM NaCl and 7 mM 2-mercaptoethanol) at 25 °C. Dissociation constants, K d , were calculated by fitting data for the difference in fluorescence emission measured for KMO-ligand complexes and free KMO at 520 nm divided by the maximum emission versus the ligand concentration (Equation  2 ).