dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular cloning Putative orthologs of Ciona robusta and Halocynthia roretzi protein-coding genes were initially identified by TBLASTN. Identified sequences were aligned to each other to support orthology relationships within Molgula and then queried by BLASTP against the NCBI nonredundant protein sequence database to further support orthology relationships to well-known tunicate and vertebrate proteins. The cDNAs were cloned by RT-PCR, and the template cDNA libraries were prepared from total RNA extracted from embryos of various stages. Upstream regulatory sequences were cloned by PCR from genomic DNA (see Additional file 4). For PCRs, we used Phusion high-fidelity polymerase (New England Biolabs, Ipswich, MA) or Pfx Platinum polymerase (Thermo Fisher). Genes are named according to the proposed unified nomenclature system for tunicate genetic elements  [52].
MATERIALS & METHODS The experiment was approved by the University of Gothenburg ethics committee and performed in accordance with the Declaration of Helsinki, and written informed consent was obtained. Microneurographic axonal recordings were made from the left antebrachial cutaneous nerve (lateral or dorsal branch) in 20 sessions from 19 healthy human participants (25 Ϯ 6 yr; 9 men, 10 women). Singleunit recordings were gained from CT and CM afferents in the forearm through an insulated, high-impedance tungsten recording electrode (FHC). Nerve signals were amplified, band-pass filtered (0. 2-4 kHz), and digitized (20. 8 kHz) with a Power1401 and Spike2 software (CED). C-mechanoreceptive units were identified by stroking or pinching the skin innervation territory, and single-unit waveforms were identified online with a combination of threshold crossing and template matching (Spike2).
Two-hertz electrical stimulation, over a period of 3 min, was used  (Obreja et al. 2010; Serra et al. 1999) , followed by 10 pulses of 0. 25-Hz stimulation, with Ͼ2 min for recovery before further electrical stimulation. High-frequency electrical stimulation consisted of four pulses at frequencies of 10, 20, 50, 100, or 200 Hz, with 30-s recovery and three repeats of all frequencies (with the exception of 10 and 20 Hz, which were given once). All trains were delivered in a randomized order. Microneurography data analysis. Analysis of microneurography data was performed in Spike2 with off-line template matching. The presence of spikes and their latency (to spike negative-going peak) were analyzed with a custom-written script. Latency changes were represented as a percentage relative to the first spike elicited by each train of stimulation.
The boxplot is given in Figure  3. Running our GLM on this second dataset we found (β 1 = 13. 3%, t 26 = 2. 28, p < 0. 001) indicating the presence of a LVF bias in the hearing group. This LVF bias was not significantly reduced in the deaf group (β 2 = -11. 19%, t 26 = -1. 35, p = 0. 18). However, the difference from 50% was not significant in the deaf group indicating an absence of LVF bias at the group level (one-sample t-test: M = 52. 14%, t 13 = 0. 37, p = 0. 71). We tested the LVF bias at the level of the participant as in Experiment 1. Filled data points in Figure  3  represent the participant for which the χ 2 statistics for 1 degree of freedom was significant at the p-value α = 0. 05 (bilateral test). The number of participants with LVF bias in the hearing and deaf group were respectively 6 and 2 (out of 14).
Eye-Tracking Data Raw position signal from the eye-tracker was processed offline. Saccades and fixations were parsed using an algorithm adapted from  Engbert and Kliegl (2003). We set the minimum amplitude for saccades to 0. 5 • of visual angle. Only trials where participants gazed at the face and with the initial fixation located on the fixation point were included in the analyses. The AOI for the mask, used to identify fixation location, were defined post-hoc using the full distribution of fixation locations (see Supplementary Figure  S1  for details and Figure  4  for an illustration of the final mask). Five areas of interest were constructed. Supplementary Figure  S1  shows the overall proportion of fixations within each AOI. The goal of the analyses was to test whether hearing and deaf participants differed with respect to face scanning and whether individual differences in face scanning could be related to the LVF bias.
General oculomotor behavior In order to check for the existence of differences between hearing and deaf participants with respect to basic aspects of oculomotor behavior, we first analyzed the distribution of fixation duration. The dataset was composed of N = 7,751 fixations and was best fitted by a lognormal model with µ = 5. 39 (219 ms) and σ = 0. 51. The mean and standard deviation in the two groups were 5. 38 (n = 4,158, SD = 0. 49) and 5. 39 (n = 3,593, SD = 0. 54) for the hearing and deaf group respectively. No differences were found between the hearing and deaf groups concerning fixation durations. Saccadic reaction time (i. e. , the time between stimulus onset and the onset of a saccade away from the fixation point) was similar in both groups (hearing: M = 180 ms, SD = 41 ms; deaf: M = 200 ms, SD = 87 ms, twosample t-test, t 26 = -0.
Statistical Analyses To test for deviation from Hardy-Weinberg Equilibrium (HWE), the computer program FINETTI (https://ihg. helmholtzmuenchen. de/cgi-bin/hw/hwa1. pl) was used to perform exact statistics, and cases and controls were separately considered. To test for genotypic association with each SNP, a standard chi-square (χ 2 ) statistic was calculated using PASW Statistics version 18 for MAC. The computer program FINETTI was used to calculate the Cochran-Armitage trend statistic to test for allelic association. UNPHASED version 3. 0. 10 program  (Dudbridge, 2003)  was applied using 3-marker slide windows to analyze for haplotypic association. UNPHASED uses the standard Expectation-Maximisation algorithm to estimate haplotypes from genotypes. The rare haplotype frequency threshold was taken as 0.
01. UNPHASED uses unconditional logistic regression to perform likelihood ratio tests under a log-linear model of the probability that an allele or haplotype belongs to the case rather than control group. The global null hypothesis is that the odds ratios of all haplotypes are equal between cases and controls. Individual haplotypes were also tested for association by grouping the frequencies of all other haplotypes together. Haploview 4. 0 program  (Barrett et al. , 2005)  was used to perform linkage disequilibrium analysis of all SNPs in our sample (data not shown). To calculate the power of our case-control sample, we used the PS program  (Dupont and Plummer, 1990). Assuming a disease allele and/or genotype with a population frequency of 0. 3, which confers risk of disease at an odds ratio of 1.
Light exposure Crabs were continuously exposed to LED-generated dim red light plus infrared light (the latter to allow video-recording during the dark phase; LEDwholesalers, CA, USA). During the photophase, light was additionally provided with LEDs in the visible spectrum (LEDwholesalers, CA, USA). The LEDs were connected to an Arduino board (Arduino Uno, www. arduino. cc), controlled via a script ran on the Arduino software (version 1. 0. 5) and synchronized by a realtime clock for accuracy (ChronoDot V2. 1 High Precision RTC, macetech LLC, CA, USA).
Behavioral data acquisition, processing and analysis The behavior of the crabs was measured using an infrared-sensitive camera (model UI-1220LE-M-GL, IDS Imaging Development Systems GmbH, Obersulm, Germany). The camera was interfaced with Yawcam (http://www. yawcam. com, version 0. 4. 1). A picture of the whole aquarium was taken every 10 sec from the top. Behavioral analysis was based on locomotor activity using a script in Matlab (version 2013a) that recognizes every individual on each picture and calculates the Euclidian distance covered by each crab between two consecutive pictures as previously described  [16]. Data were binned into 10-min intervals for further processing. Waveforms, periodograms and actograms were generated using the software El Temps (Dr Antoni Dı ´ez-Noguera, University of Barcelona, Barcelona, Spain).
Acknowledgments AM was supported by a Fellowship of the  Belgian American Educational Foundation ; VS was supported by a  FPI  grant by the  Spanish Ministry of Research Science and Technology  in the frame of the project  RITFIM  ( CTM2010-16274 ); HOD was supported by  NSF   IOS0618029  and  IOS0909716. We are grateful to  Dr. Corrado Costa  and  Dr. Paolo Menesatti  ( CRA-ING, Italy ) for the development of MATLAB functions to track locomotor activity of crabs. Authors also thank  Dr. Roelof Hut  for the discussion on the preliminary results.
Quantitative Analysis of Cell Surface Membrane Expression The confocal images were quantitatively analyzed by NIH image software (Bethesda, MD, USA). The fluorescent intensity at the plasma membrane was measured by the profile plotting function  (Yu et al. , 2006 (Yu et al. , , 2008)). For each cell, the place of non-apparent cytoplasm-labeling was selected. A line perpendicular to the cell surface was drawn cross the cell surface and the intensities of pixels along the line were recorded by the profile plotting. The mean of fluorescence intensity at the plasma membrane was measured by Gaussian fitting [y = a * log(-((x -x 0 )/b) 2 )]. Then, the measured intensities were averaged. Cell surface expression of P2X2, V60L and G353R was also verified by biotinylation-Western blotting assay. As previously described  (Jiang et al.
Patch-Clamp Recording Patch clamp recording was performed as we previously reported  (Zhu and Zhao, 2010, 2012). The culture cells were rinsed with normal extracellular solution (NES; 130 NaCl, 5. 37 KCl, 1. 47 MgCl 2 , 2 CaCl 2 , 25 Dextrose and 10 HEPES in mM; 300 mOsm and pH 7. 2) three times. Then, the culture cells were continually perfused with NES. A single, isolated cell with strong fluorescence was selected and classical whole-cell recording was performed using Axopatch 200B (Molecular Devices, CA, USA). Patch pipettes were filled with a normal intracellular solution that contained (in mM): 140 KCl, 5 EGTA, 2 MgCl 2 and 10 HEPES, pH 7. 2 with initial resistance of 2. 5-3. 5 MΩ in the bath solution. Data collection was performed with jClamp (SciSoft, New Haven, CT, USA). The signal was filtered by a 4-pole low-pass Bessel filter with a cut-off frequency of 2 kHz and digitized utilizing a Digidata 1322A A/D-D/A board (Molecular Devices, CA, USA).
ACKNOWLEDGMENTS This work was supported by  NIH   R01 DC 05989  and  R56 DC 015019  to  H-BZ  and the  Agence Nationale de la Recherche  ( ANR-14-CE11-0004-01 ) to TG. NY was supported by  Major State Basic Research Development Program of China  (No. 2014CB943002 ) and  National Natural Science Foundation of China  (No. 81470700 ).
II. DATA ACQUISITION AND PROCESSING Structural and diffusion MRI data were taken from Wakeman et al. [11]. The 1 mm isotropic resolution T1 weighted images of size 256 × 256 × 192 were acquired by a Siemens 3T. The 2 mm isotropic resolution diffusion weighted images of size 96 × 96 × 68 were collected by the same scanner (64 gradient directions and b-value = 1000 s/mm 2 ), with one b0 image (an image without diffusion gradient). The cortical surface was extracted from T1, using Freesurfer  [12] , and re-meshed to 10 4 vertices (sources). The transformation between the anatomical and diffusion space was obtained by using FSL  [13]. MEG (102 magnetometers, 204 planar gradiometers) and EEG (70 electrodes) were measured simultaneously in a magnetically shielded room. The face stimuli contain three sets of 450 gray scale photographs, one third of unfamiliar people (unknown to the participants), one third of famous people and the remaining are of scrambled faces.
2a ). Noteworthy, the abundances of these AMPAR subunits were similar among each other in either target AP and the amounts of co-purified AMPARs (defined as sum of GluA1-4 abundances/4; 15 ) exceeded by far the values obtained for any of the remaining interactors identified for FRRS1l and CPT1c. The latter are all indicated in public databases (UniProtKB/Swiss-Prot, EMBL-EBI) being membrane proteins with different topology and suggested preferred localization to the ER (amounts o0. 5% of AMPARs; Fig. 2a ). These results unraveled an almost exclusive partnership of FRRS1l and CPT1c with AMPARs and show that both proteins co-associate into the same AMPAR assemblies. This view was further corroborated by direct comparison between the entire pools of AMPARs affinity-isolated from wild-type (WT) and CPT1c knockout animals  23.
Methods Molecular biology. The cDNAs used were all verified by sequencing and had the following GenBank (www. ncbi. nlm. nih. gov/genbank) accession numbers: M38060. 1 (GluA1i, flip variant of GluA1), NM_017261. 2 (GluA2i), NM_053351 (TARP-2), NM_001025132 (CNIH-2), AF357970. 1 (CPT1c), NM_014334 (FRRS1l), and BC117752. 1 (Sac1). Biochemistry and cell biology. Affinity purification from brain membranes. Plasma-membrane-enriched protein fractions were prepared from freshly isolated WT rat or mouse brains (pools of 10-20 animals) or from three mouse brains of CPT1c knockout animals  23  , as previously described  16  , and solubilized with buffers CL-47 and CL-91 (Logopharm GmbH, Germany) for 30 min on ice (at 1 mg protein per ml). After clearing by ultracentrifugation (10 min, 150,000g), solubilisates were incubated with the respective immobilized ABs.
Right panel: correlation analysis of FRRS1l with GluA1-4 and the core subunits of AMPARs across AP data sets from different brain regions (data from ref. 15 re-evaluated). Note that maximal correlation is observed between FRRS1l and the sum of all core subunits (red bar) rather than with the sum of GluAs or individual subunits. (b) Scheme summarizing the proposed role of FRRS1l as a 'catalyst' in AMPAR biogenesis and delivery of synaptic AMPARs. Newly synthesized GluA tetramers (GluA tetra ) co-assemble with FRRS1l-CPT1c complexes during early biogenesis in the ER. These GluA-FRRS1l/CPT1c complexes prepare subsequent co-assembly with the inner core subunits TARPs and CNIHs depicted as a short-lived intermediate priming complex ('priming of assembly'). After binding of CNIHs/TARPs, FRRS1l-CPT1c complexes dissociate (arrow to the right), and the resulting GluA-CNIH/TARP assemblies represent AMPARs competent for ER exit (arrow to the left) and delivery to the plasma membrane.
The mass spectrometric data have been deposited to the Proteo-meXchange Consortium via the PRIDE partner repository with the data set identifier PXD006413 and 10. 6019/PXD006413. Protein identification. LC-MS/MS data were extracted using 'msconvert. exe' (part of ProteoWizard; http://proteowizard. sourceforge. net/, version 3. 0. 6906). Peak lists were searched against a modified UniProtKB/Swiss-Prot database (release 2017_01 for Figs 1b, 2b and 8a, release 2015_09 or newer for remaining analyses; all rat, mouse and human entries, as well as sp|P02769, sp|P00766 and sp|P00761, supplemented with the TrEMBL/NCBI entries tr|D3ZVQ3, tr|D4A4M0, tr|M0RB53, tr|D4A0X1 and XP_008765687. 1 for missing AMPAR proteome constituents) using Mascot 2. 6. 0 (Matrix Science, UK). Initially, preliminary searches with high peptide mass tolerance ( ± 50 p.
p. m. ) were performed. After linear shift mass recalibration using in-house developed software, peptide mass tolerance was reduced to ±5 p. p. m. for final searches. Fragment mass tolerance was set to ± 0. 8 Da (ion trap MS/MS spectra). One missed trypsin cleavage and common variable modifications including S/T/Y phosphorylation were accepted for peptide identification. Significance threshold was set to Po0. 05. Proteins identified by only one specific MS/MS spectrum or representing exogenous contaminations such as keratins or immunoglobulins were eliminated. Primary sequence analysis. Peak lists extracted from the LC-MS/MS data of the FRRS1l protein band were finally searched against databases containing all human UniProtKB/Swiss-Prot entries, the heterologous FRRS1l and CPT1c sequences (see above) and a series of C-terminally truncated FRRS1l sequences (truncation after P316, S317, A318, A319, Y320, Q321, T322, F323, S324 or S325 to promote Mascot identification of the C-terminal peptide of the truncated protein in the lower MW band).
Features were then aligned between different LC-MS/MS runs and assigned to peptides with retention time tolerance ±1 min and mass tolerance: ± 1. 5 p. p. m. using an in-house developed software. The resulting peptide PV tables formed the basis for protein quantification (molecular and relative abundance in Figs 1, 2 and 8 and Supplementary Figs  1b  and 5c ). Molecular abundances of AMPAR constituents (Fig. 1a ) were determined from protein profiles calibrated with a label-free QconCAT method  15, 16. First, the peptide PV data for each protein were filtered for outliers and false-positive assignments using a recently developed correlation-based method  30. For each peptide, the PVs were then normalized to their maximum over all AP data sets yielding relative peptide profiles, ranked for each protein by pairwise Pearson correlation.
Patch pipettes were positioned using two Kleindiek micromanipulators (Kleindiek Nanotechnik, Germany). A Multiclamp 700B amplifier (Molecular Devices, USA) was used for recordings. Pipette capacitance of both electrodes was compensated to 70-90%. Voltage and current signals were filtered at 10 kHz with the built-in low-pass Bessel filter and digitized at 20 kHz using a Digidata 1440A (Molecular Devices, USA). The pClamp10 software (Molecular Devices, USA) was used for stimulation and data acquisition. For dissection and storage of slices, a sucrose-containing physiological saline containing 87 mM NaCl, 25 mM NaHCO 3 , 25 mM D-glucose, 75 mM sucrose, 2. 5 mM KCl, 1. 25 mM NaH 2 PO 4 , 0. 5 mM CaCl 2 and 7 mM MgCl 2 was used. Slices were superfused with physiological extracellular solution that contained 125 mM NaCl, 25 mM NaHCO 3 , 2.
EPSCs and currents through extra-synaptic (somatic) AMPARs (Fig. 7c ) were determined with the following procedure: After recording spontaneous EPSCs in whole-cell configuration ( À 70 mV), the patch-pipette initially placed on the soma of the MC was excised into out-outside configuration and placed in front of a piezo-driven fast application system that enables solution exchanges within o100 ms (20-80%, measured from the open tip response during a switch between normal and 10 Â diluted extracellular solution). AMPAR currents were elicited by 100-ms or 1-ms applications of 10 mM glutamate. Data for all conditions (non-infected and virally transduced) were recorded in brain slices obtained from at least three different animals from three different pups; recordings from virally transduced and non-infected control cells were performed in the same slices.
Data analysis. Stimfit 0. 9 software and Igor Pro (WaveMetrics, USA) were used to analyse data from spontaneous and evoked EPSCs. The rise time 20-80% was determined as the time interval between the points corresponding to 20% and 80% of the peak amplitude. The peak current was determined as the maximum within a 2-ms window following the presynaptic action potential. For both single and paired recordings, the EPSC decay time constant (t EPSC decay ) was obtained from a mono-exponential function fitted to the decay phase of the current  15. The analysis was restricted to spontaneous and evoked EPSCs fulfilling the following criteria: (1) amplitude was 420 pA (more than twofold larger than the noise recording), (2) decay was complete, that is, traces declined to baseline and were not interfered by further synaptic events (that is, Z40 ms), (3) rise time 20-80% was between 0.
Acknowledgements We are grateful to the patients and their family members for their participation in our study. We thank  J. P. Adelman  for intense discussions and critical reading of the manuscript,  A. Haupt  for help with bioinformatics and  N. Casals  for providing CPT1c knockout brains and antibodies targeting CPT1c. This work was supported by grants of the  National Research Agency  ( ANR-10-IAHU-01 ) and the  Fondation pour la Recherche Medicale  ( DEQ20120323702 ) to L. C. and by grants of the  DFG  to  R. A. J. ( AB393/1-2  and  AB393/2-2 ) and to B. F. (SFB  746 ,  TP 16  and  Fa 332/9-1 ).
FamilyFigure 3 | 3 Figure 3 | Mutations in FRRS1l identified as disease causing in patients with severe intellectual disability. (a) Pedigree (and genotypes) of the three different families detailed in the text. Affected patients are indicated by filled symbol; slashes refer to deceased individuals. (b) Schematic representation of the FRRS1l protein (as given in the UniProtKB/Swiss-Prot database) together with the alterations identified in the indicated families and alignment of the primary sequence stretch around lysine 155 (K155) across species. TM is a predicted transmembrane domain. (c) Summary of the clinical features observed in the patients from families A-C. MA denotes mental age, NA means not investigated.
In particular, we recorded early symptomatic R6/1 mice during an operant conditioning task that relies critically on the integrity of the striatum. During random sampling of cells in the dorsal striatum only a small percent of cells recorded were MSNs  [15]. Indeed, the majority of the recorded cell types in these HD mice were qualified as fast-spiking INs in contrast to 50% being INs in WT mice. These data suggest that MSNs may suffer from functional dysregulation in vivo in R6/1 mice. Because extracellular single-unit recording technique did not allow dissociation between the sub-populations of direct and indirect pathway MSNs, a hypothesis was formulated that a few recorded MSNs in HD mice might belong to the direct pathway that may remain functional, and "unrecordable" MSNs to be part of the indirect pathway.
All analyses were performed by an experimenter blind to genotype and age. Data were expressed as percent of D1R and D2R expressing cells among c-Fos+ MSNs. Double labeling immunofluorescence experiments were performed to identify c-Fos+ INs. Striatal sections were incubated with anti-c-Fos antibody and either anti-acetylcholinesterase (ChAT), anti-parvalbumin (PV), anti-neuronal nitric oxide synthase (nNOS) or anti-calretinin (Calr) antibody according to the procedure described above. For each DMS, stacks of 5 images with a step of 5 μm were taken using Micromanager for acquisition as previously. A 20X lens was used to take mosaic image stacks of the DMS, and striatal sections were analyzed as above. Experimental design and statistical analysis. Experimental plan involved 41 WT mice and 46 R6/1 mice of 3 different ages: 2, 4 and 6 months (see Table  1 ).
To avoid this, the participants had a sufficient time to familiarize with the interface and practice taping at low and high speeds. Also, data was recorded for each single tap and its exploitability was verified in situ (as for the results given in section 4. 2, we checked both visually during the experiments and during data post-processing performed just after each tap that the gesture was performed properly). Each participant was asked to perform taps until we get at least three valid taps (correct speed and absence of contact with the ring before the obstacle).
Immunodeficient adult recipient mice were selected to avoid the potential influence of immune cytokines on cell commitment, survival, and integration. Grafted cells were analyzed 4 weeks after transplantation. A first analysis of the FACS dot plot (Figure  4A ) confirmed the previous immunostaining assessment revealing at least three different EGFP-positive cell populations showing a different body size and EGFP intensity. Because of the small retina size and, consequently, the small percentage of cells of interest at E12, all the EGFP-positive cells were sorted via FACS and transplanted. Rare EGFP-positive cells were observed in the recipient retina (data not shown). The most part of transplanted cells aggregated in the sub-retinal space, forming a consistently well-organized cell graft with rosettes (Figures  4B-4EII ).