dataesr/scientific-paragraphs-categorization huggingface dataset:
The  Framingham Heart Study  was supported by the  NHLBI  (Contract no. N01-HC-25195 ) and its contract with  Affymetrix, Inc  for genotyping services (Contract no. N02-HL-6-4278 ); some of this research used the Linux Cluster for Genetic Analysis (LinGA-II) funded by the  Robert Dawson Evans Endowment  of the  Department of Medicine at Boston University School of Medicine and Boston Medical Center ; and grants from the  National Institute of Neurological Disorders and Stroke  ( R01 NS17950 ), and the  National Institute of Aging  ( R01s AG08122 ,  AG16495 , and  AG033193 ), and the  NHLBI  ( U01 HL096917  and  R01 HL093029 ). The  Rotterdam Study Genome-Wide Association database  was funded by the  Netherlands Organization of Scientific Research (NOW ; no. 175. 010. 2005. 011 ); the study was further supported by the  Netherlands Genomics Initiative/NWO  project no.
A. Electronic structure theory calculations All quantum-mechanical calculations were carried out with the software package Molcas 7. 7. 40, 41 The reference values for the adenine in gas-phase, used to calibrate different reduced active space schemes, were obtained with a procedure discussed in Sec. II D. The effect of the geometry optimization level on the electronic structure of adenine was studied by comparing the CASSCF results to MP2 theory and DFT making use of the B3LYP functional. 42 Geometry optimizations were done using C S -symmetry. Different RASSCF schemes were assessed regarding their ability to reproduce the tran-sition energies and dipole moments of the reference calculation: SA-25-RAS(4,6|0,0|4,4), SA-25-RAS(4,6|0,0|4,3), SA-20-RAS(4,4|0,0|4,3), and a SA-15-CAS(4,4), with RAS1 described by the maximum number of holes and orbitals, RAS2 by the number of electrons and orbitals, and RAS3 by the maximum number of excitations and orbitals.
ACKNOWLEDGMENTS M. G. and G. C. acknowledge support by the  European Research Council Advanced  Grant  STRATUS (ERC-2011-AdG No. 291198 ). A. G. acknowledges financial support from  Italian Ministry of Education and Research (MIUR) -Grant No. RBFR1248UI. We also acknowledge the use of HPC resources of the " Pôle Scientifique de Modélisation Numérique " at the  ENS-Lyon, France.
9 s) or 200 frames for IP 3 R1KO neurons. All recordings were finished within 30 min after labeling. QD-SPD data were analyzed using TI workbench 2778 Cell Reports 13, 2768-2780, December 29, 2015 ª2015 The Authors software written by Dr. T. Inoue (Waseda University) as described previously  (Bannai et al. , 2009; Niwa et al. , 2012). Details of other methods are presented in the Supplemental Experimental Procedures.
ACKNOWLEDGMENTS We thank the  Research Resource Center (RIKEN BSI ) for FANTOM3 clone and for supporting antibody production. We thank  C. Hisatsune  and  S. Sakuragi  for technical supports;  T. Inoue ,  M. Dahan ,  V. Racine , and  J. B. Sibarita  for the analysis program; and  Y. Oda ,  I. Mori ,  C. Yokoyama , and  A. V. Terashima  for their valuable comments on the manuscript. This work was supported by  RIKEN  (Special Postdoctoral Researcher [SPDR] and  Foreign Postdoctoral Researcher [FPR] programs) ;  KAKENHI  ( 20700300 ,  25830058 ,  20220007 , and ''Glial assembly'' 26117509);  Japan Society for the Promotion of Science  (JSPS,  06J06775 ); research grants from the  Toyobo Biotechnology Foundation ,  Kato Memorial Bioscience Foundation , and  Toray Science Foundation ; and the  Moritani Scholarship Foundation.
Work in the A. T. laboratory was supported by the  European Research Council (ERC)  grant  PlastInhib  and the  L'Agence Nationale de la Recherche (ANR)  grant  Synaptune , The  Labex Memolife  ( ANR-10-LABX-54 ) and  PSL Research University  ( ANR-11-IDEX-0001-02 ). We thank two anonymous reviewers for their insightful and constructive comments on the manuscript.
Acknowledgment: This work was supported by a  General Research Fund  from the  Research Grants Council of Hong Kong, China , and the  Hong Kong University Seed Funding Program for Basic Research  to  Dr. Tseng. It  represents an expanded version of an invited talk given at APCV 2013 in Su-zhou, China. The talk was sponsored, in part, by a  Teaching Excellence Fellowship  of the  University of Hong Kong  (to  Prof. Chia-huei Tseng ), research funds from the  Peking-Tsinghua Center for Life Sciences, Peking University  (to  Prof. Cong Yu ), and  Chinese Academy of Sciences, Shanghai  (to  Prof. Wei Wang ). Profs. Horace Barlow ,  Charles Gilbert ,  Barbara Heider ,  Wu Li ,  Susana Martinez-Conde ,  Jerry Nelson ,  Leo Peichl ,  James Thomas ,  John Troy ,  Wei Wang ,  John S. Werner , and  Li Zhaoping  offered valuable comments on earlier versions of the manuscript.
The spectral and image decompositions are consistent with each other. A regression-based decomposition of the spectral and image Mueller matrices is also presented whereby the basic optical components are assumed to be a mirror and a circular polarizer as suggested by the Cloude decomposition. The advantage with a regression decomposition compared to a Cloude decomposition is its better stability as the matrices in the decomposition are determined a priori. The origin of the depolarizing features are discussed but from present data it is not possible to conclude whether the two major components, the mirror and the circular polarizer are laterally separated in domains in the cuticle or if the depolarization originates from the intrinsic properties of the helicoidal structure.
Introduction Mueller-matrix spectra of beetle cuticles have been reported by several authors. Goldstein  [1]  measured normal-incidence Mueller matrices on Chrysina resplendens, Chrysina gloriosa and Chrysina clypealis (In  [1]  the name Plusiotis is used instead of Chrysina). Hodgkinson et al. [2]  and our group  [3]  have reported near-normal incidence and angle-dependent Mueller-matrices, respectively, and presented polarization features including both left-handed and right-handed near-circular polarization in reflection from several scarab beetle species. Derived parameters like ellipticity, handedness, degree of polarization, depolarization and more are reported. Recently we have also presented a regression analysis approach to extract structural information and cuticle refractive indices from Mueller-matrix data of the scarab beetle Cetonia aurata  [4].
The instrument is equipped with filters and calibrated for wavelengths 532 nm and 633 nm. An objective with 20x magnification and numerical aperture of 0. 45 was used in this investigation. With this objective the diameter of the imaged spot was 90 μm and data over the θ -range 0-26 • were detected by a 512x512 pixel CCD camera (Hamamatsu). Cloude as well as regression decompositions, both of spectral and image data, were performed with Matlab.
Primary data -examples Several specimens of the beetles were studied at various setting of the instruments. Here a selection of primary data are shown to demonstrate data qualities and general optical features of the cuticles of beetles. C. aurata is a narrow-band reflector as seen in the spectral Mueller matrices shown in Fig. 2  for θ = 20 • and 65 •. We observe that the spectral features at an angle of incidence of 20 • are largest around 550 nm, e. g. in element m 41 , and that they shift to shorter wavelengths and become much smaller at θ = 65 • which is further discussed and modeled elsewhere  [3, 4]. These major features seen in m 41 , m 14 and in the diagonal elements are near-symmetric with a width at half maximum of around 55 nm (at θ = 20 • ) and with some weak oscillations on the long-wavelength side.
Regression sum decomposition of spectra Here we demonstrate regression decomposition of spectral M measured on C. aurata. A singleparameter approach is used with α as fit parameter in Eq. (7). γ = δ = 0 is assumed and with the constraint Σλ i = 1 we have β = 1 -α. An ideal mirror and a left-handed circular polarizer as used in Eq. (  9 ) are assumed for M 1 and M 2 , respectively. The regression analysis is performed in Matlab using the least-square regression algorithm. Figure  6 (a) shows α and β = 1 -α obtained in the regression analysis of M recorded on C. aurata at θ = 20 • under conditions described above. These results are very close to those from the Cloude decomposition. Notice that the difference in the two approaches are that in a regression decomposition, the fitted linear coefficients α and β are determined under an assumption of specific forms of the matrices M 1 and M 2 , whereas in a Cloude decomposition the true eigenvalues are determined independently of M 1 and M 2.
Furthermore there are no problems with magnitude sorting of eigenvalues in a regression decomposition as it is in a Cloude decomposition. For larger angles of incidence, the regression decomposition becomes more complex and circular polarizer matrices M i may have to be replaced by matrices corresponding to elliptical polarizers. Furthermore, for C. argenteola we find three non-zero eigenvalues and the regression decomposition becomes more complex. An extended regression sum decomposition of Mueller-matrix data of beetle cuticles will be presented elsewhere.
Notice that the sorting of eigenvalues after magnitude results in that λ 1 is largest, whereas for the regression β as defined in Eq. (  6 ) is largest. also has small influence as for near-normal incidence, the reflection coefficients and thereby the Mueller-matrix elements, depend only weakly on incident angle as verified by simulations (not shown here). For C. aurata the agreement between the image and spectral data is also surprisingly good in spite of the patterning observed in the images. The fact that patterning is observed in the images raises the question whether the depolarization properties of the measured Mueller matrices is due to lateral inhomogeneities implying that several types of Mueller matrices within the beam spot contribute or whether the depolarization is an intrinsic property of the cuticle structure.
In Figs. 6 and 7 noise can be observed in the eigenvalues for long and short wavelengths, respectively. Furthermore, λ 4 exhibit negative values, albeit noisy, in some spectral regions in spite of that the covariance matrix C should be positive semi-definite. The noise can be traced back to the primary data and can be seen in Figs. 2  and 3. The data become noisy because the Mueller-matrix elements are normalized to the overall reflectance which is very low at these wavelengths. The negative value of λ 4 is due to the fact that the eigenvalue algorithm uses the Σλ i = 1 and λ 4 = 1-λ 1 -λ 2 -λ 3 , i. e. a residue. Noise in the data and possibly small systematic errors can then lead to negative values of λ 4. In some Mueller-matrix elements oscillations are clearly visible, especially for C.
Concluding remarks Mueller-matrix spectra as well as Mueller-matrix images from cuticles of the beetles studied can be Cloude decomposed and their corresponding covariance matrices are found to exhibit two non-zero dominating eigenvalues. For more complex beetle cuticles additional eigenvalues are found to be non-zero. An eigenvector analysis of spectral data suggests that a mirror and a circular polarizer are basic optical components of the measured Mueller matrices and a sum decomposition reveals that in simple cases these two components in a first approximation sufficiently can describe the biological reflectors studied. It is also possible to do a regression-based decomposition assuming a set of basic optical components with a fit with no constraints on the fit parameters α, β , γ and δ.
Acknowledgments This work is dedicated to the memory of our colleague  Antonello De Martino  who suddenly passed away during the preparation of the manuscript. Specimens of C. aurata were kindly provided by  Jan Landin  and specimens of C. argenteola were on loan from  Museum of Natural History in Stockholm. Sandeep Singh  is acknowledged for help with some of the image measurements and  Jens Birch  for providing photos of the beetles. This work is supported by grants from the  Swedish Research Council  and from  Carl Tryggers foundation. Knut and  Alice Wallenberg  foundation is acknowledged for support of instrumentation.
However, there are still very few objective data on the capacity of CI users to perceive musically evoked emotions. Music appreciation in CI patients has essentially been explored using self-report questionnaires that characterize listening habits and the enjoyment of music before and after cochlear implantation. A single study reports both emotional judgments and music perception abilities in six post-lingual CI adult users and six NH participants  (Rosslau et al. , 2012). CI users were able to perceive various degrees of arousal in famous movie soundtracks, and did not show the typical difficulties in pitch, rhythm, and harmony perception, as measured by the standard MuSIC perception test battery  (Brockmeier et al. , 2011). Although these findings suggest that CI users are still able to perceive arousal conveyed by music, one should remain cautious about the interpretation of these results given the small number of participants and the familiarity of the tested musical material.
GCaMP5G fluorescence was imaged using a CoolSnap EZ camera (Photometrics, Tucson, AZ) and the appropriate filter cube (excitation 480 nm; emission 510 nm). Imaging data were analyzed using Manager 1. 4  (63). Measuring Pf%Detailed descriptions of our method are described elsewhere  (1, 62). Briefly, agonist-gated current (black trace in Fig. 1B ) was measured electrically and then integrated (red trace in Fig. 1B ) to give the total charge transfer across the cell membrane (Q T , in coulombs). At the same time, Ca 2ϩ influx was monitored from the fluorescence emitted by a high concentration (2 mM) of intracellular fura-2 K 5 (gray trace in Fig. 1B ) introduced through the recording electrode. When all of the Ca 2ϩ entering the cell was captured by the dye, then the change in 510 nm emission of fura-2 excited by 380 nm light (⌬F 380 ) was proportional to the Ca 2ϩ flux through the pore  (64).
2) where ␥ NMDG equaled 0. 72, and P Ca /P Na was calculated from the Pf % as described above (see Equation  1 ). ⌬E rev is the difference in reversal potentials measured in extracellular solutions containing either Na ϩ and Ca 2ϩ or NMDG ϩ and Ca 2ϩ. Homology Modeling of Resting and Activated rP2X7aRs-Models for the rat P2X7 receptor were built as previously described  (72). Briefly, the apo (Protein Data Bank 4DW0) and ATP-bound (Protein Data Bank 4DW1) structures of zP2X4. 1  (73)  were used as templates to generate the rP2X7aR models using the homology modeling server SWISSMODEL  (74). The rP2X7aR models were minimized using the GROMOS force-.
2D ). These data support the contention that the internal dialysis that occurs during whole cell Pf % recordings disrupts the P2Y response  (1). Confident that we could record a pure ionotropic response, we then moved to the study of the P2X7Rs. Genes encoding the P2X7aRs of dog, frog, guinea pig, human, monkey, mouse, rat, and zebrafish were individually expressed in HEK293 cells for study using patch-clamp photometry. Cells expressing transfected genes were visually identified by the fluorescence emitted from a reporter protein (eGFP or dsRed), and the Pf % was determined as described above. Transfected cells responded with robust inward currents (membrane holding potential ϭ Ϫ60 mV) and changes in fura-2 fluorescence to applications of BzATP (100 -600 M) with one exception: we failed to record agonist-gated current or a change in fura-2 fluorescence in response to BzATP (up to and including 1 mM) and ATP (6 mM) in HEK293 cells transfected with the gene encoding the Xenopus laevis P2X7aR.
Acknowledgments-We thank  Drs. Elena Adinolfi ,  Lin-Hua Jiang ,  Stefan Gru  ¨nder,  Annette Nicke ,  Richard Alan North ,  Ronald Sluyter ,  Stanko Stojilkovic , and  Mark Voigt  for supplying P2X7R plasmids. We also thank  Drs. Randy Sprague  and  Timothy Doyle  for help in isolating human macrophages,  Dr. Floretina Soto  for critiquing a presubmission version of the manuscript, and  Dr. Donald Bers  for useful discussions and initial calculations of the Ca 2ϩ buffering capacity of ATP in defined extracellular solutions.
2 and 0. 5 mm in front of the caudal edge of the area postrema and 0. 5 to 0. 7 mm lateral) and to the level of stimulation of the solitary tract (ST). Although microinjections and ST stimulations were made on either side of the medulla, all injection sites have been reported to the left side and dotted in the hatched area corresponding to the region of the interstitial and intermediate solitary tract nucleus (NTS) subnuclei. of a mechanotransducer placed around the thorax, and the electrocardiogram (ECG) by subcutaneous electrodes placed on each side of the thorax. Moreover, the electrocardiogram and swallowing EMG signals were fed to loud speakers for auditory monitoring. Rectal temperature was monitored and maintained around 37°C with a heating pad. The EMG, ECG and respiration signals were recorded on a computer using an analog-to-digital interface (PowerLab 8SP data acquisition software for Windows, ADInstruments, USA).
Image analysis and c-Fos positive neuron count. For each animal, c-Fos immunostaining analysis was performed by counting the positive nuclei on four non-consecutive sections using microphotographs acquired by a 10 fold lens with a DMX 1200 camera (Nikon) coupled to ACT-1 software. The microscope was set at a specific illumination level, as was the camera exposure time. c-Fos positive nuclei were then counted on these pictures by computer-assisted morphometry using the ImageJ software as previously described by Girardet et al. [14].
6) Statistical analyses All swallows calculated values were normalized as percents of control values. Statistical analyses were performed using one-or two-way analysis of variance (ANOVA) followed by Fisher's protected least-significant difference post-hoc test for all electrophysiological data, and using Mann-Whitney test for immunohistological data (StatView for Windows 5. 0. 1; SAS Institute). Differences were considered significant when P < 0. 05. Data were expressed as mean ± SEM.
The potential reference of the amplifier was adjusted to zero prior to breaking into the cell. Cells were held at -76 mV. Current-voltage (I-V) curves were made by a series of hyperpolarizing to depolarizing current steps immediately after breaking into the cell. Membrane resistance was estimated from the I--V curve around resting membrane potential  (Kasanetz and Manzoni, 2009). Whole cell patch-clamp recordings were performed with an Axopatch-200B amplifier. Data were low pass filtered at 2 kHz, digitized (10 kHz, DigiData 1440A, Axon Instrument), collected using Clampex 10. 2 and analyzed using Clampfit 10. 2 (all from Molecular Device, Sunnyvale, USA). Both fEPSP area and amplitude were analyzed. Stimulation was performed with a glass electrode filled with ACSF and placed ∼200 µm in the dorsalmedial direction of the recorded cell.
Data Acquisition and Analysis The magnitude of plasticity was calculated 20--30 min after the potentiation protocol as percentage of baseline responses. To determine the AMPA/NMDA ratio, the cells were voltage clamped to +40 mV and a stable dual response (AMPA + NMDA current) to afferent stimulation was recorded. The AMPAR EPSC was isolated after bath application of the NMDAR antagonist D-2-amino-5-phosphonovaleric acid (D-APV, 50 µM). The NMDAR EPSC was obtained by digital subtraction of the AMPAR EPSC from the dual response. Spontaneous EPSCs were analyzed with Axograph X (Axograph). Statistical analysis of data was performed with GraphPad Prism (GraphPad Software Inc. , La Jolla, CA) using tests indicated in the main text after outlier subtraction. All values are given as mean ± standard error and statistical significance was set at * p < 0.
PSD Size Analysis Length of PSD was measured in 100 randomly chosen synapses per animal, captured at 40,000× magnification. To ensure unbiased sampling, on average the section was imaged following two fields of view movement in the x-direction and one field of view in the y-direction between images, regardless of the shape and size of the synapse. However, synapses were only imaged when standard morphological parameters were met, including clear pre-and post-synaptic compartments and a distinct synaptic cleft. Mean lengths were generated per animal and an unpaired Student's t-test performed with the 3 wildtype vs. 3 fmr1-/y mean lengths. To ensure there were no subtle differences in the spread of PSD lengths between genotypes, the data was pooled within genotypes and then binned according to size.
Head and neck area were calculated by outlining the neck and head boundaries using ImageJ. To assess presynaptic alterations, 50 excitatory axospinous synapses were imaged at random, per animal. Active zone length was measured along the contour of the presynaptic terminal membrane and was determined by the weakly electron dense active zone directly appositional to the postsynaptic PSD. Total vesicle number was calculated by counting all intact vesicles in the presynaptic terminal. For each parameter, all values from each animal were used to create a mean value per animal. The 3 wild-type values were compared to the 3 fmr1-/y values using an unpaired Student's t-test. When mean values of individual animals belonging to the same genotype were similar the distribution of the values was compared by pooling all values per genotype and binning the data according to size.
25 ± 0. 38 SD and 1. 308 ± 0. 93 SD for wild-type and in fmr1-/y mice respectively (p = 0. 8503, Student's unpaired t-test). We also determined the excitatory postsynaptic potential-spike coupling (or E-S coupling) to directly evaluate how synaptic excitation is integrated to generate an action potential in wildtype and fmr1-/y littermates  (Thomazeau et al. , 2014). We found that the E-S coupling was similar in wild-type and in fmr1-/y mice (p = 0. 1488, two way ANOVA, Figure  3D ). We conclude that the lack of FMRP in fmr1-/y mice has no major effect on excitatory synaptic integration in accumbens MSNs. More generally, the data indicate that the lack of FMRP expression did not affect on the intrinsic properties of accumbens MSNs. We next measured field EPSPs (fEPSP) of accumbens MSNs to build input-output profiles in the two genotypes.
Acknowledgments This work was supported by the  FRAXA Foundation  (OJM, MS and DN), a  NARSAD 2010 Independent Investigator Grant  given by the  Brain and Behavior Research Foundation (OJM) ,  INSERM  ( OJM ),  ANR-Blanc France-Taiwan RescueMemo (OJM). This study was also supported by The  Momentum Program  ( LP2013-54/2013 ) of the  Hungarian Academy of Sciences  and by the  European Research Council  Grant  243153  (IK). IK is a recipient of the  Wellcome Trust   International Senior Research Fellowship  ( 090946/Z/09/Z ). CMH was a recipient of a European Molecular.
The present study examines the regulation of cytokines and antioxidants in the small and large intestine of aroused and torpid gray mouse lemurs. Multiplex and total antioxidant assays were used to determine the relative levels of pro-inflammatory cytokines, anti-inflammatory cytokines, chemokines, and antioxidant enzymes as well as antioxidant metabolites. The differential levels of cytokines in the various intestinal sections of lemurs during torpor suggest regulation of the local immune response in the gut of lemurs during hypometabolism. However, total protein levels of antioxidant enzymes did not change in response to torpor, although minimal changes in total antioxidant capacity (the sum of low molecular mass antioxidants) were observed in the ileum during torpor. These data suggest either low involvement of antioxidant defenses in the torpor response, or that antioxidant defenses are responsive to other factors not identified in the present study.